Running as unit: rb-build-arm64_14-69790.service ==================================================================================== Fri Nov 22 15:00:20 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_14) on jenkins, called using "codethink01-arm64 codethink03-arm64" as arguments. Fri Nov 22 15:00:20 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-yl9En6RD" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Nov 22 15:00:20 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Fri Nov 22 15:00:20 UTC 2024 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-JexMbD' Fri Nov 22 15:00:21 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Fri Nov 22 15:00:21 UTC 2024 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-ujnU1s' ok, let's check if primer3 is building anywhere yet… ok, primer3 is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of primer3 in unstable on arm64 on jenkins now. 1st build will be done on codethink01-arm64.debian.net. 2nd build will be done on codethink03-arm64.debian.net. ============================================================================= Fri Nov 22 15:00:43 UTC 2024 I: starting to build primer3/unstable/arm64 on jenkins on '2024-11-22 15:00' Fri Nov 22 15:00:43 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_14/69790/console.log 1732287643 arm64 unstable primer3 Fri Nov 22 15:00:43 UTC 2024 I: Downloading source for unstable/primer3=2.6.1-4 --2024-11-22 15:00:43-- http://deb.debian.org/debian/pool/main/p/primer3/primer3_2.6.1-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2243 (2.2K) [text/prs.lines.tag] Saving to: ‘primer3_2.6.1-4.dsc’ 0K .. 100% 282M=0s 2024-11-22 15:00:43 (282 MB/s) - ‘primer3_2.6.1-4.dsc’ saved [2243/2243] --2024-11-22 15:00:43-- http://deb.debian.org/debian/pool/main/p/primer3/primer3_2.6.1-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2243 (2.2K) [text/prs.lines.tag] Saving to: ‘primer3_2.6.1-4.dsc’ 0K .. 100% 282M=0s 2024-11-22 15:00:43 (282 MB/s) - ‘primer3_2.6.1-4.dsc’ saved [2243/2243] Fri Nov 22 15:00:43 UTC 2024 I: primer3_2.6.1-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: primer3 Binary: primer3, primer3-examples Architecture: any all Version: 2.6.1-4 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Homepage: http://primer3.sourceforge.net Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/primer3 Vcs-Git: https://salsa.debian.org/med-team/primer3.git Testsuite: autopkgtest Testsuite-Triggers: valgrind Build-Depends: debhelper-compat (= 13) Package-List: primer3 deb science optional arch=any primer3-examples deb science optional arch=all Checksums-Sha1: bd421d0e74ab418bd3a0b56a304853984475b469 32858944 primer3_2.6.1.orig.tar.gz 13a0a5760bbcbf6b2c9d57821c2631894a553f5f 13788 primer3_2.6.1-4.debian.tar.xz Checksums-Sha256: 805cef7ef39607cd40f0f5bb8b32e35e20007153a0a55131dd430ce644c8fb9e 32858944 primer3_2.6.1.orig.tar.gz 4ccc6bbba549b21853870b28c9c6090d3b48bc30503d4f631e3b5f4286e8e3e2 13788 primer3_2.6.1-4.debian.tar.xz Files: d18c095694b586c300c88fab4b116c8c 32858944 primer3_2.6.1.orig.tar.gz 64c16c6ba8613a8e63e479ea2ce8fd95 13788 primer3_2.6.1-4.debian.tar.xz Dgit: e1add3819d33a38aff6b5b5b286a4052cc0fcd11 debian archive/debian/2.6.1-4 https://git.dgit.debian.org/primer3 -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmNxEUcUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdr7XA/9Gt+kx6EacCA3w5ur+n4sQJlB88ph 9O6/QHrs2mH03lEn7NWWlK7n7bXlI61o6f4xnoWfK1YrK45eae9d+gS/enISNKuo h6lZ8+frcWeeLtwLxi54lJgRazlmL8UGAsr5eYyeWGe1LETzRQgM224LFLJsEqRy y7F3Gkzlo+Z9JdyTZKpWNaZ6ZabnuGOexKttqOm1CZ/Kikt1J9md3G8QnXmmTALB BHEY77gPXdTLgK4pbIyC+f1miJcav5hGttewwHix3E2fV2MJQxR2XfGSnE3DoSc2 2ACyVbJQ0PMCOa/SuyedBLlmJ9lirx9QgiVJIOEqogcIDWx65YIhWbNxBYSfHYvi Hop3FOUl5RDwjy6Zse48ULm3fPQELczBTYeaJ6VjNlGoEDWzCdz0XEGn7WfRjTkL G3DGMp4SmNZlMWLRH+Nm4EqZBuBZXqA1PPJ1X3zIx5aSIwrpyS/aHBG/xrzSLQ4y zfGGQca9rxvkyoMmxRAhvmtpin/y1c2po/lnYLC9jBHZOUn4QUhUKd6Fs07mE0RH fklXxg2PQAb9eiqIf/gwfDJk4iW8/LSsgWM35RVwrDS80lBfYmmHUH+gMI6cTo3f /X7uBxRPekVMoiVY4fUeT7VVNZpydeyNn7PsgaNHh4TECFgubcGDUgniRqk9+a2l ujh74vyei/rwJ2I= =RLJw -----END PGP SIGNATURE----- Fri Nov 22 15:00:43 UTC 2024 I: Checking whether the package is not for us Fri Nov 22 15:00:43 UTC 2024 I: Starting 1st build on remote node codethink01-arm64.debian.net. Fri Nov 22 15:00:43 UTC 2024 I: Preparing to do remote build '1' on codethink01-arm64.debian.net. Fri Nov 22 15:00:43 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Fri Nov 22 15:00:43 UTC 2024 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-HF1enJ' ==================================================================================== Thu Dec 25 21:23:45 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink01-arm64, called using "1 primer3 unstable /srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO 2.6.1-4" as arguments. Thu Dec 25 21:23:45 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-5asFjObT" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Dec 25 21:23:45 UTC 2025 I: Downloading source for unstable/primer3=2.6.1-4 Reading package lists... NOTICE: 'primer3' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/primer3.git Please use: git clone https://salsa.debian.org/med-team/primer3.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 32.9 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main primer3 2.6.1-4 (dsc) [2243 B] Get:2 http://deb.debian.org/debian unstable/main primer3 2.6.1-4 (tar) [32.9 MB] Get:3 http://deb.debian.org/debian unstable/main primer3 2.6.1-4 (diff) [13.8 kB] Fetched 32.9 MB in 1s (39.4 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'primer3' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/primer3.git Please use: git clone https://salsa.debian.org/med-team/primer3.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 32.9 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main primer3 2.6.1-4 (dsc) [2243 B] Get:2 http://deb.debian.org/debian unstable/main primer3 2.6.1-4 (tar) [32.9 MB] Get:3 http://deb.debian.org/debian unstable/main primer3 2.6.1-4 (diff) [13.8 kB] Fetched 32.9 MB in 1s (39.4 MB/s) Download complete and in download only mode ============================================================================= Building primer3 in unstable on arm64 on codethink01-arm64 now. Date: Thu Dec 25 21:23:46 GMT 2025 Date UTC: Thu Dec 25 21:23:46 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Dec 25 09:23:46 -12 2025 I: pbuilder-time-stamp: 1766697826 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 [primer3_2.6.1-4.dsc] I: copying [./primer3_2.6.1.orig.tar.gz] I: copying [./primer3_2.6.1-4.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Nov 13 15:46:15 2022 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./primer3_2.6.1-4.dsc: no acceptable signature found dpkg-source: info: extracting primer3 in primer3-2.6.1 dpkg-source: info: unpacking primer3_2.6.1.orig.tar.gz dpkg-source: info: unpacking primer3_2.6.1-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch dpkg-source: info: applying primer_thermodynamic_parameters_path_2_etc.patch dpkg-source: info: applying set_prefix.patch dpkg-source: info: applying buildflags.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1014008/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='1da4862480c84894992fd79a1df8efa0' 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='1014008' 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.7QxZNohO/pbuilderrc_il3F --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.7QxZNohO/b1 --logfile b1/build.log primer3_2.6.1-4.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink01-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1014008/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20084 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 19.4 MB of archives. After unpacking 77.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Fetched 19.4 MB in 0s (99.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20084 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../23-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... 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_13.20_all.deb ... Unpacking debhelper (13.20) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... 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/primer3-2.6.1/ && 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 > ../primer3_2.6.1-4_source.changes dpkg-buildpackage: info: source package primer3 dpkg-buildpackage: info: source version 2.6.1-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j12 clean make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1/src' no windows rm -f *.o primer3_core ntdpal ntthal amplicon3_core oligotm long_seq_tm_test primer3_masker *~ libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a libprimer3.so.1.0.0 libdpal.a.so.1.0.0 libthal.a.so.1.0.0 libthalpara.a.so.1.0.0 libamplicontm.so.1.0.0 liboligotm.so.1.2.0 libmasker.a.so.1.0.0 example.for example.rev example.int core ../*~ cd ../test/; make clean make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/test' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. echo; echo; echo 'CLEAN UP TEST DIRECTORIES'; echo; echo; CLEAN UP TEST DIRECTORIES rm -rf primer_list_tmp/* rm -rf primer1_list_tmp/* rm -rf primer1_th_list_tmp/* rm -rf th-w-other-tasks_list_tmp/* rm -f primer_global_err/*.tmp primer_global_err/*.tmp2 primer_global_err/*.bak rm -f amplicon3/*.tmp amplicon3/*.jpg amplicon3/decipher* rm -f *.tmp *.bak *.tmp.err *~ rm -f hyb_probe_only.for hyb_probe_only.int rm -f right_only.for right_only.rev left_only.for rm -f pcr_primers_and_io.int pcr_primers_and_io.rev pcr_primers_and_io.for rm -f pcr_primers.rev pcr_primers.for rm -f pick_primer_list_and_file_flag_th_[1-4].for pick_primer_list_and_file_flag_th_[1-4].rev rm -f pick_primer_list_and_file_flag_th_[1-4].int rm -f syntax[0-1][0-9].for syntax[0-1][0-9].int syntax[0-1][0-9].rev rm -f oligotm.*.valg # valgrind output from oligotm_test.pl --valgrind rm -f ntdpal.*.valg # valgrind output from dpal_test.pl --valgrind rm -f ntthal.*.valg # valgrind output from thal_test.pl --valgrind rm -f masker.*.valg # valgrind output from thal_test.pl --valgrind rm -f oligotm.*.valg.* # valgrind output from oligotm_test.pl --valgrind rm -f ntdpal.*.valg.* # valgrind output from dpal_test.pl --valgrind rm -f ntthal.*.valg.* # valgrind output from thal_test.pl --valgrind rm -f masker.*.valg.* # valgrind output from masker_test.pl --valgrind rm -f *.vg */*.vg # valgrind output from p3test{,z}.pl --valgrind rm -f *.vg.core.* # core files from crashed valgrind test rm -f ./core # in case we crashed and left a core file make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1/test' make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1/src' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1' dh_auto_build -- 'CPP=$(CXX)' cd src && make -j12 "INSTALL=install --strip-program=true" CPP=\$\(CXX\) make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/src' no windows cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g primer3_boulder_main.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o format_output.o format_output.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o read_boulder.o read_boulder.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o print_boulder.o print_boulder.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -std=c++11 -Wl,-z,relro -Wl,-z,now -g -o libprimer3.o libprimer3.cc cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o p3_seq_lib.o p3_seq_lib.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o dpal_primer.o dpal.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal_primer.o thal.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal_parameters.o thal_parameters.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o oligotm.o oligotm.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicontm.o amplicontm.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g masker.c format_output.c: In function 'print_seq': format_output.c:418:61: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress] 418 | if (pa->pick_right_primer && (&retval->rev) != NULL | ^~ In file included from format_output.h:41, from format_output.c:40: libprimer3.h:927:26: note: 'rev' declared here 927 | oligo_array fwd, intl, rev; | ^~~ format_output.c:429:60: warning: the comparison will always evaluate as 'true' for the address of 'fwd' will never be NULL [-Waddress] 429 | if (pa->pick_left_primer && (&retval->fwd) != NULL | ^~ libprimer3.h:927:15: note: 'fwd' declared here 927 | oligo_array fwd, intl, rev; | ^~~ format_output.c: In function 'format_oligos': format_output.c:851:51: warning: the comparison will always evaluate as 'true' for the address of 'fwd' will never be NULL [-Waddress] 851 | if ((pa->pick_left_primer) && ((&retval->fwd) != NULL ) | ^~ libprimer3.h:927:15: note: 'fwd' declared here 927 | oligo_array fwd, intl, rev; | ^~~ format_output.c:858:55: warning: the comparison will always evaluate as 'true' for the address of 'intl' will never be NULL [-Waddress] 858 | if ((pa->pick_internal_oligo) && ((&retval->intl) != NULL ) | ^~ libprimer3.h:927:20: note: 'intl' declared here 927 | oligo_array fwd, intl, rev; | ^~~~ format_output.c:865:52: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress] 865 | if ((pa->pick_right_primer) && ((&retval->rev) != NULL ) | ^~ libprimer3.h:927:26: note: 'rev' declared here 927 | oligo_array fwd, intl, rev; | ^~~ format_output.c:888:49: warning: the comparison will always evaluate as 'true' for the address of 'fwd' will never be NULL [-Waddress] 888 | if ((pa->pick_left_primer) && ((&retval->fwd) != NULL ) | ^~ libprimer3.h:927:15: note: 'fwd' declared here 927 | oligo_array fwd, intl, rev; | ^~~ format_output.c:907:53: warning: the comparison will always evaluate as 'true' for the address of 'intl' will never be NULL [-Waddress] 907 | if ((pa->pick_internal_oligo) && ((&retval->intl) != NULL ) | ^~ libprimer3.h:927:20: note: 'intl' declared here 927 | oligo_array fwd, intl, rev; | ^~~~ format_output.c:926:50: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress] 926 | if ((pa->pick_right_primer) && ((&retval->rev) != NULL ) | ^~ libprimer3.h:927:26: note: 'rev' declared here 927 | oligo_array fwd, intl, rev; | ^~~ cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -g -Wall -Wl,-z,relro -Wl,-z,now -g -o ntdpal_main.o ntdpal_main.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o dpal.o dpal.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o thal_main.o thal_main.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal.o thal.c ar rv libthalpara.a thal_parameters.o ar: creating libthalpara.a a - thal_parameters.o ranlib libthalpara.a libprimer3.cc: In function 'char* strstr_nocase(char*, char*)': libprimer3.cc:6168:29: warning: pointer 'p' used after 'void free(void*)' [-Wuse-after-free] 6168 | else {free(tmp); return p;} | ^ libprimer3.cc:6168:15: note: call to 'void free(void*)' here 6168 | else {free(tmp); return p;} | ~~~~^~~~~ ar rv liboligotm.a oligotm.o ar: cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm creating liboligotm.a a - oligotm.o ranlib liboligotm.a cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o oligotm oligotm_main.c liboligotm.a -lm ar rv libmasker.a masker.o ar: creating libmasker.a a - masker.o ranlib libmasker.a In file included from /usr/include/string.h:548, from thal.c:43: In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'calc_hairpin' at thal.c:1922:19: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' ar rv libamplicontm.a amplicontm.o ar: creating libamplicontm.a a - amplicontm.o ranlib libamplicontm.a cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o amplicon3_core amplicontm_main.c libamplicontm.a -lm ar rv libdpal.a dpal_primer.o ar: creating libdpal.a a - dpal_primer.o ranlib libdpal.a In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'calc_bulge_internal.isra' at thal.c:2000:19: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'maxTM' at thal.c:1542:19, inlined from 'fillMatrix' at thal.c:1473:16: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntdpal ntdpal_main.o dpal.o In file included from /usr/include/string.h:548, from thal.c:43: In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'calc_hairpin' at thal.c:1922:19: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'calc_bulge_internal.isra' at thal.c:2000:19: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'maxTM' at thal.c:1542:19, inlined from 'fillMatrix' at thal.c:1473:16: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' ar rv libthal.a thal_primer.o ar: creating libthal.a a - thal_primer.o ranlib libthal.a cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntthal thal_main.o thal.o thal_parameters.o -lm ar rv libprimer3.a libprimer3.o p3_seq_lib.o ar: creating libprimer3.a a - libprimer3.o a - p3_seq_lib.o ranlib libprimer3.a g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -std=c++11 -lstdc++ -Wl,-z,relro -Wl,-z,now -g -o primer3_core primer3_boulder_main.o format_output.o read_boulder.o print_boulder.o libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -std=c++11 -lstdc++ -Wl,-z,relro -Wl,-z,now -g -o primer3_masker masker_main.c libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a -lm cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1/src' make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1' dh_auto_test --no-parallel --sourcedirectory=test cd test && make -j1 test make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/test' cd ../src; make make[3]: Entering directory '/build/reproducible-path/primer3-2.6.1/src' no windows make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/primer3-2.6.1/src' perl cmdline_test.pl TESTING command line arguments Test 1... [OK] Test 2... [OK] Test 3... [OK] Test 4... [OK] Test 5... [OK] Passed all tests - [OK] perl oligotm_test.pl TESTING Tm CALCULATIONS Tm tests nr 1-50: [OK] echo; echo; echo 'TESTING ALIGNMENT CALCS'; echo; perl dpal_test.pl ; TESTING ALIGNMENT CALCS Error handling of too-long sequence...[OK] Default implementations + alignment...[OK] Default implementations + NO alignment 1...[OK] Default implementations + NO alignment 2...[OK] Force _dpal_generic...[OK] Force _dpal_long_nopath_generic 1...[OK] Force _dpal_long_nopath_generic 2...[OK] Force long maxgap1 functions 1...[OK] Force long maxgap1 functions 2...[OK] echo; echo; echo 'TESTING THERMODYNAMIC ALIGNMENT CALCS'; echo; perl thal_test.pl ; TESTING THERMODYNAMIC ALIGNMENT CALCS Error handling of too-long sequence... 1................................... [OK] Default implementations + alignment...[OK] Default implementations + NO alignment 1...[OK] Default implementations + NO alignment 2...[OK] Default implementations + alignment (interactive)...[OK] Default implementations + NO alignment 1 (interactive)...[OK] Default implementations + NO alignment 2 (interactive)...[OK] Default implementations + alignment (interactive batch inputs)...[OK] Default implementations + alignment + HAIRPIN (interactive batch inputs)...[OK] echo; echo; echo 'TESTING MASKER'; echo; perl masker_test.pl ; TESTING MASKER Default implementations...[OK] echo; echo; echo 'TESTING amplicon3_core'; echo; perl a3test.pl TESTING amplicon3_core a3test.pl for amplicon3_core version 2.5.0 a3test.pl: testing ../src/amplicon3_core START, Thu Dec 25 21:24:41 2025 plain_WNT9B...0s [OK] plain_TBX18...0s [OK] plain_RYK...0s [OK] plain_WNT2...0s [OK] plain_ROCK2...0s [OK] plain_SFRP3...0s [OK] plain_IFT20...0s [OK] plain_DVL1...0s [OK] plain_IFT88...0s [OK] plain_FZD2...0s [OK] plain_GAPDH...0s [OK] plain_WNT1...0s [OK] plain_MYH6...0s [OK] plain_on_command_line_WNT9B...0s [OK] plain_on_command_line_TBX18...0s [OK] plain_on_command_line_RYK...0s [OK] plain_on_command_line_WNT2...0s [OK] plain_on_command_line_ROCK2...0s [OK] plain_on_command_line_SFRP3...0s [OK] plain_on_command_line_IFT20...0s [OK] plain_on_command_line_DVL1...0s [OK] plain_on_command_line_IFT88...0s [OK] plain_on_command_line_FZD2...0s [OK] plain_on_command_line_GAPDH...0s [OK] plain_on_command_line_WNT1...0s [OK] plain_on_command_line_MYH6...0s [OK] classic_WNT9B...0s [OK] classic_TBX18...0s [OK] classic_RYK...0s [OK] classic_WNT2...0s [OK] classic_ROCK2...0s [OK] classic_SFRP3...0s [OK] classic_IFT20...0s [OK] classic_DVL1...0s [OK] classic_IFT88...0s [OK] classic_FZD2...0s [OK] classic_GAPDH...0s [OK] classic_WNT1...0s [OK] classic_MYH6...0s [OK] heli_WNT9B...0s [OK] heli_TBX18...0s [OK] heli_RYK...0s [OK] heli_WNT2...0s [OK] heli_ROCK2...0s [OK] heli_SFRP3...0s [OK] heli_IFT20...0s [OK] heli_DVL1...0s [OK] heli_IFT88...0s [OK] heli_FZD2...0s [OK] heli_GAPDH...1s [OK] heli_WNT1...0s [OK] heli_MYH6...0s [OK] long_WNT9B...0s [OK] long_TBX18...0s [OK] long_RYK...0s [OK] long_WNT2...0s [OK] long_ROCK2...0s [OK] long_SFRP3...0s [OK] long_IFT20...0s [OK] long_DVL1...0s [OK] long_IFT88...0s [OK] long_FZD2...0s [OK] long_GAPDH...0s [OK] long_WNT1...0s [OK] long_MYH6...0s [OK] optimal_WNT9B...0s [OK] optimal_TBX18...0s [OK] optimal_RYK...0s [OK] optimal_WNT2...0s [OK] optimal_ROCK2...0s [OK] optimal_SFRP3...0s [OK] optimal_IFT20...0s [OK] optimal_DVL1...0s [OK] optimal_IFT88...0s [OK] optimal_FZD2...0s [OK] optimal_GAPDH...0s [OK] optimal_WNT1...0s [OK] optimal_MYH6...0s [OK] only_mv_WNT9B...0s [OK] only_mv_TBX18...0s [OK] only_mv_RYK...0s [OK] only_mv_WNT2...0s [OK] only_mv_ROCK2...0s [OK] only_mv_SFRP3...0s [OK] only_mv_IFT20...0s [OK] only_mv_DVL1...0s [OK] only_mv_IFT88...0s [OK] only_mv_FZD2...0s [OK] only_mv_GAPDH...0s [OK] only_mv_WNT1...0s [OK] only_mv_MYH6...0s [OK] no_dmso_WNT9B...0s [OK] no_dmso_TBX18...0s [OK] no_dmso_RYK...0s [OK] no_dmso_WNT2...0s [OK] no_dmso_ROCK2...0s [OK] no_dmso_SFRP3...0s [OK] no_dmso_IFT20...0s [OK] no_dmso_DVL1...0s [OK] no_dmso_IFT88...0s [OK] no_dmso_FZD2...0s [OK] no_dmso_GAPDH...0s [OK] no_dmso_WNT1...0s [OK] no_dmso_MYH6...0s [OK] Tests in a3test.pl ran for 1 s (0.0166666666666667 min) DONE Thu Dec 25 21:24:42 2025 Passed all tests - [OK] echo; echo; echo 'TESTING primer3_core'; echo; perl p3test.pl TESTING primer3_core mkdir: ../test/primer_list_tmp mkdir: ../test/primer1_list_tmp mkdir: ../test/primer1_th_list_tmp mkdir: ../test/th-w-other-tasks_list_tmp p3test.pl for primer3_core version 2.6.1 p3test.pl: testing ../src/primer3_core START, Thu Dec 25 21:24:42 2025 testing fatal errors... ./primer_global_err/annealing_temp_salt Testing --output and --error flags on ../src/primer3_core --strict_tags ./primer_global_err/annealing_temp_salt.in --output ./primer_global_err/annealing_temp_salt.tmp --error ./primer_global_err/annealing_temp_salt.tmp2 ./primer_global_err/bad_divalent_dntp_conc_1 ./primer_global_err/bad_divalent_dntp_conc_2 ./primer_global_err/bad_divalent_dntp_conc_3 ./primer_global_err/bad_divalent_dntp_conc_4 ./primer_global_err/bad_dna_conc ./primer_global_err/bad_first_base_index ./primer_global_err/bad_float_1 ./primer_global_err/bad_float_2 ./primer_global_err/bad_float_3 ./primer_global_err/bad_float_4 ./primer_global_err/bad_gc_1 ./primer_global_err/bad_gc_2 ./primer_global_err/bad_gc_3 ./primer_global_err/bad_gc_int_1 ./primer_global_err/bad_gc_int_2 ./primer_global_err/bad_gc_int_3 ./primer_global_err/bad_min_three_prime_distance ./primer_global_err/bad_num_ns ./primer_global_err/bad_num_ns_int ./primer_global_err/bad_product_sizes_1 ./primer_global_err/bad_product_sizes_2 ./primer_global_err/bad_product_sizes_3 ./primer_global_err/bad_product_sizes_4 ./primer_global_err/bad_salt_conc ./primer_global_err/bad_self_any ./primer_global_err/bad_self_any_int ./primer_global_err/bad_self_end ./primer_global_err/bad_self_end_int ./primer_global_err/bad_settings0 ./primer_global_err/bad_settings1 ./primer_global_err/bad_settings2 ./primer_global_err/bad_settings3 ./primer_global_err/bad_settings4 ./primer_global_err/bad_settings5 ./primer_global_err/bad_settings6 ./primer_global_err/empty_1 ./primer_global_err/empty_product_size ./primer_global_err/gc_clamp_min_size ./primer_global_err/incorrect_task ./primer_global_err/io_gc_content_obj_fn ./primer_global_err/io_obj_fn ./primer_global_err/junction_overlap_max_size ./primer_global_err/junction_overlap_min_size ./primer_global_err/max_annealing_temp ./primer_global_err/max_min_bound ./primer_global_err/max_min_bound_int ./primer_global_err/max_min_tm ./primer_global_err/max_min_tm_int ./primer_global_err/max_opt_bound ./primer_global_err/max_opt_bound_int ./primer_global_err/max_opt_tm ./primer_global_err/max_opt_tm_int ./primer_global_err/MAX_PRIMER_LENGTH ./primer_global_err/max_size_limit_int ./primer_global_err/max_size_limit_with_overhang ./primer_global_err/max_size_min_product ./primer_global_err/max_size_min_product_int ./primer_global_err/min_opt_tm ./primer_global_err/min_opt_tm_int ./primer_global_err/mishyb_obj_fn ./primer_global_err/mispr_obj_fn ./primer_global_err/must_match_length_0 ./primer_global_err/must_match_length_1 ./primer_global_err/must_match_length_10 ./primer_global_err/must_match_length_2 ./primer_global_err/must_match_length_3 ./primer_global_err/must_match_length_4 ./primer_global_err/must_match_length_5 ./primer_global_err/must_match_length_6 ./primer_global_err/must_match_length_7 ./primer_global_err/must_match_length_8 ./primer_global_err/must_match_length_9 ./primer_global_err/no_equal ./primer_global_err/no_terminal_equal ./primer_global_err/opt_max_size ./primer_global_err/opt_max_size_int ./primer_global_err/opt_min_size ./primer_global_err/opt_min_size_int ./primer_global_err/pair_mispr ./primer_global_err/pr_gc_content_obj_fn ./primer_global_err/product_size_obj_fn ./primer_global_err/product_tm_obj_fn ./primer_global_err/repeat_lib_err ./primer_global_err/repeat_lib_err1 ./primer_global_err/repeat_lib_err2 ./primer_global_err/repeat_lib_err3 ./primer_global_err/repeat_lib_err4 ./primer_global_err/repeat_lib_err5 ./primer_global_err/repeat_lib_err6 ./primer_global_err/repeat_lib_int_err ./primer_global_err/repeat_lib_int_err1 ./primer_global_err/repeat_lib_int_err2 ./primer_global_err/repeat_lib_int_err3 ./primer_global_err/repeat_lib_int_err4 ./primer_global_err/repeat_lib_int_err5 ./primer_global_err/repeat_lib_int_err6 ./primer_global_err/seq_quality1 ./primer_global_err/seq_quality2 ./primer_global_err/seq_quality3 ./primer_global_err/seq_quality4 ./primer_global_err/too_many_product_sizes ./primer_global_err/zero_min_size ./primer_global_err/zero_num_return [OK] primer_must_use_th...0s [OK] primer_sec_struct_dpal...0s [OK] primer_task_th...1s [OK] primer_thal_args...0s [OK] primer_thal_max_seq_error...1s [OK] primer_first_base_index...0s [OK] primer_must_match...0s [OK] test_compl_error...0s [OK] test_left_to_right_of_right...0s [OK] dv_conc_vs_dntp_conc...0s [OK] primer_boundary...0s [OK] primer_boundary1...0s [OK] primer_boundary_formatted...0s [OK] primer_boundary1_formatted...0s [OK] primer3_v1_1_4_default_settings...0s [OK] primer3web_v0_4_0_default_settings...0s [OK] primer3web_v3_0_0_default_settings...1s [OK] primer3web_v4_0_0_default_settings...1s [OK] primer_internal...0s [OK] primer_internal1...0s [OK] primer_internal_formatted...0s [OK] primer_internal1_formatted...0s [OK] primer_ok_regions...0s [OK] primer_ok_regions_formatted...0s [OK] primer_ok_regions2...7s [OK] primer_tm_lc_masking...0s [OK] primer_tm_lc_masking_formatted...0s [OK] primer_start_codon...0s [OK] primer_task...0s [OK] primer_task_formatted...0s [OK] primer_renewed_tasks...0s [OK] primer_dmso_formamide...0s [OK] primer_new_tasks...0s [OK] primer_new_tasks_formatted...1s [OK] primer_internal_position...0s [OK] primer_annealing_temp...0s [OK] primer_windows_newlines...1s [OK] primer_must_overlap_point...0s [OK] primer_overlap_junction...0s [OK] primer_all_settingsfiles...0s [OK] primer_high_tm_load_set...0s [OK] primer_high_gc_load_set...0s [OK] primer_gc_end...1s [OK] primer_check...0s [OK] primer_must_use...0s [OK] primer_must_use_formatted...0s [OK] primer_syntax...0s [OK] primer_end_pathology...0s [OK] primer_num_best...0s [OK] primer_quality_boundary...0s [OK] primer...1s [OK] primer_list_files...[OK] primer1...0s [OK] primer1_list_files...[OK] primer_mispriming...0s [OK] primer_mispriming_formatted...0s [OK] primer_mispriming_boundary1...0s [OK] primer_mispriming_boundary1_formatted...1s [OK] primer_mispriming_boundary2...0s [OK] primer_mispriming_boundary2_formatted...0s [OK] primer_mispriming_long_lib...0s [OK] primer_rat...0s [OK] primer_human...1s [OK] long_seq...0s [OK] primer_position_penalty...0s [OK] primer_position_penalty_formatted...1s [OK] p3-tmpl-mispriming...0s [OK] primer_poly_x...0s [OK] primer_three_prime_distance...0s [OK] primer_obj_fn...2s [OK] p3_3_prime_n...0s [OK] primer_masker...2s [OK] primer_masker_formatted...2s [OK] primer_overhang...0s [OK] primer_overhang_th...11s [OK] primer_mispriming_th...8s [OK] th-w-other-tasks...12s [OK] th-w-other-tasks_list_files...[OK] primer_new_tasks_th...16s [OK] primer_sec_struct_thal...12s [OK] primer_thermod_align...36s [OK] primer_thermod_align_formatted...36s [OK] primer1_th...98s [OK] primer1_th_list_files...[OK] primer_lib_amb_codes... NOTE: this test takes _much_ longer than the others (5 to 20 minutes or more). starting primer_lib_amb_codes at Thu Dec 25 21:28:56 2025...107s [OK] Tests in p3test.pl ran for 361 s (6.01666666666667 min) DONE Thu Dec 25 21:30:43 2025 Passed all tests - [OK] echo; echo; echo "Testing completed. You must check the test output for the string FAILED"; echo; echo; Testing completed. You must check the test output for the string FAILED make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1/test' dh clean --sourcedirectory=test dh_auto_clean -O--sourcedirectory=test cd test && make -j12 clean make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/test' echo; echo; echo 'CLEAN UP TEST DIRECTORIES'; echo; echo; CLEAN UP TEST DIRECTORIES rm -rf primer_list_tmp/* rm -rf primer1_list_tmp/* rm -rf primer1_th_list_tmp/* rm -rf th-w-other-tasks_list_tmp/* rm -f primer_global_err/*.tmp primer_global_err/*.tmp2 primer_global_err/*.bak rm -f amplicon3/*.tmp amplicon3/*.jpg amplicon3/decipher* rm -f *.tmp *.bak *.tmp.err *~ rm -f hyb_probe_only.for hyb_probe_only.int rm -f right_only.for right_only.rev left_only.for rm -f pcr_primers_and_io.int pcr_primers_and_io.rev pcr_primers_and_io.for rm -f pcr_primers.rev pcr_primers.for rm -f pick_primer_list_and_file_flag_th_[1-4].for pick_primer_list_and_file_flag_th_[1-4].rev rm -f pick_primer_list_and_file_flag_th_[1-4].int rm -f syntax[0-1][0-9].for syntax[0-1][0-9].int syntax[0-1][0-9].rev rm -f oligotm.*.valg # valgrind output from oligotm_test.pl --valgrind rm -f ntdpal.*.valg # valgrind output from dpal_test.pl --valgrind rm -f ntthal.*.valg # valgrind output from thal_test.pl --valgrind rm -f masker.*.valg # valgrind output from thal_test.pl --valgrind rm -f oligotm.*.valg.* # valgrind output from oligotm_test.pl --valgrind rm -f ntdpal.*.valg.* # valgrind output from dpal_test.pl --valgrind rm -f ntthal.*.valg.* # valgrind output from thal_test.pl --valgrind rm -f masker.*.valg.* # valgrind output from masker_test.pl --valgrind rm -f *.vg */*.vg # valgrind output from p3test{,z}.pl --valgrind rm -f *.vg.core.* # core files from crashed valgrind test rm -f ./core # in case we crashed and left a core file make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1/test' dh_autoreconf_clean -O--sourcedirectory=test dh_clean -O--sourcedirectory=test make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1' dh_auto_install -- PREFIX=debian/primer3/usr cd src && make -j12 install DESTDIR=/build/reproducible-path/primer3-2.6.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=debian/primer3/usr make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/src' no windows install -d "debian/primer3/usr/bin" install -m 755 primer3_core ntdpal ntthal amplicon3_core oligotm long_seq_tm_test primer3_masker "debian/primer3/usr/bin" make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1/src' make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1' dh_install -O--sourcedirectory=src dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1' dh_installexamples mkdir -p /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test; mkdir -p /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/src; mkdir -p /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/settings_files; mkdir -p /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/kmer_lists; cp -aR ./test/* /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test; cp -aR ./src/humrep_and_simple.txt /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/src; cp -a settings_files/primer*.txt /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/settings_files; cp -aR ./kmer_lists/*.list /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/kmer_lists; chmod -x /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test/thal* chmod -x /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test/amplicon3/amplicons.csv chmod -x /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test/primer_windows_newlines_input sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test/long_seq_tm_test.pl ; sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test/vgrep.pl ; make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1' dh_installman -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_lintian -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'primer3' in '../primer3_2.6.1-4_arm64.deb'. dpkg-deb: building package 'primer3-examples' in '../primer3-examples_2.6.1-4_all.deb'. dpkg-deb: building package 'primer3-dbgsym' in '../primer3-dbgsym_2.6.1-4_arm64.deb'. dpkg-genbuildinfo --build=binary -O../primer3_2.6.1-4_arm64.buildinfo dpkg-genchanges --build=binary -O../primer3_2.6.1-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1014008 and its subdirectories I: Current time: Thu Dec 25 09:32:35 -12 2025 I: pbuilder-time-stamp: 1766698355 Thu Dec 25 21:32:35 UTC 2025 I: Signing ./b1/primer3_2.6.1-4_arm64.buildinfo as primer3_2.6.1-4_arm64.buildinfo.asc Thu Dec 25 21:32:35 UTC 2025 I: Signed ./b1/primer3_2.6.1-4_arm64.buildinfo as ./b1/primer3_2.6.1-4_arm64.buildinfo.asc Thu Dec 25 21:32:35 UTC 2025 - build #1 for primer3/unstable/arm64 on codethink01-arm64 done. Starting cleanup. All cleanup done. Thu Dec 25 21:32:35 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-5asFjObT, removing. /srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 15:09 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 15:00 b2 -rw-r--r-- 1 jenkins jenkins 2243 Nov 13 2022 primer3_2.6.1-4.dsc -rw------- 1 jenkins jenkins 3353 Nov 22 15:00 rbuildlog.JLrjCS8 /srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO/b1: total 31660 -rw-r--r-- 1 jenkins jenkins 54932 Nov 22 15:09 build.log -rw-r--r-- 1 jenkins jenkins 434948 Nov 22 15:09 primer3-dbgsym_2.6.1-4_arm64.deb -rw-r--r-- 1 jenkins jenkins 31644144 Nov 22 15:09 primer3-examples_2.6.1-4_all.deb -rw-r--r-- 1 jenkins jenkins 13788 Nov 22 15:09 primer3_2.6.1-4.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2243 Nov 22 15:09 primer3_2.6.1-4.dsc -rw-r--r-- 1 jenkins jenkins 5227 Nov 22 15:09 primer3_2.6.1-4_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6109 Nov 22 15:09 primer3_2.6.1-4_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1840 Nov 22 15:09 primer3_2.6.1-4_arm64.changes -rw-r--r-- 1 jenkins jenkins 186456 Nov 22 15:09 primer3_2.6.1-4_arm64.deb -rw-r--r-- 1 jenkins jenkins 1293 Nov 22 15:09 primer3_2.6.1-4_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO/b2: total 0 Fri Nov 22 15:09:44 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Dec 25 09:23:46 -12 2025 I: pbuilder-time-stamp: 1766697826 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 [primer3_2.6.1-4.dsc] I: copying [./primer3_2.6.1.orig.tar.gz] I: copying [./primer3_2.6.1-4.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Nov 13 15:46:15 2022 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./primer3_2.6.1-4.dsc: no acceptable signature found dpkg-source: info: extracting primer3 in primer3-2.6.1 dpkg-source: info: unpacking primer3_2.6.1.orig.tar.gz dpkg-source: info: unpacking primer3_2.6.1-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch dpkg-source: info: applying primer_thermodynamic_parameters_path_2_etc.patch dpkg-source: info: applying set_prefix.patch dpkg-source: info: applying buildflags.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1014008/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='1da4862480c84894992fd79a1df8efa0' 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='1014008' 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.7QxZNohO/pbuilderrc_il3F --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.7QxZNohO/b1 --logfile b1/build.log primer3_2.6.1-4.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink01-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1014008/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20084 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 19.4 MB of archives. After unpacking 77.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Fetched 19.4 MB in 0s (99.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20084 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../23-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... 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_13.20_all.deb ... Unpacking debhelper (13.20) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... 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/primer3-2.6.1/ && 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 > ../primer3_2.6.1-4_source.changes dpkg-buildpackage: info: source package primer3 dpkg-buildpackage: info: source version 2.6.1-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j12 clean make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1/src' no windows rm -f *.o primer3_core ntdpal ntthal amplicon3_core oligotm long_seq_tm_test primer3_masker *~ libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a libprimer3.so.1.0.0 libdpal.a.so.1.0.0 libthal.a.so.1.0.0 libthalpara.a.so.1.0.0 libamplicontm.so.1.0.0 liboligotm.so.1.2.0 libmasker.a.so.1.0.0 example.for example.rev example.int core ../*~ cd ../test/; make clean make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/test' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. echo; echo; echo 'CLEAN UP TEST DIRECTORIES'; echo; echo; CLEAN UP TEST DIRECTORIES rm -rf primer_list_tmp/* rm -rf primer1_list_tmp/* rm -rf primer1_th_list_tmp/* rm -rf th-w-other-tasks_list_tmp/* rm -f primer_global_err/*.tmp primer_global_err/*.tmp2 primer_global_err/*.bak rm -f amplicon3/*.tmp amplicon3/*.jpg amplicon3/decipher* rm -f *.tmp *.bak *.tmp.err *~ rm -f hyb_probe_only.for hyb_probe_only.int rm -f right_only.for right_only.rev left_only.for rm -f pcr_primers_and_io.int pcr_primers_and_io.rev pcr_primers_and_io.for rm -f pcr_primers.rev pcr_primers.for rm -f pick_primer_list_and_file_flag_th_[1-4].for pick_primer_list_and_file_flag_th_[1-4].rev rm -f pick_primer_list_and_file_flag_th_[1-4].int rm -f syntax[0-1][0-9].for syntax[0-1][0-9].int syntax[0-1][0-9].rev rm -f oligotm.*.valg # valgrind output from oligotm_test.pl --valgrind rm -f ntdpal.*.valg # valgrind output from dpal_test.pl --valgrind rm -f ntthal.*.valg # valgrind output from thal_test.pl --valgrind rm -f masker.*.valg # valgrind output from thal_test.pl --valgrind rm -f oligotm.*.valg.* # valgrind output from oligotm_test.pl --valgrind rm -f ntdpal.*.valg.* # valgrind output from dpal_test.pl --valgrind rm -f ntthal.*.valg.* # valgrind output from thal_test.pl --valgrind rm -f masker.*.valg.* # valgrind output from masker_test.pl --valgrind rm -f *.vg */*.vg # valgrind output from p3test{,z}.pl --valgrind rm -f *.vg.core.* # core files from crashed valgrind test rm -f ./core # in case we crashed and left a core file make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1/test' make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1/src' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1' dh_auto_build -- 'CPP=$(CXX)' cd src && make -j12 "INSTALL=install --strip-program=true" CPP=\$\(CXX\) make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/src' no windows cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g primer3_boulder_main.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o format_output.o format_output.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o read_boulder.o read_boulder.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o print_boulder.o print_boulder.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -std=c++11 -Wl,-z,relro -Wl,-z,now -g -o libprimer3.o libprimer3.cc cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o p3_seq_lib.o p3_seq_lib.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o dpal_primer.o dpal.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal_primer.o thal.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal_parameters.o thal_parameters.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o oligotm.o oligotm.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicontm.o amplicontm.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g masker.c format_output.c: In function 'print_seq': format_output.c:418:61: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress] 418 | if (pa->pick_right_primer && (&retval->rev) != NULL | ^~ In file included from format_output.h:41, from format_output.c:40: libprimer3.h:927:26: note: 'rev' declared here 927 | oligo_array fwd, intl, rev; | ^~~ format_output.c:429:60: warning: the comparison will always evaluate as 'true' for the address of 'fwd' will never be NULL [-Waddress] 429 | if (pa->pick_left_primer && (&retval->fwd) != NULL | ^~ libprimer3.h:927:15: note: 'fwd' declared here 927 | oligo_array fwd, intl, rev; | ^~~ format_output.c: In function 'format_oligos': format_output.c:851:51: warning: the comparison will always evaluate as 'true' for the address of 'fwd' will never be NULL [-Waddress] 851 | if ((pa->pick_left_primer) && ((&retval->fwd) != NULL ) | ^~ libprimer3.h:927:15: note: 'fwd' declared here 927 | oligo_array fwd, intl, rev; | ^~~ format_output.c:858:55: warning: the comparison will always evaluate as 'true' for the address of 'intl' will never be NULL [-Waddress] 858 | if ((pa->pick_internal_oligo) && ((&retval->intl) != NULL ) | ^~ libprimer3.h:927:20: note: 'intl' declared here 927 | oligo_array fwd, intl, rev; | ^~~~ format_output.c:865:52: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress] 865 | if ((pa->pick_right_primer) && ((&retval->rev) != NULL ) | ^~ libprimer3.h:927:26: note: 'rev' declared here 927 | oligo_array fwd, intl, rev; | ^~~ format_output.c:888:49: warning: the comparison will always evaluate as 'true' for the address of 'fwd' will never be NULL [-Waddress] 888 | if ((pa->pick_left_primer) && ((&retval->fwd) != NULL ) | ^~ libprimer3.h:927:15: note: 'fwd' declared here 927 | oligo_array fwd, intl, rev; | ^~~ format_output.c:907:53: warning: the comparison will always evaluate as 'true' for the address of 'intl' will never be NULL [-Waddress] 907 | if ((pa->pick_internal_oligo) && ((&retval->intl) != NULL ) | ^~ libprimer3.h:927:20: note: 'intl' declared here 927 | oligo_array fwd, intl, rev; | ^~~~ format_output.c:926:50: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress] 926 | if ((pa->pick_right_primer) && ((&retval->rev) != NULL ) | ^~ libprimer3.h:927:26: note: 'rev' declared here 927 | oligo_array fwd, intl, rev; | ^~~ cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -g -Wall -Wl,-z,relro -Wl,-z,now -g -o ntdpal_main.o ntdpal_main.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o dpal.o dpal.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o thal_main.o thal_main.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal.o thal.c ar rv libthalpara.a thal_parameters.o ar: creating libthalpara.a a - thal_parameters.o ranlib libthalpara.a libprimer3.cc: In function 'char* strstr_nocase(char*, char*)': libprimer3.cc:6168:29: warning: pointer 'p' used after 'void free(void*)' [-Wuse-after-free] 6168 | else {free(tmp); return p;} | ^ libprimer3.cc:6168:15: note: call to 'void free(void*)' here 6168 | else {free(tmp); return p;} | ~~~~^~~~~ ar rv liboligotm.a oligotm.o ar: cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm creating liboligotm.a a - oligotm.o ranlib liboligotm.a cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o oligotm oligotm_main.c liboligotm.a -lm ar rv libmasker.a masker.o ar: creating libmasker.a a - masker.o ranlib libmasker.a In file included from /usr/include/string.h:548, from thal.c:43: In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'calc_hairpin' at thal.c:1922:19: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' ar rv libamplicontm.a amplicontm.o ar: creating libamplicontm.a a - amplicontm.o ranlib libamplicontm.a cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o amplicon3_core amplicontm_main.c libamplicontm.a -lm ar rv libdpal.a dpal_primer.o ar: creating libdpal.a a - dpal_primer.o ranlib libdpal.a In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'calc_bulge_internal.isra' at thal.c:2000:19: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'maxTM' at thal.c:1542:19, inlined from 'fillMatrix' at thal.c:1473:16: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntdpal ntdpal_main.o dpal.o In file included from /usr/include/string.h:548, from thal.c:43: In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'calc_hairpin' at thal.c:1922:19: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'calc_bulge_internal.isra' at thal.c:2000:19: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'maxTM' at thal.c:1542:19, inlined from 'fillMatrix' at thal.c:1473:16: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' ar rv libthal.a thal_primer.o ar: creating libthal.a a - thal_primer.o ranlib libthal.a cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntthal thal_main.o thal.o thal_parameters.o -lm ar rv libprimer3.a libprimer3.o p3_seq_lib.o ar: creating libprimer3.a a - libprimer3.o a - p3_seq_lib.o ranlib libprimer3.a g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -std=c++11 -lstdc++ -Wl,-z,relro -Wl,-z,now -g -o primer3_core primer3_boulder_main.o format_output.o read_boulder.o print_boulder.o libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -std=c++11 -lstdc++ -Wl,-z,relro -Wl,-z,now -g -o primer3_masker masker_main.c libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a -lm cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1/src' make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1' dh_auto_test --no-parallel --sourcedirectory=test cd test && make -j1 test make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/test' cd ../src; make make[3]: Entering directory '/build/reproducible-path/primer3-2.6.1/src' no windows make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/primer3-2.6.1/src' perl cmdline_test.pl TESTING command line arguments Test 1... [OK] Test 2... [OK] Test 3... [OK] Test 4... [OK] Test 5... [OK] Passed all tests - [OK] perl oligotm_test.pl TESTING Tm CALCULATIONS Tm tests nr 1-50: [OK] echo; echo; echo 'TESTING ALIGNMENT CALCS'; echo; perl dpal_test.pl ; TESTING ALIGNMENT CALCS Error handling of too-long sequence...[OK] Default implementations + alignment...[OK] Default implementations + NO alignment 1...[OK] Default implementations + NO alignment 2...[OK] Force _dpal_generic...[OK] Force _dpal_long_nopath_generic 1...[OK] Force _dpal_long_nopath_generic 2...[OK] Force long maxgap1 functions 1...[OK] Force long maxgap1 functions 2...[OK] echo; echo; echo 'TESTING THERMODYNAMIC ALIGNMENT CALCS'; echo; perl thal_test.pl ; TESTING THERMODYNAMIC ALIGNMENT CALCS Error handling of too-long sequence... 1................................... [OK] Default implementations + alignment...[OK] Default implementations + NO alignment 1...[OK] Default implementations + NO alignment 2...[OK] Default implementations + alignment (interactive)...[OK] Default implementations + NO alignment 1 (interactive)...[OK] Default implementations + NO alignment 2 (interactive)...[OK] Default implementations + alignment (interactive batch inputs)...[OK] Default implementations + alignment + HAIRPIN (interactive batch inputs)...[OK] echo; echo; echo 'TESTING MASKER'; echo; perl masker_test.pl ; TESTING MASKER Default implementations...[OK] echo; echo; echo 'TESTING amplicon3_core'; echo; perl a3test.pl TESTING amplicon3_core a3test.pl for amplicon3_core version 2.5.0 a3test.pl: testing ../src/amplicon3_core START, Thu Dec 25 21:24:41 2025 plain_WNT9B...0s [OK] plain_TBX18...0s [OK] plain_RYK...0s [OK] plain_WNT2...0s [OK] plain_ROCK2...0s [OK] plain_SFRP3...0s [OK] plain_IFT20...0s [OK] plain_DVL1...0s [OK] plain_IFT88...0s [OK] plain_FZD2...0s [OK] plain_GAPDH...0s [OK] plain_WNT1...0s [OK] plain_MYH6...0s [OK] plain_on_command_line_WNT9B...0s [OK] plain_on_command_line_TBX18...0s [OK] plain_on_command_line_RYK...0s [OK] plain_on_command_line_WNT2...0s [OK] plain_on_command_line_ROCK2...0s [OK] plain_on_command_line_SFRP3...0s [OK] plain_on_command_line_IFT20...0s [OK] plain_on_command_line_DVL1...0s [OK] plain_on_command_line_IFT88...0s [OK] plain_on_command_line_FZD2...0s [OK] plain_on_command_line_GAPDH...0s [OK] plain_on_command_line_WNT1...0s [OK] plain_on_command_line_MYH6...0s [OK] classic_WNT9B...0s [OK] classic_TBX18...0s [OK] classic_RYK...0s [OK] classic_WNT2...0s [OK] classic_ROCK2...0s [OK] classic_SFRP3...0s [OK] classic_IFT20...0s [OK] classic_DVL1...0s [OK] classic_IFT88...0s [OK] classic_FZD2...0s [OK] classic_GAPDH...0s [OK] classic_WNT1...0s [OK] classic_MYH6...0s [OK] heli_WNT9B...0s [OK] heli_TBX18...0s [OK] heli_RYK...0s [OK] heli_WNT2...0s [OK] heli_ROCK2...0s [OK] heli_SFRP3...0s [OK] heli_IFT20...0s [OK] heli_DVL1...0s [OK] heli_IFT88...0s [OK] heli_FZD2...0s [OK] heli_GAPDH...1s [OK] heli_WNT1...0s [OK] heli_MYH6...0s [OK] long_WNT9B...0s [OK] long_TBX18...0s [OK] long_RYK...0s [OK] long_WNT2...0s [OK] long_ROCK2...0s [OK] long_SFRP3...0s [OK] long_IFT20...0s [OK] long_DVL1...0s [OK] long_IFT88...0s [OK] long_FZD2...0s [OK] long_GAPDH...0s [OK] long_WNT1...0s [OK] long_MYH6...0s [OK] optimal_WNT9B...0s [OK] optimal_TBX18...0s [OK] optimal_RYK...0s [OK] optimal_WNT2...0s [OK] optimal_ROCK2...0s [OK] optimal_SFRP3...0s [OK] optimal_IFT20...0s [OK] optimal_DVL1...0s [OK] optimal_IFT88...0s [OK] optimal_FZD2...0s [OK] optimal_GAPDH...0s [OK] optimal_WNT1...0s [OK] optimal_MYH6...0s [OK] only_mv_WNT9B...0s [OK] only_mv_TBX18...0s [OK] only_mv_RYK...0s [OK] only_mv_WNT2...0s [OK] only_mv_ROCK2...0s [OK] only_mv_SFRP3...0s [OK] only_mv_IFT20...0s [OK] only_mv_DVL1...0s [OK] only_mv_IFT88...0s [OK] only_mv_FZD2...0s [OK] only_mv_GAPDH...0s [OK] only_mv_WNT1...0s [OK] only_mv_MYH6...0s [OK] no_dmso_WNT9B...0s [OK] no_dmso_TBX18...0s [OK] no_dmso_RYK...0s [OK] no_dmso_WNT2...0s [OK] no_dmso_ROCK2...0s [OK] no_dmso_SFRP3...0s [OK] no_dmso_IFT20...0s [OK] no_dmso_DVL1...0s [OK] no_dmso_IFT88...0s [OK] no_dmso_FZD2...0s [OK] no_dmso_GAPDH...0s [OK] no_dmso_WNT1...0s [OK] no_dmso_MYH6...0s [OK] Tests in a3test.pl ran for 1 s (0.0166666666666667 min) DONE Thu Dec 25 21:24:42 2025 Passed all tests - [OK] echo; echo; echo 'TESTING primer3_core'; echo; perl p3test.pl TESTING primer3_core mkdir: ../test/primer_list_tmp mkdir: ../test/primer1_list_tmp mkdir: ../test/primer1_th_list_tmp mkdir: ../test/th-w-other-tasks_list_tmp p3test.pl for primer3_core version 2.6.1 p3test.pl: testing ../src/primer3_core START, Thu Dec 25 21:24:42 2025 testing fatal errors... ./primer_global_err/annealing_temp_salt Testing --output and --error flags on ../src/primer3_core --strict_tags ./primer_global_err/annealing_temp_salt.in --output ./primer_global_err/annealing_temp_salt.tmp --error ./primer_global_err/annealing_temp_salt.tmp2 ./primer_global_err/bad_divalent_dntp_conc_1 ./primer_global_err/bad_divalent_dntp_conc_2 ./primer_global_err/bad_divalent_dntp_conc_3 ./primer_global_err/bad_divalent_dntp_conc_4 ./primer_global_err/bad_dna_conc ./primer_global_err/bad_first_base_index ./primer_global_err/bad_float_1 ./primer_global_err/bad_float_2 ./primer_global_err/bad_float_3 ./primer_global_err/bad_float_4 ./primer_global_err/bad_gc_1 ./primer_global_err/bad_gc_2 ./primer_global_err/bad_gc_3 ./primer_global_err/bad_gc_int_1 ./primer_global_err/bad_gc_int_2 ./primer_global_err/bad_gc_int_3 ./primer_global_err/bad_min_three_prime_distance ./primer_global_err/bad_num_ns ./primer_global_err/bad_num_ns_int ./primer_global_err/bad_product_sizes_1 ./primer_global_err/bad_product_sizes_2 ./primer_global_err/bad_product_sizes_3 ./primer_global_err/bad_product_sizes_4 ./primer_global_err/bad_salt_conc ./primer_global_err/bad_self_any ./primer_global_err/bad_self_any_int ./primer_global_err/bad_self_end ./primer_global_err/bad_self_end_int ./primer_global_err/bad_settings0 ./primer_global_err/bad_settings1 ./primer_global_err/bad_settings2 ./primer_global_err/bad_settings3 ./primer_global_err/bad_settings4 ./primer_global_err/bad_settings5 ./primer_global_err/bad_settings6 ./primer_global_err/empty_1 ./primer_global_err/empty_product_size ./primer_global_err/gc_clamp_min_size ./primer_global_err/incorrect_task ./primer_global_err/io_gc_content_obj_fn ./primer_global_err/io_obj_fn ./primer_global_err/junction_overlap_max_size ./primer_global_err/junction_overlap_min_size ./primer_global_err/max_annealing_temp ./primer_global_err/max_min_bound ./primer_global_err/max_min_bound_int ./primer_global_err/max_min_tm ./primer_global_err/max_min_tm_int ./primer_global_err/max_opt_bound ./primer_global_err/max_opt_bound_int ./primer_global_err/max_opt_tm ./primer_global_err/max_opt_tm_int ./primer_global_err/MAX_PRIMER_LENGTH ./primer_global_err/max_size_limit_int ./primer_global_err/max_size_limit_with_overhang ./primer_global_err/max_size_min_product ./primer_global_err/max_size_min_product_int ./primer_global_err/min_opt_tm ./primer_global_err/min_opt_tm_int ./primer_global_err/mishyb_obj_fn ./primer_global_err/mispr_obj_fn ./primer_global_err/must_match_length_0 ./primer_global_err/must_match_length_1 ./primer_global_err/must_match_length_10 ./primer_global_err/must_match_length_2 ./primer_global_err/must_match_length_3 ./primer_global_err/must_match_length_4 ./primer_global_err/must_match_length_5 ./primer_global_err/must_match_length_6 ./primer_global_err/must_match_length_7 ./primer_global_err/must_match_length_8 ./primer_global_err/must_match_length_9 ./primer_global_err/no_equal ./primer_global_err/no_terminal_equal ./primer_global_err/opt_max_size ./primer_global_err/opt_max_size_int ./primer_global_err/opt_min_size ./primer_global_err/opt_min_size_int ./primer_global_err/pair_mispr ./primer_global_err/pr_gc_content_obj_fn ./primer_global_err/product_size_obj_fn ./primer_global_err/product_tm_obj_fn ./primer_global_err/repeat_lib_err ./primer_global_err/repeat_lib_err1 ./primer_global_err/repeat_lib_err2 ./primer_global_err/repeat_lib_err3 ./primer_global_err/repeat_lib_err4 ./primer_global_err/repeat_lib_err5 ./primer_global_err/repeat_lib_err6 ./primer_global_err/repeat_lib_int_err ./primer_global_err/repeat_lib_int_err1 ./primer_global_err/repeat_lib_int_err2 ./primer_global_err/repeat_lib_int_err3 ./primer_global_err/repeat_lib_int_err4 ./primer_global_err/repeat_lib_int_err5 ./primer_global_err/repeat_lib_int_err6 ./primer_global_err/seq_quality1 ./primer_global_err/seq_quality2 ./primer_global_err/seq_quality3 ./primer_global_err/seq_quality4 ./primer_global_err/too_many_product_sizes ./primer_global_err/zero_min_size ./primer_global_err/zero_num_return [OK] primer_must_use_th...0s [OK] primer_sec_struct_dpal...0s [OK] primer_task_th...1s [OK] primer_thal_args...0s [OK] primer_thal_max_seq_error...1s [OK] primer_first_base_index...0s [OK] primer_must_match...0s [OK] test_compl_error...0s [OK] test_left_to_right_of_right...0s [OK] dv_conc_vs_dntp_conc...0s [OK] primer_boundary...0s [OK] primer_boundary1...0s [OK] primer_boundary_formatted...0s [OK] primer_boundary1_formatted...0s [OK] primer3_v1_1_4_default_settings...0s [OK] primer3web_v0_4_0_default_settings...0s [OK] primer3web_v3_0_0_default_settings...1s [OK] primer3web_v4_0_0_default_settings...1s [OK] primer_internal...0s [OK] primer_internal1...0s [OK] primer_internal_formatted...0s [OK] primer_internal1_formatted...0s [OK] primer_ok_regions...0s [OK] primer_ok_regions_formatted...0s [OK] primer_ok_regions2...7s [OK] primer_tm_lc_masking...0s [OK] primer_tm_lc_masking_formatted...0s [OK] primer_start_codon...0s [OK] primer_task...0s [OK] primer_task_formatted...0s [OK] primer_renewed_tasks...0s [OK] primer_dmso_formamide...0s [OK] primer_new_tasks...0s [OK] primer_new_tasks_formatted...1s [OK] primer_internal_position...0s [OK] primer_annealing_temp...0s [OK] primer_windows_newlines...1s [OK] primer_must_overlap_point...0s [OK] primer_overlap_junction...0s [OK] primer_all_settingsfiles...0s [OK] primer_high_tm_load_set...0s [OK] primer_high_gc_load_set...0s [OK] primer_gc_end...1s [OK] primer_check...0s [OK] primer_must_use...0s [OK] primer_must_use_formatted...0s [OK] primer_syntax...0s [OK] primer_end_pathology...0s [OK] primer_num_best...0s [OK] primer_quality_boundary...0s [OK] primer...1s [OK] primer_list_files...[OK] primer1...0s [OK] primer1_list_files...[OK] primer_mispriming...0s [OK] primer_mispriming_formatted...0s [OK] primer_mispriming_boundary1...0s [OK] primer_mispriming_boundary1_formatted...1s [OK] primer_mispriming_boundary2...0s [OK] primer_mispriming_boundary2_formatted...0s [OK] primer_mispriming_long_lib...0s [OK] primer_rat...0s [OK] primer_human...1s [OK] long_seq...0s [OK] primer_position_penalty...0s [OK] primer_position_penalty_formatted...1s [OK] p3-tmpl-mispriming...0s [OK] primer_poly_x...0s [OK] primer_three_prime_distance...0s [OK] primer_obj_fn...2s [OK] p3_3_prime_n...0s [OK] primer_masker...2s [OK] primer_masker_formatted...2s [OK] primer_overhang...0s [OK] primer_overhang_th...11s [OK] primer_mispriming_th...8s [OK] th-w-other-tasks...12s [OK] th-w-other-tasks_list_files...[OK] primer_new_tasks_th...16s [OK] primer_sec_struct_thal...12s [OK] primer_thermod_align...36s [OK] primer_thermod_align_formatted...36s [OK] primer1_th...98s [OK] primer1_th_list_files...[OK] primer_lib_amb_codes... NOTE: this test takes _much_ longer than the others (5 to 20 minutes or more). starting primer_lib_amb_codes at Thu Dec 25 21:28:56 2025...107s [OK] Tests in p3test.pl ran for 361 s (6.01666666666667 min) DONE Thu Dec 25 21:30:43 2025 Passed all tests - [OK] echo; echo; echo "Testing completed. You must check the test output for the string FAILED"; echo; echo; Testing completed. You must check the test output for the string FAILED make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1/test' dh clean --sourcedirectory=test dh_auto_clean -O--sourcedirectory=test cd test && make -j12 clean make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/test' echo; echo; echo 'CLEAN UP TEST DIRECTORIES'; echo; echo; CLEAN UP TEST DIRECTORIES rm -rf primer_list_tmp/* rm -rf primer1_list_tmp/* rm -rf primer1_th_list_tmp/* rm -rf th-w-other-tasks_list_tmp/* rm -f primer_global_err/*.tmp primer_global_err/*.tmp2 primer_global_err/*.bak rm -f amplicon3/*.tmp amplicon3/*.jpg amplicon3/decipher* rm -f *.tmp *.bak *.tmp.err *~ rm -f hyb_probe_only.for hyb_probe_only.int rm -f right_only.for right_only.rev left_only.for rm -f pcr_primers_and_io.int pcr_primers_and_io.rev pcr_primers_and_io.for rm -f pcr_primers.rev pcr_primers.for rm -f pick_primer_list_and_file_flag_th_[1-4].for pick_primer_list_and_file_flag_th_[1-4].rev rm -f pick_primer_list_and_file_flag_th_[1-4].int rm -f syntax[0-1][0-9].for syntax[0-1][0-9].int syntax[0-1][0-9].rev rm -f oligotm.*.valg # valgrind output from oligotm_test.pl --valgrind rm -f ntdpal.*.valg # valgrind output from dpal_test.pl --valgrind rm -f ntthal.*.valg # valgrind output from thal_test.pl --valgrind rm -f masker.*.valg # valgrind output from thal_test.pl --valgrind rm -f oligotm.*.valg.* # valgrind output from oligotm_test.pl --valgrind rm -f ntdpal.*.valg.* # valgrind output from dpal_test.pl --valgrind rm -f ntthal.*.valg.* # valgrind output from thal_test.pl --valgrind rm -f masker.*.valg.* # valgrind output from masker_test.pl --valgrind rm -f *.vg */*.vg # valgrind output from p3test{,z}.pl --valgrind rm -f *.vg.core.* # core files from crashed valgrind test rm -f ./core # in case we crashed and left a core file make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1/test' dh_autoreconf_clean -O--sourcedirectory=test dh_clean -O--sourcedirectory=test make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1' dh_auto_install -- PREFIX=debian/primer3/usr cd src && make -j12 install DESTDIR=/build/reproducible-path/primer3-2.6.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=debian/primer3/usr make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/src' no windows install -d "debian/primer3/usr/bin" install -m 755 primer3_core ntdpal ntthal amplicon3_core oligotm long_seq_tm_test primer3_masker "debian/primer3/usr/bin" make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1/src' make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1' dh_install -O--sourcedirectory=src dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1' dh_installexamples mkdir -p /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test; mkdir -p /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/src; mkdir -p /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/settings_files; mkdir -p /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/kmer_lists; cp -aR ./test/* /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test; cp -aR ./src/humrep_and_simple.txt /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/src; cp -a settings_files/primer*.txt /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/settings_files; cp -aR ./kmer_lists/*.list /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/kmer_lists; chmod -x /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test/thal* chmod -x /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test/amplicon3/amplicons.csv chmod -x /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test/primer_windows_newlines_input sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test/long_seq_tm_test.pl ; sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test/vgrep.pl ; make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1' dh_installman -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_lintian -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'primer3' in '../primer3_2.6.1-4_arm64.deb'. dpkg-deb: building package 'primer3-examples' in '../primer3-examples_2.6.1-4_all.deb'. dpkg-deb: building package 'primer3-dbgsym' in '../primer3-dbgsym_2.6.1-4_arm64.deb'. dpkg-genbuildinfo --build=binary -O../primer3_2.6.1-4_arm64.buildinfo dpkg-genchanges --build=binary -O../primer3_2.6.1-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1014008 and its subdirectories I: Current time: Thu Dec 25 09:32:35 -12 2025 I: pbuilder-time-stamp: 1766698355 Fri Nov 22 15:09:45 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Fri Nov 22 15:09:45 UTC 2024 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Fri Nov 22 15:09:45 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Fri Nov 22 15:09:45 UTC 2024 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-3mlata' ==================================================================================== Thu Dec 25 21:32:47 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "2 primer3 unstable /srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO 2.6.1-4" as arguments. Thu Dec 25 21:32:47 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-EaGivI0T" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Dec 25 21:32:47 UTC 2025 I: Downloading source for unstable/primer3=2.6.1-4 Reading package lists... NOTICE: 'primer3' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/primer3.git Please use: git clone https://salsa.debian.org/med-team/primer3.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 32.9 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main primer3 2.6.1-4 (dsc) [2243 B] Get:2 http://deb.debian.org/debian unstable/main primer3 2.6.1-4 (tar) [32.9 MB] Get:3 http://deb.debian.org/debian unstable/main primer3 2.6.1-4 (diff) [13.8 kB] Fetched 32.9 MB in 0s (126 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'primer3' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/primer3.git Please use: git clone https://salsa.debian.org/med-team/primer3.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 32.9 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main primer3 2.6.1-4 (dsc) [2243 B] Get:2 http://deb.debian.org/debian unstable/main primer3 2.6.1-4 (tar) [32.9 MB] Get:3 http://deb.debian.org/debian unstable/main primer3 2.6.1-4 (diff) [13.8 kB] Fetched 32.9 MB in 0s (126 MB/s) Download complete and in download only mode ============================================================================= Re-Building primer3 in unstable on arm64 on codethink03-arm64 now. Date: Thu Dec 25 21:32:47 GMT 2025 Date UTC: Thu Dec 25 21:32:47 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO/pbuilderrc_cZhZ + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' primer3 = debian-installer -o primer3 = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' primer3 = u-boot ']' + case "${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.7QxZNohO/pbuilderrc_cZhZ --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.7QxZNohO/b2 --logfile b2/build.log primer3_2.6.1-4.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: Fri Dec 26 11:32:48 +14 2025 I: pbuilder-time-stamp: 1766698368 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 [primer3_2.6.1-4.dsc] I: copying [./primer3_2.6.1.orig.tar.gz] I: copying [./primer3_2.6.1-4.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Nov 13 15:46:15 2022 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./primer3_2.6.1-4.dsc: no acceptable signature found dpkg-source: info: extracting primer3 in primer3-2.6.1 dpkg-source: info: unpacking primer3_2.6.1.orig.tar.gz dpkg-source: info: unpacking primer3_2.6.1-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch dpkg-source: info: applying primer_thermodynamic_parameters_path_2_etc.patch dpkg-source: info: applying set_prefix.patch dpkg-source: info: applying buildflags.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4141199/tmp/hooks/D01_modify_environment starting debug: Running on codethink03-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Dec 25 21:32 /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/4141199/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/4141199/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=0cd3988f9b104511adb0464f67e54a03 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=4141199 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.7QxZNohO/pbuilderrc_cZhZ --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.7QxZNohO/b2 --logfile b2/build.log primer3_2.6.1-4.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4141199/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20084 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 19.4 MB of archives. After unpacking 77.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Fetched 19.4 MB in 0s (125 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20084 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../23-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... 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_13.20_all.deb ... Unpacking debhelper (13.20) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... 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/4141199/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/4141199/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/primer3-2.6.1/ && 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 > ../primer3_2.6.1-4_source.changes dpkg-buildpackage: info: source package primer3 dpkg-buildpackage: info: source version 2.6.1-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j12 clean make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1/src' no windows rm -f *.o primer3_core ntdpal ntthal amplicon3_core oligotm long_seq_tm_test primer3_masker *~ libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a libprimer3.so.1.0.0 libdpal.a.so.1.0.0 libthal.a.so.1.0.0 libthalpara.a.so.1.0.0 libamplicontm.so.1.0.0 liboligotm.so.1.2.0 libmasker.a.so.1.0.0 example.for example.rev example.int core ../*~ cd ../test/; make clean make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/test' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. echo; echo; echo 'CLEAN UP TEST DIRECTORIES'; echo; echo; CLEAN UP TEST DIRECTORIES rm -rf primer_list_tmp/* rm -rf primer1_list_tmp/* rm -rf primer1_th_list_tmp/* rm -rf th-w-other-tasks_list_tmp/* rm -f primer_global_err/*.tmp primer_global_err/*.tmp2 primer_global_err/*.bak rm -f amplicon3/*.tmp amplicon3/*.jpg amplicon3/decipher* rm -f *.tmp *.bak *.tmp.err *~ rm -f hyb_probe_only.for hyb_probe_only.int rm -f right_only.for right_only.rev left_only.for rm -f pcr_primers_and_io.int pcr_primers_and_io.rev pcr_primers_and_io.for rm -f pcr_primers.rev pcr_primers.for rm -f pick_primer_list_and_file_flag_th_[1-4].for pick_primer_list_and_file_flag_th_[1-4].rev rm -f pick_primer_list_and_file_flag_th_[1-4].int rm -f syntax[0-1][0-9].for syntax[0-1][0-9].int syntax[0-1][0-9].rev rm -f oligotm.*.valg # valgrind output from oligotm_test.pl --valgrind rm -f ntdpal.*.valg # valgrind output from dpal_test.pl --valgrind rm -f ntthal.*.valg # valgrind output from thal_test.pl --valgrind rm -f masker.*.valg # valgrind output from thal_test.pl --valgrind rm -f oligotm.*.valg.* # valgrind output from oligotm_test.pl --valgrind rm -f ntdpal.*.valg.* # valgrind output from dpal_test.pl --valgrind rm -f ntthal.*.valg.* # valgrind output from thal_test.pl --valgrind rm -f masker.*.valg.* # valgrind output from masker_test.pl --valgrind rm -f *.vg */*.vg # valgrind output from p3test{,z}.pl --valgrind rm -f *.vg.core.* # core files from crashed valgrind test rm -f ./core # in case we crashed and left a core file make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1/test' make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1/src' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1' dh_auto_build -- 'CPP=$(CXX)' cd src && make -j12 "INSTALL=install --strip-program=true" CPP=\$\(CXX\) make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/src' no windows cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g primer3_boulder_main.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o format_output.o format_output.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o read_boulder.o read_boulder.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o print_boulder.o print_boulder.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -std=c++11 -Wl,-z,relro -Wl,-z,now -g -o libprimer3.o libprimer3.cc cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o p3_seq_lib.o p3_seq_lib.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o dpal_primer.o dpal.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal_primer.o thal.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal_parameters.o thal_parameters.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o oligotm.o oligotm.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicontm.o amplicontm.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g masker.c cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ format_output.c: In function 'print_seq': format_output.c:418:61: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress] 418 | if (pa->pick_right_primer && (&retval->rev) != NULL | ^~ In file included from format_output.h:41, from format_output.c:40: libprimer3.h:927:26: note: 'rev' declared here 927 | oligo_array fwd, intl, rev; | ^~~ format_output.c:429:60: warning: the comparison will always evaluate as 'true' for the address of 'fwd' will never be NULL [-Waddress] 429 | if (pa->pick_left_primer && (&retval->fwd) != NULL | ^~ libprimer3.h:927:15: note: 'fwd' declared here 927 | oligo_array fwd, intl, rev; | ^~~ format_output.c: In function 'format_oligos': format_output.c:851:51: warning: the comparison will always evaluate as 'true' for the address of 'fwd' will never be NULL [-Waddress] 851 | if ((pa->pick_left_primer) && ((&retval->fwd) != NULL ) | ^~ libprimer3.h:927:15: note: 'fwd' declared here 927 | oligo_array fwd, intl, rev; | ^~~ format_output.c:858:55: warning: the comparison will always evaluate as 'true' for the address of 'intl' will never be NULL [-Waddress] 858 | if ((pa->pick_internal_oligo) && ((&retval->intl) != NULL ) | ^~ libprimer3.h:927:20: note: 'intl' declared here 927 | oligo_array fwd, intl, rev; | ^~~~ format_output.c:865:52: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress] 865 | if ((pa->pick_right_primer) && ((&retval->rev) != NULL ) | ^~ libprimer3.h:927:26: note: 'rev' declared here 927 | oligo_array fwd, intl, rev; | ^~~ format_output.c:888:49: warning: the comparison will always evaluate as 'true' for the address of 'fwd' will never be NULL [-Waddress] 888 | if ((pa->pick_left_primer) && ((&retval->fwd) != NULL ) | ^~ libprimer3.h:927:15: note: 'fwd' declared here 927 | oligo_array fwd, intl, rev; | ^~~ format_output.c:907:53: warning: the comparison will always evaluate as 'true' for the address of 'intl' will never be NULL [-Waddress] 907 | if ((pa->pick_internal_oligo) && ((&retval->intl) != NULL ) | ^~ libprimer3.h:927:20: note: 'intl' declared here 927 | oligo_array fwd, intl, rev; | ^~~~ format_output.c:926:50: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress] 926 | if ((pa->pick_right_primer) && ((&retval->rev) != NULL ) | ^~ libprimer3.h:927:26: note: 'rev' declared here 927 | oligo_array fwd, intl, rev; | ^~~ cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -g -Wall -Wl,-z,relro -Wl,-z,now -g -o ntdpal_main.o ntdpal_main.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o dpal.o dpal.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o thal_main.o thal_main.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal.o thal.c ar rv libthalpara.a thal_parameters.o ar: creating libthalpara.a a - thal_parameters.o ranlib libthalpara.a ar rv liboligotm.a oligotm.o ar: creating liboligotm.a a - oligotm.o ranlib liboligotm.a cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o oligotm oligotm_main.c liboligotm.a -lm ar rv libmasker.a masker.o ar: creating libmasker.a a - masker.o ranlib libmasker.a ar rv libamplicontm.a amplicontm.o ar: creating libamplicontm.a a - amplicontm.o ranlib libamplicontm.a cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o amplicon3_core amplicontm_main.c libamplicontm.a -lm libprimer3.cc: In function 'char* strstr_nocase(char*, char*)': libprimer3.cc:6168:29: warning: pointer 'p' used after 'void free(void*)' [-Wuse-after-free] 6168 | else {free(tmp); return p;} | ^ libprimer3.cc:6168:15: note: call to 'void free(void*)' here 6168 | else {free(tmp); return p;} | ~~~~^~~~~ In file included from /usr/include/string.h:548, from thal.c:43: In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'calc_hairpin' at thal.c:1922:19: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' ar rv libdpal.a dpal_primer.o ar: creating libdpal.a a - dpal_primer.o ranlib libdpal.a In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'calc_bulge_internal.isra' at thal.c:2000:19: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'maxTM' at thal.c:1542:19, inlined from 'fillMatrix' at thal.c:1473:16: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntdpal ntdpal_main.o dpal.o In file included from /usr/include/string.h:548, from thal.c:43: In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'calc_hairpin' at thal.c:1922:19: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'calc_bulge_internal.isra' at thal.c:2000:19: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'maxTM' at thal.c:1542:19, inlined from 'fillMatrix' at thal.c:1473:16: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' ar rv libthal.a thal_primer.o ar: creating libthal.a a - thal_primer.o ranlib libthal.a cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntthal thal_main.o thal.o thal_parameters.o -lm ar rv libprimer3.a libprimer3.o p3_seq_lib.o ar: creating libprimer3.a a - libprimer3.o a - p3_seq_lib.o ranlib libprimer3.a g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -std=c++11 -lstdc++ -Wl,-z,relro -Wl,-z,now -g -o primer3_core primer3_boulder_main.o format_output.o read_boulder.o print_boulder.o libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -std=c++11 -lstdc++ -Wl,-z,relro -Wl,-z,now -g -o primer3_masker masker_main.c libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a -lm cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1/src' make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1' dh_auto_test --no-parallel --sourcedirectory=test cd test && make -j1 test make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/test' cd ../src; make make[3]: Entering directory '/build/reproducible-path/primer3-2.6.1/src' no windows make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/primer3-2.6.1/src' perl cmdline_test.pl TESTING command line arguments Test 1... [OK] Test 2... [OK] Test 3... [OK] Test 4... [OK] Test 5... [OK] Passed all tests - [OK] perl oligotm_test.pl TESTING Tm CALCULATIONS Tm tests nr 1-50: [OK] echo; echo; echo 'TESTING ALIGNMENT CALCS'; echo; perl dpal_test.pl ; TESTING ALIGNMENT CALCS Error handling of too-long sequence...[OK] Default implementations + alignment...[OK] Default implementations + NO alignment 1...[OK] Default implementations + NO alignment 2...[OK] Force _dpal_generic...[OK] Force _dpal_long_nopath_generic 1...[OK] Force _dpal_long_nopath_generic 2...[OK] Force long maxgap1 functions 1...[OK] Force long maxgap1 functions 2...[OK] echo; echo; echo 'TESTING THERMODYNAMIC ALIGNMENT CALCS'; echo; perl thal_test.pl ; TESTING THERMODYNAMIC ALIGNMENT CALCS Error handling of too-long sequence... 1................................... [OK] Default implementations + alignment...[OK] Default implementations + NO alignment 1...[OK] Default implementations + NO alignment 2...[OK] Default implementations + alignment (interactive)...[OK] Default implementations + NO alignment 1 (interactive)...[OK] Default implementations + NO alignment 2 (interactive)...[OK] Default implementations + alignment (interactive batch inputs)...[OK] Default implementations + alignment + HAIRPIN (interactive batch inputs)...[OK] echo; echo; echo 'TESTING MASKER'; echo; perl masker_test.pl ; TESTING MASKER Default implementations...[OK] echo; echo; echo 'TESTING amplicon3_core'; echo; perl a3test.pl TESTING amplicon3_core a3test.pl for amplicon3_core version 2.5.0 a3test.pl: testing ../src/amplicon3_core START, Thu Dec 25 21:33:40 2025 plain_WNT9B...0s [OK] plain_TBX18...0s [OK] plain_RYK...0s [OK] plain_WNT2...0s [OK] plain_ROCK2...0s [OK] plain_SFRP3...0s [OK] plain_IFT20...0s [OK] plain_DVL1...0s [OK] plain_IFT88...0s [OK] plain_FZD2...0s [OK] plain_GAPDH...0s [OK] plain_WNT1...0s [OK] plain_MYH6...0s [OK] plain_on_command_line_WNT9B...0s [OK] plain_on_command_line_TBX18...0s [OK] plain_on_command_line_RYK...0s [OK] plain_on_command_line_WNT2...0s [OK] plain_on_command_line_ROCK2...0s [OK] plain_on_command_line_SFRP3...0s [OK] plain_on_command_line_IFT20...0s [OK] plain_on_command_line_DVL1...0s [OK] plain_on_command_line_IFT88...0s [OK] plain_on_command_line_FZD2...0s [OK] plain_on_command_line_GAPDH...0s [OK] plain_on_command_line_WNT1...0s [OK] plain_on_command_line_MYH6...0s [OK] classic_WNT9B...0s [OK] classic_TBX18...0s [OK] classic_RYK...0s [OK] classic_WNT2...0s [OK] classic_ROCK2...0s [OK] classic_SFRP3...0s [OK] classic_IFT20...0s [OK] classic_DVL1...0s [OK] classic_IFT88...0s [OK] classic_FZD2...0s [OK] classic_GAPDH...0s [OK] classic_WNT1...0s [OK] classic_MYH6...0s [OK] heli_WNT9B...0s [OK] heli_TBX18...0s [OK] heli_RYK...0s [OK] heli_WNT2...0s [OK] heli_ROCK2...0s [OK] heli_SFRP3...0s [OK] heli_IFT20...0s [OK] heli_DVL1...0s [OK] heli_IFT88...0s [OK] heli_FZD2...0s [OK] heli_GAPDH...0s [OK] heli_WNT1...0s [OK] heli_MYH6...0s [OK] long_WNT9B...0s [OK] long_TBX18...0s [OK] long_RYK...0s [OK] long_WNT2...0s [OK] long_ROCK2...0s [OK] long_SFRP3...0s [OK] long_IFT20...0s [OK] long_DVL1...0s [OK] long_IFT88...0s [OK] long_FZD2...0s [OK] long_GAPDH...0s [OK] long_WNT1...0s [OK] long_MYH6...0s [OK] optimal_WNT9B...1s [OK] optimal_TBX18...0s [OK] optimal_RYK...0s [OK] optimal_WNT2...0s [OK] optimal_ROCK2...0s [OK] optimal_SFRP3...0s [OK] optimal_IFT20...0s [OK] optimal_DVL1...0s [OK] optimal_IFT88...0s [OK] optimal_FZD2...0s [OK] optimal_GAPDH...0s [OK] optimal_WNT1...0s [OK] optimal_MYH6...0s [OK] only_mv_WNT9B...0s [OK] only_mv_TBX18...0s [OK] only_mv_RYK...0s [OK] only_mv_WNT2...0s [OK] only_mv_ROCK2...0s [OK] only_mv_SFRP3...0s [OK] only_mv_IFT20...0s [OK] only_mv_DVL1...0s [OK] only_mv_IFT88...0s [OK] only_mv_FZD2...0s [OK] only_mv_GAPDH...0s [OK] only_mv_WNT1...0s [OK] only_mv_MYH6...0s [OK] no_dmso_WNT9B...0s [OK] no_dmso_TBX18...0s [OK] no_dmso_RYK...0s [OK] no_dmso_WNT2...0s [OK] no_dmso_ROCK2...0s [OK] no_dmso_SFRP3...0s [OK] no_dmso_IFT20...0s [OK] no_dmso_DVL1...0s [OK] no_dmso_IFT88...0s [OK] no_dmso_FZD2...0s [OK] no_dmso_GAPDH...0s [OK] no_dmso_WNT1...0s [OK] no_dmso_MYH6...0s [OK] Tests in a3test.pl ran for 1 s (0.0166666666666667 min) DONE Thu Dec 25 21:33:41 2025 Passed all tests - [OK] echo; echo; echo 'TESTING primer3_core'; echo; perl p3test.pl TESTING primer3_core mkdir: ../test/primer_list_tmp mkdir: ../test/primer1_list_tmp mkdir: ../test/primer1_th_list_tmp mkdir: ../test/th-w-other-tasks_list_tmp p3test.pl for primer3_core version 2.6.1 p3test.pl: testing ../src/primer3_core START, Thu Dec 25 21:33:41 2025 testing fatal errors... ./primer_global_err/annealing_temp_salt Testing --output and --error flags on ../src/primer3_core --strict_tags ./primer_global_err/annealing_temp_salt.in --output ./primer_global_err/annealing_temp_salt.tmp --error ./primer_global_err/annealing_temp_salt.tmp2 ./primer_global_err/bad_divalent_dntp_conc_1 ./primer_global_err/bad_divalent_dntp_conc_2 ./primer_global_err/bad_divalent_dntp_conc_3 ./primer_global_err/bad_divalent_dntp_conc_4 ./primer_global_err/bad_dna_conc ./primer_global_err/bad_first_base_index ./primer_global_err/bad_float_1 ./primer_global_err/bad_float_2 ./primer_global_err/bad_float_3 ./primer_global_err/bad_float_4 ./primer_global_err/bad_gc_1 ./primer_global_err/bad_gc_2 ./primer_global_err/bad_gc_3 ./primer_global_err/bad_gc_int_1 ./primer_global_err/bad_gc_int_2 ./primer_global_err/bad_gc_int_3 ./primer_global_err/bad_min_three_prime_distance ./primer_global_err/bad_num_ns ./primer_global_err/bad_num_ns_int ./primer_global_err/bad_product_sizes_1 ./primer_global_err/bad_product_sizes_2 ./primer_global_err/bad_product_sizes_3 ./primer_global_err/bad_product_sizes_4 ./primer_global_err/bad_salt_conc ./primer_global_err/bad_self_any ./primer_global_err/bad_self_any_int ./primer_global_err/bad_self_end ./primer_global_err/bad_self_end_int ./primer_global_err/bad_settings0 ./primer_global_err/bad_settings1 ./primer_global_err/bad_settings2 ./primer_global_err/bad_settings3 ./primer_global_err/bad_settings4 ./primer_global_err/bad_settings5 ./primer_global_err/bad_settings6 ./primer_global_err/empty_1 ./primer_global_err/empty_product_size ./primer_global_err/gc_clamp_min_size ./primer_global_err/incorrect_task ./primer_global_err/io_gc_content_obj_fn ./primer_global_err/io_obj_fn ./primer_global_err/junction_overlap_max_size ./primer_global_err/junction_overlap_min_size ./primer_global_err/max_annealing_temp ./primer_global_err/max_min_bound ./primer_global_err/max_min_bound_int ./primer_global_err/max_min_tm ./primer_global_err/max_min_tm_int ./primer_global_err/max_opt_bound ./primer_global_err/max_opt_bound_int ./primer_global_err/max_opt_tm ./primer_global_err/max_opt_tm_int ./primer_global_err/MAX_PRIMER_LENGTH ./primer_global_err/max_size_limit_int ./primer_global_err/max_size_limit_with_overhang ./primer_global_err/max_size_min_product ./primer_global_err/max_size_min_product_int ./primer_global_err/min_opt_tm ./primer_global_err/min_opt_tm_int ./primer_global_err/mishyb_obj_fn ./primer_global_err/mispr_obj_fn ./primer_global_err/must_match_length_0 ./primer_global_err/must_match_length_1 ./primer_global_err/must_match_length_10 ./primer_global_err/must_match_length_2 ./primer_global_err/must_match_length_3 ./primer_global_err/must_match_length_4 ./primer_global_err/must_match_length_5 ./primer_global_err/must_match_length_6 ./primer_global_err/must_match_length_7 ./primer_global_err/must_match_length_8 ./primer_global_err/must_match_length_9 ./primer_global_err/no_equal ./primer_global_err/no_terminal_equal ./primer_global_err/opt_max_size ./primer_global_err/opt_max_size_int ./primer_global_err/opt_min_size ./primer_global_err/opt_min_size_int ./primer_global_err/pair_mispr ./primer_global_err/pr_gc_content_obj_fn ./primer_global_err/product_size_obj_fn ./primer_global_err/product_tm_obj_fn ./primer_global_err/repeat_lib_err ./primer_global_err/repeat_lib_err1 ./primer_global_err/repeat_lib_err2 ./primer_global_err/repeat_lib_err3 ./primer_global_err/repeat_lib_err4 ./primer_global_err/repeat_lib_err5 ./primer_global_err/repeat_lib_err6 ./primer_global_err/repeat_lib_int_err ./primer_global_err/repeat_lib_int_err1 ./primer_global_err/repeat_lib_int_err2 ./primer_global_err/repeat_lib_int_err3 ./primer_global_err/repeat_lib_int_err4 ./primer_global_err/repeat_lib_int_err5 ./primer_global_err/repeat_lib_int_err6 ./primer_global_err/seq_quality1 ./primer_global_err/seq_quality2 ./primer_global_err/seq_quality3 ./primer_global_err/seq_quality4 ./primer_global_err/too_many_product_sizes ./primer_global_err/zero_min_size ./primer_global_err/zero_num_return [OK] primer_must_use_th...0s [OK] primer_sec_struct_dpal...0s [OK] primer_task_th...1s [OK] primer_thal_args...0s [OK] primer_thal_max_seq_error...0s [OK] primer_first_base_index...1s [OK] primer_must_match...0s [OK] test_compl_error...0s [OK] test_left_to_right_of_right...0s [OK] dv_conc_vs_dntp_conc...0s [OK] primer_boundary...0s [OK] primer_boundary1...0s [OK] primer_boundary_formatted...0s [OK] primer_boundary1_formatted...0s [OK] primer3_v1_1_4_default_settings...0s [OK] primer3web_v0_4_0_default_settings...0s [OK] primer3web_v3_0_0_default_settings...1s [OK] primer3web_v4_0_0_default_settings...1s [OK] primer_internal...0s [OK] primer_internal1...0s [OK] primer_internal_formatted...0s [OK] primer_internal1_formatted...0s [OK] primer_ok_regions...0s [OK] primer_ok_regions_formatted...0s [OK] primer_ok_regions2...6s [OK] primer_tm_lc_masking...0s [OK] primer_tm_lc_masking_formatted...0s [OK] primer_start_codon...0s [OK] primer_task...0s [OK] primer_task_formatted...0s [OK] primer_renewed_tasks...0s [OK] primer_dmso_formamide...0s [OK] primer_new_tasks...0s [OK] primer_new_tasks_formatted...1s [OK] primer_internal_position...0s [OK] primer_annealing_temp...0s [OK] primer_windows_newlines...1s [OK] primer_must_overlap_point...0s [OK] primer_overlap_junction...0s [OK] primer_all_settingsfiles...0s [OK] primer_high_tm_load_set...0s [OK] primer_high_gc_load_set...0s [OK] primer_gc_end...1s [OK] primer_check...0s [OK] primer_must_use...0s [OK] primer_must_use_formatted...0s [OK] primer_syntax...0s [OK] primer_end_pathology...0s [OK] primer_num_best...0s [OK] primer_quality_boundary...0s [OK] primer...1s [OK] primer_list_files...[OK] primer1...0s [OK] primer1_list_files...[OK] primer_mispriming...0s [OK] primer_mispriming_formatted...0s [OK] primer_mispriming_boundary1...0s [OK] primer_mispriming_boundary1_formatted...0s [OK] primer_mispriming_boundary2...0s [OK] primer_mispriming_boundary2_formatted...1s [OK] primer_mispriming_long_lib...0s [OK] primer_rat...0s [OK] primer_human...1s [OK] long_seq...0s [OK] primer_position_penalty...0s [OK] primer_position_penalty_formatted...1s [OK] p3-tmpl-mispriming...0s [OK] primer_poly_x...0s [OK] primer_three_prime_distance...0s [OK] primer_obj_fn...2s [OK] p3_3_prime_n...0s [OK] primer_masker...2s [OK] primer_masker_formatted...1s [OK] primer_overhang...1s [OK] primer_overhang_th...10s [OK] primer_mispriming_th...9s [OK] th-w-other-tasks...12s [OK] th-w-other-tasks_list_files...[OK] primer_new_tasks_th...15s [OK] primer_sec_struct_thal...12s [OK] primer_thermod_align...37s [OK] primer_thermod_align_formatted...36s [OK] primer1_th...96s [OK] primer1_th_list_files...[OK] primer_lib_amb_codes... NOTE: this test takes _much_ longer than the others (5 to 20 minutes or more). starting primer_lib_amb_codes at Thu Dec 25 21:37:52 2025...112s [OK] Tests in p3test.pl ran for 363 s (6.05 min) DONE Thu Dec 25 21:39:44 2025 Passed all tests - [OK] echo; echo; echo "Testing completed. You must check the test output for the string FAILED"; echo; echo; Testing completed. You must check the test output for the string FAILED make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1/test' dh clean --sourcedirectory=test dh_auto_clean -O--sourcedirectory=test cd test && make -j12 clean make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/test' echo; echo; echo 'CLEAN UP TEST DIRECTORIES'; echo; echo; CLEAN UP TEST DIRECTORIES rm -rf primer_list_tmp/* rm -rf primer1_list_tmp/* rm -rf primer1_th_list_tmp/* rm -rf th-w-other-tasks_list_tmp/* rm -f primer_global_err/*.tmp primer_global_err/*.tmp2 primer_global_err/*.bak rm -f amplicon3/*.tmp amplicon3/*.jpg amplicon3/decipher* rm -f *.tmp *.bak *.tmp.err *~ rm -f hyb_probe_only.for hyb_probe_only.int rm -f right_only.for right_only.rev left_only.for rm -f pcr_primers_and_io.int pcr_primers_and_io.rev pcr_primers_and_io.for rm -f pcr_primers.rev pcr_primers.for rm -f pick_primer_list_and_file_flag_th_[1-4].for pick_primer_list_and_file_flag_th_[1-4].rev rm -f pick_primer_list_and_file_flag_th_[1-4].int rm -f syntax[0-1][0-9].for syntax[0-1][0-9].int syntax[0-1][0-9].rev rm -f oligotm.*.valg # valgrind output from oligotm_test.pl --valgrind rm -f ntdpal.*.valg # valgrind output from dpal_test.pl --valgrind rm -f ntthal.*.valg # valgrind output from thal_test.pl --valgrind rm -f masker.*.valg # valgrind output from thal_test.pl --valgrind rm -f oligotm.*.valg.* # valgrind output from oligotm_test.pl --valgrind rm -f ntdpal.*.valg.* # valgrind output from dpal_test.pl --valgrind rm -f ntthal.*.valg.* # valgrind output from thal_test.pl --valgrind rm -f masker.*.valg.* # valgrind output from masker_test.pl --valgrind rm -f *.vg */*.vg # valgrind output from p3test{,z}.pl --valgrind rm -f *.vg.core.* # core files from crashed valgrind test rm -f ./core # in case we crashed and left a core file make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1/test' dh_autoreconf_clean -O--sourcedirectory=test dh_clean -O--sourcedirectory=test make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1' dh_auto_install -- PREFIX=debian/primer3/usr cd src && make -j12 install DESTDIR=/build/reproducible-path/primer3-2.6.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=debian/primer3/usr make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/src' no windows install -d "debian/primer3/usr/bin" install -m 755 primer3_core ntdpal ntthal amplicon3_core oligotm long_seq_tm_test primer3_masker "debian/primer3/usr/bin" make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1/src' make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1' dh_install -O--sourcedirectory=src dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1' dh_installexamples mkdir -p /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test; mkdir -p /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/src; mkdir -p /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/settings_files; mkdir -p /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/kmer_lists; cp -aR ./test/* /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test; cp -aR ./src/humrep_and_simple.txt /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/src; cp -a settings_files/primer*.txt /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/settings_files; cp -aR ./kmer_lists/*.list /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/kmer_lists; chmod -x /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test/thal* chmod -x /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test/amplicon3/amplicons.csv chmod -x /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test/primer_windows_newlines_input sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test/long_seq_tm_test.pl ; sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' /build/reproducible-path/primer3-2.6.1/debian/primer3-examples/usr/share/doc/primer3/examples/test/vgrep.pl ; make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1' dh_installman -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_lintian -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'primer3-dbgsym' in '../primer3-dbgsym_2.6.1-4_arm64.deb'. dpkg-deb: building package 'primer3' in '../primer3_2.6.1-4_arm64.deb'. dpkg-deb: building package 'primer3-examples' in '../primer3-examples_2.6.1-4_all.deb'. dpkg-genbuildinfo --build=binary -O../primer3_2.6.1-4_arm64.buildinfo dpkg-genchanges --build=binary -O../primer3_2.6.1-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/4141199/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/4141199/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/4141199 and its subdirectories I: Current time: Fri Dec 26 11:41:53 +14 2025 I: pbuilder-time-stamp: 1766698913 + false + set +x Thu Dec 25 21:41:53 UTC 2025 I: Signing ./b2/primer3_2.6.1-4_arm64.buildinfo as primer3_2.6.1-4_arm64.buildinfo.asc Thu Dec 25 21:41:53 UTC 2025 I: Signed ./b2/primer3_2.6.1-4_arm64.buildinfo as ./b2/primer3_2.6.1-4_arm64.buildinfo.asc Thu Dec 25 21:41:53 UTC 2025 - build #2 for primer3/unstable/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Thu Dec 25 21:41:53 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-EaGivI0T, removing. /srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO: total 76 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 15:09 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 15:18 b2 -rw-r--r-- 1 jenkins jenkins 2243 Nov 13 2022 primer3_2.6.1-4.dsc -rw------- 1 jenkins jenkins 58586 Nov 22 15:09 rbuildlog.JLrjCS8 /srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO/b1: total 31664 -rw-r--r-- 1 jenkins jenkins 54932 Nov 22 15:09 build.log -rw-r--r-- 1 jenkins jenkins 434948 Nov 22 15:09 primer3-dbgsym_2.6.1-4_arm64.deb -rw-r--r-- 1 jenkins jenkins 31644144 Nov 22 15:09 primer3-examples_2.6.1-4_all.deb -rw-r--r-- 1 jenkins jenkins 13788 Nov 22 15:09 primer3_2.6.1-4.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2243 Nov 22 15:09 primer3_2.6.1-4.dsc -rw-r--r-- 1 jenkins jenkins 5227 Nov 22 15:09 primer3_2.6.1-4_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6109 Nov 22 15:09 primer3_2.6.1-4_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1840 Nov 22 15:09 primer3_2.6.1-4_arm64.changes -rw-r--r-- 1 jenkins jenkins 186456 Nov 22 15:09 primer3_2.6.1-4_arm64.deb -rw-r--r-- 1 jenkins jenkins 1293 Nov 22 15:09 primer3_2.6.1-4_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO/b2: total 31616 -rw-r--r-- 1 jenkins jenkins 56864 Nov 22 15:18 build.log -rw-r--r-- 1 jenkins jenkins 434948 Nov 22 15:18 primer3-dbgsym_2.6.1-4_arm64.deb -rw-r--r-- 1 jenkins jenkins 31644144 Nov 22 15:18 primer3-examples_2.6.1-4_all.deb -rw-r--r-- 1 jenkins jenkins 13788 Nov 22 15:18 primer3_2.6.1-4.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2243 Nov 22 15:18 primer3_2.6.1-4.dsc -rw-r--r-- 1 jenkins jenkins 5227 Nov 22 15:18 primer3_2.6.1-4_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6109 Nov 22 15:18 primer3_2.6.1-4_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1840 Nov 22 15:18 primer3_2.6.1-4_arm64.changes -rw-r--r-- 1 jenkins jenkins 186456 Nov 22 15:18 primer3_2.6.1-4_arm64.deb -rw-r--r-- 1 jenkins jenkins 1293 Nov 22 15:18 primer3_2.6.1-4_source.changes Fri Nov 22 15:18:55 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Fri Nov 22 15:18:56 UTC 2024 I: primer3_2.6.1-4_arm64.changes: Format: 1.8 Date: Sun, 13 Nov 2022 11:49:48 +0100 Source: primer3 Binary: primer3 primer3-dbgsym primer3-examples Architecture: arm64 all Version: 2.6.1-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: primer3 - tool to design flanking oligo nucleotides for DNA amplification primer3-examples - tool to design flanking oligo nucleotides for DNA amplification ( Closes: 1023823 Changes: primer3 (2.6.1-4) unstable; urgency=medium . * Team upload. . [ Lukas Märdian ] * d/t/run-unit-test: fix autopkgtest sed commands on s390x. (Closes: #1023823) Checksums-Sha1: 879e308cd7a27dba267aac1a8693ad21668cdafe 434948 primer3-dbgsym_2.6.1-4_arm64.deb df8edaf64af395a56512ca7d375dc0a30465d246 31644144 primer3-examples_2.6.1-4_all.deb d6c7939766effc40793fc34026343e9b62cf0446 5227 primer3_2.6.1-4_arm64.buildinfo aba9ff0b9b385fb1ae7e31cde4848845e6ac2a1d 186456 primer3_2.6.1-4_arm64.deb Checksums-Sha256: 353120e8c95bf6d52dcf171b75a12d6af7a6991134a16640758229301d136636 434948 primer3-dbgsym_2.6.1-4_arm64.deb 1570823d07b9e4b19652d3f32cf60120531e272bfcd204b2cb36a41696999035 31644144 primer3-examples_2.6.1-4_all.deb 61f11e6dc7407d290a3a272df8aa54c07f8ea2f47ff5d8c18e26a3ca391c3d83 5227 primer3_2.6.1-4_arm64.buildinfo 070c1ecafba297c12224bffb0eaaae83ab732d4127dda4d4cd32580ff13b905f 186456 primer3_2.6.1-4_arm64.deb Files: 89842fa052cf19ad8f314b6cc8f0abbe 434948 debug optional primer3-dbgsym_2.6.1-4_arm64.deb 1d8dae15f3ebdbff2d1ae505ce7d7fef 31644144 science optional primer3-examples_2.6.1-4_all.deb be15183ae0899eeaeea2178a9ba27c73 5227 science optional primer3_2.6.1-4_arm64.buildinfo f835f55bcf0f7e9d434671cb2fbe8571 186456 science optional primer3_2.6.1-4_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/primer3_2.6.1-4.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/primer3_2.6.1-4.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/primer3_2.6.1-4.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/primer3_2.6.1-4.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/arm64/primer3_2.6.1-4_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/primer3_2.6.1-4.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-11-22 15:09:36.037322550 +0000 +++ b2/build.log 2024-11-22 15:18:54.420117240 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Dec 25 09:23:46 -12 2025 -I: pbuilder-time-stamp: 1766697826 +I: Current time: Fri Dec 26 11:32:48 +14 2025 +I: pbuilder-time-stamp: 1766698368 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying buildflags.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1014008/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4141199/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 25 21:32 /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/4141199/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4141199/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='1da4862480c84894992fd79a1df8efa0' - 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='1014008' - PS1='# ' - PS2='> ' + INVOCATION_ID=0cd3988f9b104511adb0464f67e54a03 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=4141199 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.7QxZNohO/pbuilderrc_il3F --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.7QxZNohO/b1 --logfile b1/build.log primer3_2.6.1-4.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO/pbuilderrc_cZhZ --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.7QxZNohO/b2 --logfile b2/build.log primer3_2.6.1-4.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink01-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1014008/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/4141199/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: 27 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] -Fetched 19.4 MB in 0s (99.1 MB/s) +Fetched 19.4 MB in 0s (125 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20084 files and directories currently installed.) @@ -272,7 +304,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/primer3-2.6.1/ && 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 > ../primer3_2.6.1-4_source.changes +I: user script /srv/workspace/pbuilder/4141199/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/4141199/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/primer3-2.6.1/ && 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 > ../primer3_2.6.1-4_source.changes dpkg-buildpackage: info: source package primer3 dpkg-buildpackage: info: source version 2.6.1-4 dpkg-buildpackage: info: source distribution unstable @@ -345,9 +381,9 @@ cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal_primer.o thal.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal_parameters.o thal_parameters.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o oligotm.o oligotm.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicontm.o amplicontm.c cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g masker.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ format_output.c: In function 'print_seq': format_output.c:418:61: warning: the comparison will always evaluate as 'true' for the address of 'rev' will never be NULL [-Waddress] 418 | if (pa->pick_right_primer && (&retval->rev) != NULL @@ -408,23 +444,28 @@ ar: creating libthalpara.a a - thal_parameters.o ranlib libthalpara.a -libprimer3.cc: In function 'char* strstr_nocase(char*, char*)': -libprimer3.cc:6168:29: warning: pointer 'p' used after 'void free(void*)' [-Wuse-after-free] - 6168 | else {free(tmp); return p;} - | ^ -libprimer3.cc:6168:15: note: call to 'void free(void*)' here - 6168 | else {free(tmp); return p;} - | ~~~~^~~~~ ar rv liboligotm.a oligotm.o -ar: cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm -creating liboligotm.a +ar: creating liboligotm.a a - oligotm.o ranlib liboligotm.a +cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o oligotm oligotm_main.c liboligotm.a -lm ar rv libmasker.a masker.o ar: creating libmasker.a a - masker.o ranlib libmasker.a +ar rv libamplicontm.a amplicontm.o +ar: creating libamplicontm.a +a - amplicontm.o +ranlib libamplicontm.a +cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o amplicon3_core amplicontm_main.c libamplicontm.a -lm +libprimer3.cc: In function 'char* strstr_nocase(char*, char*)': +libprimer3.cc:6168:29: warning: pointer 'p' used after 'void free(void*)' [-Wuse-after-free] + 6168 | else {free(tmp); return p;} + | ^ +libprimer3.cc:6168:15: note: call to 'void free(void*)' here + 6168 | else {free(tmp); return p;} + | ~~~~^~~~~ In file included from /usr/include/string.h:548, from thal.c:43: In function 'strcpy', @@ -434,11 +475,6 @@ 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' -ar rv libamplicontm.a amplicontm.o -ar: creating libamplicontm.a -a - amplicontm.o -ranlib libamplicontm.a -cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/primer3-2.6.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o amplicon3_core amplicontm_main.c libamplicontm.a -lm ar rv libdpal.a dpal_primer.o ar: creating libdpal.a a - dpal_primer.o @@ -573,7 +609,7 @@ a3test.pl: testing ../src/amplicon3_core -START, Thu Dec 25 21:24:41 2025 +START, Thu Dec 25 21:33:40 2025 plain_WNT9B...0s [OK] plain_TBX18...0s [OK] plain_RYK...0s [OK] @@ -623,7 +659,7 @@ heli_DVL1...0s [OK] heli_IFT88...0s [OK] heli_FZD2...0s [OK] -heli_GAPDH...1s [OK] +heli_GAPDH...0s [OK] heli_WNT1...0s [OK] heli_MYH6...0s [OK] long_WNT9B...0s [OK] @@ -639,7 +675,7 @@ long_GAPDH...0s [OK] long_WNT1...0s [OK] long_MYH6...0s [OK] -optimal_WNT9B...0s [OK] +optimal_WNT9B...1s [OK] optimal_TBX18...0s [OK] optimal_RYK...0s [OK] optimal_WNT2...0s [OK] @@ -681,7 +717,7 @@ Tests in a3test.pl ran for 1 s (0.0166666666666667 min) -DONE Thu Dec 25 21:24:42 2025 Passed all tests - [OK] +DONE Thu Dec 25 21:33:41 2025 Passed all tests - [OK] echo; echo; echo 'TESTING primer3_core'; echo; perl p3test.pl @@ -698,7 +734,7 @@ p3test.pl: testing ../src/primer3_core -START, Thu Dec 25 21:24:42 2025 +START, Thu Dec 25 21:33:41 2025 testing fatal errors... ./primer_global_err/annealing_temp_salt @@ -812,8 +848,8 @@ primer_sec_struct_dpal...0s [OK] primer_task_th...1s [OK] primer_thal_args...0s [OK] -primer_thal_max_seq_error...1s [OK] -primer_first_base_index...0s [OK] +primer_thal_max_seq_error...0s [OK] +primer_first_base_index...1s [OK] primer_must_match...0s [OK] test_compl_error...0s [OK] test_left_to_right_of_right...0s [OK] @@ -832,7 +868,7 @@ primer_internal1_formatted...0s [OK] primer_ok_regions...0s [OK] primer_ok_regions_formatted...0s [OK] -primer_ok_regions2...7s [OK] +primer_ok_regions2...6s [OK] primer_tm_lc_masking...0s [OK] primer_tm_lc_masking_formatted...0s [OK] primer_start_codon...0s [OK] @@ -865,9 +901,9 @@ primer_mispriming...0s [OK] primer_mispriming_formatted...0s [OK] primer_mispriming_boundary1...0s [OK] -primer_mispriming_boundary1_formatted...1s [OK] +primer_mispriming_boundary1_formatted...0s [OK] primer_mispriming_boundary2...0s [OK] -primer_mispriming_boundary2_formatted...0s [OK] +primer_mispriming_boundary2_formatted...1s [OK] primer_mispriming_long_lib...0s [OK] primer_rat...0s [OK] primer_human...1s [OK] @@ -880,25 +916,25 @@ primer_obj_fn...2s [OK] p3_3_prime_n...0s [OK] primer_masker...2s [OK] -primer_masker_formatted...2s [OK] -primer_overhang...0s [OK] -primer_overhang_th...11s [OK] -primer_mispriming_th...8s [OK] +primer_masker_formatted...1s [OK] +primer_overhang...1s [OK] +primer_overhang_th...10s [OK] +primer_mispriming_th...9s [OK] th-w-other-tasks...12s [OK] th-w-other-tasks_list_files...[OK] -primer_new_tasks_th...16s [OK] +primer_new_tasks_th...15s [OK] primer_sec_struct_thal...12s [OK] -primer_thermod_align...36s [OK] +primer_thermod_align...37s [OK] primer_thermod_align_formatted...36s [OK] -primer1_th...98s [OK] +primer1_th...96s [OK] primer1_th_list_files...[OK] primer_lib_amb_codes... NOTE: this test takes _much_ longer than the others (5 to 20 minutes or more). -starting primer_lib_amb_codes at Thu Dec 25 21:28:56 2025...107s [OK] +starting primer_lib_amb_codes at Thu Dec 25 21:37:52 2025...112s [OK] -Tests in p3test.pl ran for 361 s (6.01666666666667 min) +Tests in p3test.pl ran for 363 s (6.05 min) -DONE Thu Dec 25 21:30:43 2025 Passed all tests - [OK] +DONE Thu Dec 25 21:39:44 2025 Passed all tests - [OK] echo; echo; echo "Testing completed. You must check the test output for the string FAILED"; echo; echo; @@ -1001,9 +1037,9 @@ dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src +dpkg-deb: building package 'primer3-dbgsym' in '../primer3-dbgsym_2.6.1-4_arm64.deb'. dpkg-deb: building package 'primer3' in '../primer3_2.6.1-4_arm64.deb'. dpkg-deb: building package 'primer3-examples' in '../primer3-examples_2.6.1-4_all.deb'. -dpkg-deb: building package 'primer3-dbgsym' in '../primer3-dbgsym_2.6.1-4_arm64.deb'. dpkg-genbuildinfo --build=binary -O../primer3_2.6.1-4_arm64.buildinfo dpkg-genchanges --build=binary -O../primer3_2.6.1-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1011,12 +1047,14 @@ 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/4141199/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4141199/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/1014008 and its subdirectories -I: Current time: Thu Dec 25 09:32:35 -12 2025 -I: pbuilder-time-stamp: 1766698355 +I: removing directory /srv/workspace/pbuilder/4141199 and its subdirectories +I: Current time: Fri Dec 26 11:41:53 +14 2025 +I: pbuilder-time-stamp: 1766698913 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/primer3_2.6.1-4.diff: 72.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/primer3_2.6.1-4.diff.gz b2/build.log: 81.3% -- replaced with stdout Compressing the 1st log... b1/build.log: 81.9% -- replaced with stdout Fri Nov 22 15:18:57 UTC 2024 I: diffoscope 283 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_primer3_unstable_arm64_1732288737 + touch /var/log/reproducible-builds/diffoscope_stamp_primer3_unstable_arm64_1732288737 + RESULT=0 + systemd-run '--description=diffoscope on primer3/2.6.1-4 in unstable/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_14-69790 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO --run-session -c jenkins-reproducible-unstable-diffoscope-a93cc3ab-879d-478b-be76-b1b32b5a6236 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO/dbd-tmp-o5HNS8Y ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO/primer3_2.6.1-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO/primer3_2.6.1-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO/primer3_2.6.1-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO/b1/primer3_2.6.1-4_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO/b2/primer3_2.6.1-4_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_14-69790.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO/primer3_2.6.1-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO/primer3_2.6.1-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO/primer3_2.6.1-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO/b1/primer3_2.6.1-4_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.7QxZNohO/b2/primer3_2.6.1-4_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.604s) 0.604s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.293s) 0.293s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 894ms CPU time consumed: 895ms _ _____ _ __ _ __(_)_ __ ___ ___ _ _|___ / | '_ \| '__| | '_ ` _ \ / _ \ '__||_ \ | |_) | | | | | | | | | __/ | ___) | | .__/|_| |_|_| |_| |_|\___|_| |____/ |_| Fri Nov 22 15:18:58 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Fri Nov 22 15:18:58 UTC 2024 I: primer3 from unstable built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-22 15:18:59] INFO: Starting at 2024-11-22 15:18:59.007692 [2024-11-22 15:18:59] INFO: Generating the pages of 1 package(s) [2024-11-22 15:18:59] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/primer3 didn't produce a buildlog, even though it has been built. [2024-11-22 15:18:59] INFO: Finished at 2024-11-22 15:18:59.445269, took: 0:00:00.437583 Fri Nov 22 15:18:59 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/primer3.html Fri Nov 22 15:18:59 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Nov 22 15:18:59 UTC 2024 I: Submitting 8.0K b1/primer3_2.6.1-4_arm64.buildinfo.asc https://buildinfo.debian.net/d6c7939766effc40793fc34026343e9b62cf0446/primer3_2.6.1-4_all Fri Nov 22 15:19:00 UTC 2024 I: Submitting 8.0K b2/primer3_2.6.1-4_arm64.buildinfo.asc https://buildinfo.debian.net/b8f0e2f5ce2af5dd4283751b29d669846aa70fe2/primer3_2.6.1-4_all Fri Nov 22 15:19:01 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Nov 22 15:19:01 UTC 2024 I: Done submitting .buildinfo files. Fri Nov 22 15:19:01 UTC 2024 I: Removing signed primer3_2.6.1-4_arm64.buildinfo.asc files: removed './b1/primer3_2.6.1-4_arm64.buildinfo.asc' removed './b2/primer3_2.6.1-4_arm64.buildinfo.asc' 1732288741 arm64 unstable primer3 Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/primer3_2.6.1-4.rbuild.log: 78.8% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/primer3_2.6.1-4.rbuild.log.gz [2024-11-22 15:19:01] INFO: Starting at 2024-11-22 15:19:01.453210 [2024-11-22 15:19:01] INFO: Generating the pages of 1 package(s) [2024-11-22 15:19:01] INFO: Finished at 2024-11-22 15:19:01.913469, took: 0:00:00.460267 All cleanup done. Fri Nov 22 15:19:02 UTC 2024 - total duration: 0h 18m 38s. Fri Nov 22 15:19:02 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-yl9En6RD, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 18min 41.374s CPU time consumed: 8.228s