Running as unit: rb-build-amd64_8-45948.service ==================================================================================== Tue Jan 21 18:01:38 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_8) on jenkins, called using "ionos15-amd64 ionos11-amd64" as arguments. Tue Jan 21 18:01:38 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-EKlfyBVp" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Jan 21 18:01:38 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Tue Jan 21 18:01:38 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-ebIxRZ' Tue Jan 21 18:01:39 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Tue Jan 21 18:01:39 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-FKErnK' 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 amd64 on jenkins now. 1st build will be done on ionos15-amd64.debian.net. 2nd build will be done on ionos11-amd64.debian.net. ============================================================================= Tue Jan 21 18:02:01 UTC 2025 I: starting to build primer3/unstable/amd64 on jenkins on '2025-01-21 18:01' Tue Jan 21 18:02:01 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_8/45948/console.log 1737482521 amd64 unstable primer3 Tue Jan 21 18:02:01 UTC 2025 I: Downloading source for unstable/primer3=2.6.1-5 --2025-01-21 18:02:01-- http://deb.debian.org/debian/pool/main/p/primer3/primer3_2.6.1-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2101 (2.1K) [text/prs.lines.tag] Saving to: ‘primer3_2.6.1-5.dsc’ 0K .. 100% 276M=0s 2025-01-21 18:02:01 (276 MB/s) - ‘primer3_2.6.1-5.dsc’ saved [2101/2101] --2025-01-21 18:02:01-- http://deb.debian.org/debian/pool/main/p/primer3/primer3_2.6.1-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2101 (2.1K) [text/prs.lines.tag] Saving to: ‘primer3_2.6.1-5.dsc’ 0K .. 100% 276M=0s 2025-01-21 18:02:01 (276 MB/s) - ‘primer3_2.6.1-5.dsc’ saved [2101/2101] Tue Jan 21 18:02:01 UTC 2025 I: primer3_2.6.1-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: primer3 Binary: primer3, primer3-examples Architecture: any all Version: 2.6.1-5 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Homepage: http://primer3.sourceforge.net Standards-Version: 4.7.0 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 2c5ec5e1be386c69b4e6b686b0765f31ca4257d6 13976 primer3_2.6.1-5.debian.tar.xz Checksums-Sha256: 805cef7ef39607cd40f0f5bb8b32e35e20007153a0a55131dd430ce644c8fb9e 32858944 primer3_2.6.1.orig.tar.gz 6a5b39ad2920ba085d5c1799f6e41c028bfe34db4c21b9c58b31998f98a17f42 13976 primer3_2.6.1-5.debian.tar.xz Files: d18c095694b586c300c88fab4b116c8c 32858944 primer3_2.6.1.orig.tar.gz 28b989a292909a073f143fabc5d430ee 13976 primer3_2.6.1-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEUtW9Dn1NsITjS1hl1KQc+t2yDbUFAmdMUawACgkQ1KQc+t2y DbWZIBAAqzmSnkkRlDwr5JutlukF4KCSewjSTINug9uS/YZF0WFEo3gmyI8nURnH ZxMsl1CPrzHBD+GR7QrrfI+xEGNazP/h3FT7xKUw17GX1gYcuCFHlnLmWG0JG+jv i/aowZKSh0a3b2FB42ThkGG6sDwVYU0AI331mbcT5kSWMRbf/xfzAUYEtaartzBi otF6e+pbp8Rz23EcPSZ21AEfJWU9LEcgpt4p2EAzo+pS9khIrxjXuwuVv7+6ATz9 K6ny7WwnOkovBGi4xBD9jXXneZhqLha42hvQsqCW7WtaLt23MFQOSzxZOdhqJ9Df 5qE3BpYD5pWchx+Uj0ii0ee5XlgNTQzJV9/9VQLutnP/kfJMD/YdJWZ5T75Tm/nR UXQi2jnz0J+rSMNmmV/PvjKNomDkKXp9aDwFow+GZAYyJYQH8goq+5AUS6Za7zc6 7ssmzqwcJQknCT1mVpRPDVT8RjdhGtDSXRKc0xhpufJr6PW8mHqRBy3Z6T0xL5Rx Mb3d2aatPUA0FQZLxTEth5ICqaJd3mlsPTJyR66y3A9m3Wa9PXgFcE83n2GdgdLu MU+R5PoMoDOP4wY8VwVoSeGszoW1wyV9qIkF52WpcEVbk4OPl9Dp7W6vJHCJAJ5+ IZmXbmmvHv7hRAEZaexWvNL2KfjXC3xTrgM5FzFNE+4K6ESVN+I= =Na+R -----END PGP SIGNATURE----- Tue Jan 21 18:02:01 UTC 2025 I: Checking whether the package is not for us Tue Jan 21 18:02:01 UTC 2025 I: Starting 1st build on remote node ionos15-amd64.debian.net. Tue Jan 21 18:02:01 UTC 2025 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Tue Jan 21 18:02:01 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Tue Jan 21 18:02:01 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-u7c2o9' ==================================================================================== Tue Feb 24 00:25:04 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "1 primer3 unstable /srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7 2.6.1-5" as arguments. Tue Feb 24 00:25:04 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-dTuOrJnd" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Feb 24 00:25:04 UTC 2026 I: Downloading source for unstable/primer3=2.6.1-5 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 2.6.1-5 (dsc) [2101 B] Get:2 http://deb.debian.org/debian unstable/main primer3 2.6.1-5 (tar) [32.9 MB] Get:3 http://deb.debian.org/debian unstable/main primer3 2.6.1-5 (diff) [14.0 kB] Fetched 32.9 MB in 1s (49.1 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 2.6.1-5 (dsc) [2101 B] Get:2 http://deb.debian.org/debian unstable/main primer3 2.6.1-5 (tar) [32.9 MB] Get:3 http://deb.debian.org/debian unstable/main primer3 2.6.1-5 (diff) [14.0 kB] Fetched 32.9 MB in 1s (49.1 MB/s) Download complete and in download only mode ============================================================================= Building primer3 in unstable on amd64 on ionos15-amd64 now. Date: Tue Feb 24 00:25:05 UTC 2026 Date UTC: Tue Feb 24 00:25:05 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Mon Feb 23 12:25:05 -12 2026 I: pbuilder-time-stamp: 1771892705 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_2.6.1-5.dsc] I: copying [./primer3_2.6.1.orig.tar.gz] I: copying [./primer3_2.6.1-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./primer3_2.6.1-5.dsc: unsupported subcommand 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_2.6.1-5.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/638090/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='18eaeed902294d418b16ad1f8786c072' 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='638090' 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.zFxAXyg7/pbuilderrc_jXoK --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.zFxAXyg7/b1 --logfile b1/build.log primer3_2.6.1-5.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.11.10+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1~bpo12+1 (2024-12-19) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/638090/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19851 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} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 20.5 MB of archives. After unpacking 77.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-1 [92.2 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-2 [539 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Fetched 20.5 MB in 0s (70.2 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19851 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_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-1_amd64.deb ... Unpacking bsdextrautils (2.40.4-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-5_amd64.deb ... Unpacking m4 (1.4.19-5) ... 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_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-2_all.deb ... Unpacking libtool (2.5.4-2) ... 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_1.14.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-1_amd64.deb ... Unpacking libunistring5:amd64 (1.3-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-6_amd64.deb ... Unpacking libicu72:amd64 (72.1-6) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_amd64.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libicu72:amd64 (72.1-6) ... Setting up bsdextrautils (2.40.4-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... 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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_2.6.1-5_source.changes dpkg-buildpackage: info: source package primer3 dpkg-buildpackage: info: source version 2.6.1-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Ananthu C V dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j42 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' 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' debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1' rm -rf /build/reproducible-path/primer3-2.6.1/src/debian make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1' 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 -j42 "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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal_parameters.o thal_parameters.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g masker.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal.o thal.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; | ^~~ ar rv libthalpara.a thal_parameters.o ar: creating libthalpara.a a - thal_parameters.o ranlib libthalpara.a ar rv liboligotm.a oligotm.o 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 -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm 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 -fcf-protection -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 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 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 -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o amplicon3_core amplicontm_main.c libamplicontm.a -lm 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: 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 -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntdpal ntdpal_main.o dpal.o /usr/include/x86_64-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/x86_64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' 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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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 -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntthal thal_main.o thal.o thal_parameters.o -lm ar rv libthal.a thal_primer.o ar: creating libthal.a a - thal_primer.o ranlib libthal.a 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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, Tue Feb 24 00:27:48 2026 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...1s [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 Tue Feb 24 00:27:49 2026 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, Tue Feb 24 00:27:49 2026 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...4s [OK] primer_thal_args...1s [OK] primer_thal_max_seq_error...0s [OK] primer_first_base_index...0s [OK] primer_must_match...0s [OK] test_compl_error...0s [OK] test_left_to_right_of_right...1s [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...2s [OK] primer3web_v4_0_0_default_settings...0s [OK] primer_internal...0s [OK] primer_internal1...0s [OK] primer_internal_formatted...0s [OK] primer_internal1_formatted...1s [OK] primer_ok_regions...0s [OK] primer_ok_regions_formatted...0s [OK] primer_ok_regions2...15s [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...1s [OK] primer_new_tasks...0s [OK] primer_new_tasks_formatted...0s [OK] primer_internal_position...1s [OK] primer_annealing_temp...0s [OK] primer_windows_newlines...1s [OK] primer_must_overlap_point...1s [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...0s [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...5s [OK] primer_list_files...[OK] primer1...0s [OK] primer1_list_files...[OK] primer_mispriming...1s [OK] primer_mispriming_formatted...1s [OK] primer_mispriming_boundary1...0s [OK] primer_mispriming_boundary1_formatted...1s [OK] primer_mispriming_boundary2...0s [OK] primer_mispriming_boundary2_formatted...1s [OK] primer_mispriming_long_lib...0s [OK] primer_rat...4s [OK] primer_human...3s [OK] long_seq...0s [OK] primer_position_penalty...2s [OK] primer_position_penalty_formatted...6s [OK] p3-tmpl-mispriming...1s [OK] primer_poly_x...0s [OK] primer_three_prime_distance...0s [OK] primer_obj_fn...3s [OK] p3_3_prime_n...0s [OK] primer_masker...7s [OK] primer_masker_formatted...7s [OK] primer_overhang...0s [OK] primer_overhang_th...27s [OK] primer_mispriming_th...18s [OK] th-w-other-tasks...27s [OK] th-w-other-tasks_list_files...[OK] primer_new_tasks_th...40s [OK] primer_sec_struct_thal...36s [OK] primer_thermod_align...91s [OK] primer_thermod_align_formatted...82s [OK] primer1_th...228s [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 Tue Feb 24 00:38:10 2026...323s [OK] Tests in p3test.pl ran for 944 s (15.7333333333333 min) DONE Tue Feb 24 00:43:33 2026 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 -j42 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' debian/rules execute_after_dh_auto_clean make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1' rm -rf /build/reproducible-path/primer3-2.6.1/src/debian make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1' 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 -j42 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 dh_installexamples -O--sourcedirectory=src debian/rules execute_after_dh_installexamples make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1' 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 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_2.6.1-5_amd64.deb'. dpkg-deb: building package 'primer3' in '../primer3_2.6.1-5_amd64.deb'. dpkg-deb: building package 'primer3-examples' in '../primer3-examples_2.6.1-5_all.deb'. dpkg-genbuildinfo --build=binary -O../primer3_2.6.1-5_amd64.buildinfo dpkg-genchanges --build=binary -O../primer3_2.6.1-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/638090 and its subdirectories I: Current time: Mon Feb 23 12:45:25 -12 2026 I: pbuilder-time-stamp: 1771893925 Tue Feb 24 00:45:25 UTC 2026 I: Signing ./b1/primer3_2.6.1-5_amd64.buildinfo as primer3_2.6.1-5_amd64.buildinfo.asc Tue Feb 24 00:45:25 UTC 2026 I: Signed ./b1/primer3_2.6.1-5_amd64.buildinfo as ./b1/primer3_2.6.1-5_amd64.buildinfo.asc Tue Feb 24 00:45:25 UTC 2026 - build #1 for primer3/unstable/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Tue Feb 24 00:45:25 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-dTuOrJnd, removing. /srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Jan 21 18:22 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jan 21 18:02 b2 -rw-r--r-- 1 jenkins jenkins 2101 Dec 1 12:18 primer3_2.6.1-5.dsc -rw------- 1 jenkins jenkins 3202 Jan 21 18:02 rbuildlog.rpHixzU /srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7/b1: total 31632 -rw-r--r-- 1 jenkins jenkins 54815 Jan 21 18:22 build.log -rw-r--r-- 1 jenkins jenkins 435480 Jan 21 18:22 primer3-dbgsym_2.6.1-5_amd64.deb -rw-r--r-- 1 jenkins jenkins 31644736 Jan 21 18:22 primer3-examples_2.6.1-5_all.deb -rw-r--r-- 1 jenkins jenkins 13976 Jan 21 18:22 primer3_2.6.1-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2101 Jan 21 18:22 primer3_2.6.1-5.dsc -rw-r--r-- 1 jenkins jenkins 5250 Jan 21 18:22 primer3_2.6.1-5_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6132 Jan 21 18:22 primer3_2.6.1-5_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1981 Jan 21 18:22 primer3_2.6.1-5_amd64.changes -rw-r--r-- 1 jenkins jenkins 203972 Jan 21 18:22 primer3_2.6.1-5_amd64.deb -rw-r--r-- 1 jenkins jenkins 1434 Jan 21 18:22 primer3_2.6.1-5_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7/b2: total 0 Tue Jan 21 18:22:27 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Feb 23 12:25:05 -12 2026 I: pbuilder-time-stamp: 1771892705 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_2.6.1-5.dsc] I: copying [./primer3_2.6.1.orig.tar.gz] I: copying [./primer3_2.6.1-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./primer3_2.6.1-5.dsc: unsupported subcommand 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_2.6.1-5.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/638090/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='18eaeed902294d418b16ad1f8786c072' 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='638090' 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.zFxAXyg7/pbuilderrc_jXoK --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.zFxAXyg7/b1 --logfile b1/build.log primer3_2.6.1-5.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.11.10+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1~bpo12+1 (2024-12-19) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/638090/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19851 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} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 20.5 MB of archives. After unpacking 77.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-1 [92.2 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-2 [539 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Fetched 20.5 MB in 0s (70.2 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19851 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_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-1_amd64.deb ... Unpacking bsdextrautils (2.40.4-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-5_amd64.deb ... Unpacking m4 (1.4.19-5) ... 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_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-2_all.deb ... Unpacking libtool (2.5.4-2) ... 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_1.14.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-1_amd64.deb ... Unpacking libunistring5:amd64 (1.3-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-6_amd64.deb ... Unpacking libicu72:amd64 (72.1-6) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_amd64.deb ... Unpacking gettext (0.23.1-1) ... 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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_2.6.1-5_source.changes dpkg-buildpackage: info: source package primer3 dpkg-buildpackage: info: source version 2.6.1-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Ananthu C V dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j42 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' 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' debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1' rm -rf /build/reproducible-path/primer3-2.6.1/src/debian make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1' 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 -j42 "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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal_parameters.o thal_parameters.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g masker.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal.o thal.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; | ^~~ ar rv libthalpara.a thal_parameters.o ar: creating libthalpara.a a - thal_parameters.o ranlib libthalpara.a ar rv liboligotm.a oligotm.o 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 -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm 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 -fcf-protection -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 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 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 -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o amplicon3_core amplicontm_main.c libamplicontm.a -lm 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: 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 -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntdpal ntdpal_main.o dpal.o /usr/include/x86_64-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/x86_64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' 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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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 -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntthal thal_main.o thal.o thal_parameters.o -lm ar rv libthal.a thal_primer.o ar: creating libthal.a a - thal_primer.o ranlib libthal.a 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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, Tue Feb 24 00:27:48 2026 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...1s [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 Tue Feb 24 00:27:49 2026 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, Tue Feb 24 00:27:49 2026 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...4s [OK] primer_thal_args...1s [OK] primer_thal_max_seq_error...0s [OK] primer_first_base_index...0s [OK] primer_must_match...0s [OK] test_compl_error...0s [OK] test_left_to_right_of_right...1s [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...2s [OK] primer3web_v4_0_0_default_settings...0s [OK] primer_internal...0s [OK] primer_internal1...0s [OK] primer_internal_formatted...0s [OK] primer_internal1_formatted...1s [OK] primer_ok_regions...0s [OK] primer_ok_regions_formatted...0s [OK] primer_ok_regions2...15s [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...1s [OK] primer_new_tasks...0s [OK] primer_new_tasks_formatted...0s [OK] primer_internal_position...1s [OK] primer_annealing_temp...0s [OK] primer_windows_newlines...1s [OK] primer_must_overlap_point...1s [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...0s [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...5s [OK] primer_list_files...[OK] primer1...0s [OK] primer1_list_files...[OK] primer_mispriming...1s [OK] primer_mispriming_formatted...1s [OK] primer_mispriming_boundary1...0s [OK] primer_mispriming_boundary1_formatted...1s [OK] primer_mispriming_boundary2...0s [OK] primer_mispriming_boundary2_formatted...1s [OK] primer_mispriming_long_lib...0s [OK] primer_rat...4s [OK] primer_human...3s [OK] long_seq...0s [OK] primer_position_penalty...2s [OK] primer_position_penalty_formatted...6s [OK] p3-tmpl-mispriming...1s [OK] primer_poly_x...0s [OK] primer_three_prime_distance...0s [OK] primer_obj_fn...3s [OK] p3_3_prime_n...0s [OK] primer_masker...7s [OK] primer_masker_formatted...7s [OK] primer_overhang...0s [OK] primer_overhang_th...27s [OK] primer_mispriming_th...18s [OK] th-w-other-tasks...27s [OK] th-w-other-tasks_list_files...[OK] primer_new_tasks_th...40s [OK] primer_sec_struct_thal...36s [OK] primer_thermod_align...91s [OK] primer_thermod_align_formatted...82s [OK] primer1_th...228s [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 Tue Feb 24 00:38:10 2026...323s [OK] Tests in p3test.pl ran for 944 s (15.7333333333333 min) DONE Tue Feb 24 00:43:33 2026 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 -j42 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' debian/rules execute_after_dh_auto_clean make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1' rm -rf /build/reproducible-path/primer3-2.6.1/src/debian make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1' 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 -j42 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 dh_installexamples -O--sourcedirectory=src debian/rules execute_after_dh_installexamples make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1' 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 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_2.6.1-5_amd64.deb'. dpkg-deb: building package 'primer3' in '../primer3_2.6.1-5_amd64.deb'. dpkg-deb: building package 'primer3-examples' in '../primer3-examples_2.6.1-5_all.deb'. dpkg-genbuildinfo --build=binary -O../primer3_2.6.1-5_amd64.buildinfo dpkg-genchanges --build=binary -O../primer3_2.6.1-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/638090 and its subdirectories I: Current time: Mon Feb 23 12:45:25 -12 2026 I: pbuilder-time-stamp: 1771893925 Tue Jan 21 18:22:27 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Tue Jan 21 18:22:27 UTC 2025 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Tue Jan 21 18:22:27 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Tue Jan 21 18:22:27 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-JQ016t' ==================================================================================== Tue Jan 21 18:22:28 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos11-amd64, called using "2 primer3 unstable /srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7 2.6.1-5" as arguments. Tue Jan 21 18:22:28 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-hCZknKKW" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Jan 21 18:22:29 UTC 2025 I: Downloading source for unstable/primer3=2.6.1-5 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 2.6.1-5 (dsc) [2101 B] Get:2 http://deb.debian.org/debian unstable/main primer3 2.6.1-5 (tar) [32.9 MB] Get:3 http://deb.debian.org/debian unstable/main primer3 2.6.1-5 (diff) [14.0 kB] Fetched 32.9 MB in 2s (21.3 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 2.6.1-5 (dsc) [2101 B] Get:2 http://deb.debian.org/debian unstable/main primer3 2.6.1-5 (tar) [32.9 MB] Get:3 http://deb.debian.org/debian unstable/main primer3 2.6.1-5 (diff) [14.0 kB] Fetched 32.9 MB in 2s (21.3 MB/s) Download complete and in download only mode ============================================================================= Re-Building primer3 in unstable on amd64 on ionos11-amd64 now. Date: Tue Jan 21 18:22:30 UTC 2025 Date UTC: Tue Jan 21 18:22:30 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7 + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7/pbuilderrc_gqIm + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' primer3 = debian-installer -o primer3 = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' primer3 = u-boot ']' + case "${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.zFxAXyg7/pbuilderrc_gqIm --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.zFxAXyg7/b2 --logfile b2/build.log primer3_2.6.1-5.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: Wed Jan 22 08:22:31 +14 2025 I: pbuilder-time-stamp: 1737483751 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_2.6.1-5.dsc] I: copying [./primer3_2.6.1.orig.tar.gz] I: copying [./primer3_2.6.1-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./primer3_2.6.1-5.dsc: unsupported subcommand 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_2.6.1-5.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/3256846/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jan 21 18:23 /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/3256846/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3256846/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]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=4291bbdd4ef847fda01a9fd29eabf059 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3256846 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.zFxAXyg7/pbuilderrc_gqIm --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.zFxAXyg7/b2 --logfile b2/build.log primer3_2.6.1-5.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3256846/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19851 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} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 20.5 MB of archives. After unpacking 77.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-1 [92.2 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-2 [539 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Fetched 20.5 MB in 1s (34.4 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19851 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_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_amd64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_amd64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-1_amd64.deb ... Unpacking bsdextrautils (2.40.4-1) ... Selecting previously unselected package libpipeline1:amd64. 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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/3256846/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/3256846/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_2.6.1-5_source.changes dpkg-buildpackage: info: source package primer3 dpkg-buildpackage: info: source version 2.6.1-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Ananthu C V dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j20 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' 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' debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1' rm -rf /build/reproducible-path/primer3-2.6.1/src/debian make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1' 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 -j20 "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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g masker.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal.o thal.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; | ^~~ 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o amplicon3_core amplicontm_main.c libamplicontm.a -lm 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/x86_64-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/x86_64-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/x86_64-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/x86_64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' 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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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/x86_64-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 -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntdpal ntdpal_main.o dpal.o 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 -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntthal thal_main.o thal.o thal_parameters.o -lm ar rv libthal.a thal_primer.o ar: creating libthal.a a - thal_primer.o ranlib libthal.a 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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, Tue Jan 21 18:24:41 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...1s [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...1s [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...1s [OK] heli_FZD2...0s [OK] heli_GAPDH...0s [OK] heli_WNT1...0s [OK] heli_MYH6...1s [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...1s [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...1s [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 7 s (0.116666666666667 min) DONE Tue Jan 21 18:24:48 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, Tue Jan 21 18:24:48 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...3s [OK] primer_thal_args...1s [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...1s [OK] primer3_v1_1_4_default_settings...0s [OK] primer3web_v0_4_0_default_settings...0s [OK] primer3web_v3_0_0_default_settings...3s [OK] primer3web_v4_0_0_default_settings...0s [OK] primer_internal...0s [OK] primer_internal1...0s [OK] primer_internal_formatted...1s [OK] primer_internal1_formatted...0s [OK] primer_ok_regions...0s [OK] primer_ok_regions_formatted...0s [OK] primer_ok_regions2...26s [OK] primer_tm_lc_masking...0s [OK] primer_tm_lc_masking_formatted...0s [OK] primer_start_codon...0s [OK] primer_task...1s [OK] primer_task_formatted...0s [OK] primer_renewed_tasks...0s [OK] primer_dmso_formamide...1s [OK] primer_new_tasks...0s [OK] primer_new_tasks_formatted...1s [OK] primer_internal_position...1s [OK] primer_annealing_temp...0s [OK] primer_windows_newlines...3s [OK] primer_must_overlap_point...2s [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...0s [OK] primer_check...0s [OK] primer_must_use...1s [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...3s [OK] primer_list_files...[OK] primer1...0s [OK] primer1_list_files...[OK] primer_mispriming...1s [OK] primer_mispriming_formatted...1s [OK] primer_mispriming_boundary1...0s [OK] primer_mispriming_boundary1_formatted...0s [OK] primer_mispriming_boundary2...0s [OK] primer_mispriming_boundary2_formatted...0s [OK] primer_mispriming_long_lib...0s [OK] primer_rat...1s [OK] primer_human...2s [OK] long_seq...1s [OK] primer_position_penalty...1s [OK] primer_position_penalty_formatted...2s [OK] p3-tmpl-mispriming...0s [OK] primer_poly_x...0s [OK] primer_three_prime_distance...0s [OK] primer_obj_fn...5s [OK] p3_3_prime_n...0s [OK] primer_masker...6s [OK] primer_masker_formatted...5s [OK] primer_overhang...0s [OK] primer_overhang_th...27s [OK] primer_mispriming_th...22s [OK] th-w-other-tasks...28s [OK] th-w-other-tasks_list_files...[OK] primer_new_tasks_th...42s [OK] primer_sec_struct_thal...34s [OK] primer_thermod_align...110s [OK] primer_thermod_align_formatted...111s [OK] primer1_th...274s [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 Tue Jan 21 18:36:55 2025...217s [OK] Tests in p3test.pl ran for 944 s (15.7333333333333 min) DONE Tue Jan 21 18:40:32 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 -j20 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' debian/rules execute_after_dh_auto_clean make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1' rm -rf /build/reproducible-path/primer3-2.6.1/src/debian make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1' 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 -j20 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 dh_installexamples -O--sourcedirectory=src debian/rules execute_after_dh_installexamples make[1]: Entering directory '/build/reproducible-path/primer3-2.6.1' 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 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_2.6.1-5_amd64.deb'. dpkg-deb: building package 'primer3' in '../primer3_2.6.1-5_amd64.deb'. dpkg-deb: building package 'primer3-examples' in '../primer3-examples_2.6.1-5_all.deb'. dpkg-genbuildinfo --build=binary -O../primer3_2.6.1-5_amd64.buildinfo dpkg-genchanges --build=binary -O../primer3_2.6.1-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3256846/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3256846/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/3256846 and its subdirectories I: Current time: Wed Jan 22 08:43:58 +14 2025 I: pbuilder-time-stamp: 1737485038 + false + set +x Tue Jan 21 18:43:58 UTC 2025 I: Signing ./b2/primer3_2.6.1-5_amd64.buildinfo as primer3_2.6.1-5_amd64.buildinfo.asc Tue Jan 21 18:43:58 UTC 2025 I: Signed ./b2/primer3_2.6.1-5_amd64.buildinfo as ./b2/primer3_2.6.1-5_amd64.buildinfo.asc Tue Jan 21 18:43:58 UTC 2025 - build #2 for primer3/unstable/amd64 on ionos11-amd64 done. Starting cleanup. All cleanup done. Tue Jan 21 18:43:58 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-hCZknKKW, removing. /srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7: total 76 drwxr-xr-x 2 jenkins jenkins 4096 Jan 21 18:22 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jan 21 18:43 b2 -rw-r--r-- 1 jenkins jenkins 2101 Dec 1 12:18 primer3_2.6.1-5.dsc -rw------- 1 jenkins jenkins 58306 Jan 21 18:22 rbuildlog.rpHixzU /srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7/b1: total 31680 -rw-r--r-- 1 jenkins jenkins 54815 Jan 21 18:22 build.log -rw-r--r-- 1 jenkins jenkins 435480 Jan 21 18:22 primer3-dbgsym_2.6.1-5_amd64.deb -rw-r--r-- 1 jenkins jenkins 31644736 Jan 21 18:22 primer3-examples_2.6.1-5_all.deb -rw-r--r-- 1 jenkins jenkins 13976 Jan 21 18:22 primer3_2.6.1-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2101 Jan 21 18:22 primer3_2.6.1-5.dsc -rw-r--r-- 1 jenkins jenkins 5250 Jan 21 18:22 primer3_2.6.1-5_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6132 Jan 21 18:22 primer3_2.6.1-5_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1981 Jan 21 18:22 primer3_2.6.1-5_amd64.changes -rw-r--r-- 1 jenkins jenkins 203972 Jan 21 18:22 primer3_2.6.1-5_amd64.deb -rw-r--r-- 1 jenkins jenkins 1434 Jan 21 18:22 primer3_2.6.1-5_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7/b2: total 31632 -rw-r--r-- 1 jenkins jenkins 56739 Jan 21 18:43 build.log -rw-r--r-- 1 jenkins jenkins 435480 Jan 21 18:43 primer3-dbgsym_2.6.1-5_amd64.deb -rw-r--r-- 1 jenkins jenkins 31644736 Jan 21 18:43 primer3-examples_2.6.1-5_all.deb -rw-r--r-- 1 jenkins jenkins 13976 Jan 21 18:43 primer3_2.6.1-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2101 Jan 21 18:43 primer3_2.6.1-5.dsc -rw-r--r-- 1 jenkins jenkins 5239 Jan 21 18:43 primer3_2.6.1-5_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6121 Jan 21 18:43 primer3_2.6.1-5_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1981 Jan 21 18:43 primer3_2.6.1-5_amd64.changes -rw-r--r-- 1 jenkins jenkins 203972 Jan 21 18:43 primer3_2.6.1-5_amd64.deb -rw-r--r-- 1 jenkins jenkins 1434 Jan 21 18:43 primer3_2.6.1-5_source.changes Tue Jan 21 18:43:59 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Tue Jan 21 18:44:00 UTC 2025 I: primer3_2.6.1-5_amd64.changes: Format: 1.8 Date: Sun, 01 Dec 2024 17:24:55 +0530 Source: primer3 Binary: primer3 primer3-dbgsym primer3-examples Architecture: amd64 all Version: 2.6.1-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Ananthu C V Description: primer3 - tool to design flanking oligo nucleotides for DNA amplification primer3-examples - tool to design flanking oligo nucleotides for DNA amplification ( Closes: 1045454 Changes: primer3 (2.6.1-5) unstable; urgency=medium . * Team upload. * Clean up source directory properly (Closes: #1045454) * Use execute_after hook over overrides in d/rules * Bump standards version to 4.7.0 (no changes needed) * Correct patch header metadata * Drop deprecated an-trap macro from manpage Checksums-Sha1: caaa136865112dde426b5e6f62c4c1e3bdd5aca6 435480 primer3-dbgsym_2.6.1-5_amd64.deb a187d54fb5a21c73073833cc4a56379c1f45d659 31644736 primer3-examples_2.6.1-5_all.deb 59253a5319c76988e39275434ea040498526fcf9 5250 primer3_2.6.1-5_amd64.buildinfo 6690e4399aed23e8546bc4b27ecefe8c5a61d3e7 203972 primer3_2.6.1-5_amd64.deb Checksums-Sha256: d18f0465f11c801bc6332f621d35741a21061edba5f4f378afba0bb4109446f7 435480 primer3-dbgsym_2.6.1-5_amd64.deb e361a7c0694b9a49581b408b1de3adbd0f072a8c9b280ad98d04d31a77227f6d 31644736 primer3-examples_2.6.1-5_all.deb 5ab4a31af84af99ab54109f05ff25d909b60b280e9ff05f759d42f0c5cdf52f0 5250 primer3_2.6.1-5_amd64.buildinfo a5269681f766affef457da3f69f50b7848a76e5d26476f6cdcb0a2a94d935231 203972 primer3_2.6.1-5_amd64.deb Files: d0d7ea16659b1c391eabec7a9671876f 435480 debug optional primer3-dbgsym_2.6.1-5_amd64.deb bf597aea4f63012f68040f66f549e60b 31644736 science optional primer3-examples_2.6.1-5_all.deb bd34c411efe5c26f47f672ecc922cb2e 5250 science optional primer3_2.6.1-5_amd64.buildinfo c3c3c3b0f317257313b3cef72c697f29 203972 science optional primer3_2.6.1-5_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/primer3_2.6.1-5.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/primer3_2.6.1-5.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/primer3_2.6.1-5.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/primer3_2.6.1-5.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/primer3_2.6.1-5_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/primer3_2.6.1-5.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-01-21 18:22:27.143249624 +0000 +++ b2/build.log 2025-01-21 18:43:59.272943478 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Feb 23 12:25:05 -12 2026 -I: pbuilder-time-stamp: 1771892705 +I: Current time: Wed Jan 22 08:22:31 +14 2025 +I: pbuilder-time-stamp: 1737483751 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -27,52 +27,84 @@ dpkg-source: info: applying buildflags.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/638090/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3256846/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jan 21 18:23 /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/3256846/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3256846/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='18eaeed902294d418b16ad1f8786c072' - 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='638090' - PS1='# ' - PS2='> ' + INVOCATION_ID=4291bbdd4ef847fda01a9fd29eabf059 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3256846 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.zFxAXyg7/pbuilderrc_jXoK --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.zFxAXyg7/b1 --logfile b1/build.log primer3_2.6.1-5.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7/pbuilderrc_gqIm --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.zFxAXyg7/b2 --logfile b2/build.log primer3_2.6.1-5.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.11.10+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1~bpo12+1 (2024-12-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/638090/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3256846/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -138,7 +170,7 @@ Get: 28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] -Fetched 20.5 MB in 0s (70.2 MB/s) +Fetched 20.5 MB in 1s (34.4 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19851 files and directories currently installed.) @@ -273,7 +305,11 @@ 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_2.6.1-5_source.changes +I: user script /srv/workspace/pbuilder/3256846/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3256846/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_2.6.1-5_source.changes dpkg-buildpackage: info: source package primer3 dpkg-buildpackage: info: source version 2.6.1-5 dpkg-buildpackage: info: source distribution unstable @@ -283,7 +319,7 @@ debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src - cd src && make -j42 clean + cd src && make -j20 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 ../*~ @@ -336,7 +372,7 @@ 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 -j42 "INSTALL=install --strip-program=true" CPP=\$\(CXX\) + cd src && make -j20 "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 -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g primer3_boulder_main.c @@ -348,8 +384,8 @@ 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -g -Wall -O2 -ffloat-store -Wl,-z,relro -Wl,-z,now -g -o thal_parameters.o thal_parameters.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g masker.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 -fcf-protection -g -Wall -O2 -g -Wall -Wl,-z,relro -Wl,-z,now -g -o ntdpal_main.o ntdpal_main.c @@ -412,9 +448,16 @@ 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 -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 -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm -ar: creating liboligotm.a +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 -fcf-protection -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 -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o oligotm oligotm_main.c liboligotm.a -lm @@ -422,13 +465,6 @@ ar: creating libmasker.a a - masker.o ranlib libmasker.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 libamplicontm.a amplicontm.o ar: creating libamplicontm.a a - amplicontm.o @@ -439,27 +475,22 @@ In function 'strcpy', inlined from 'safe_malloc' at thal.c:804:7, inlined from 'calc_hairpin' at thal.c:1922:19: -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 -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntdpal ntdpal_main.o dpal.o /usr/include/x86_64-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/x86_64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function '__builtin___memcpy_chk' -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: + inlined from 'calc_bulge_internal.isra' at thal.c:2000:19: /usr/include/x86_64-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/x86_64-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 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_bulge_internal.isra' at thal.c:2000:19: + inlined from 'calc_hairpin' at thal.c:1922:19: /usr/include/x86_64-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)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -472,6 +503,10 @@ 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-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: @@ -487,6 +522,7 @@ 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/x86_64-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 -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntdpal ntdpal_main.o dpal.o 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 -fcf-protection -g -Wall -O2 -Wl,-z,relro -Wl,-z,now -g -o ntthal thal_main.o thal.o thal_parameters.o -lm ar rv libthal.a thal_primer.o ar: creating libthal.a @@ -577,7 +613,7 @@ a3test.pl: testing ../src/amplicon3_core -START, Tue Feb 24 00:27:48 2026 +START, Tue Jan 21 18:24:41 2025 plain_WNT9B...0s [OK] plain_TBX18...0s [OK] plain_RYK...0s [OK] @@ -591,7 +627,7 @@ plain_GAPDH...0s [OK] plain_WNT1...0s [OK] plain_MYH6...0s [OK] -plain_on_command_line_WNT9B...0s [OK] +plain_on_command_line_WNT9B...1s [OK] plain_on_command_line_TBX18...0s [OK] plain_on_command_line_RYK...0s [OK] plain_on_command_line_WNT2...0s [OK] @@ -615,7 +651,7 @@ classic_IFT88...0s [OK] classic_FZD2...0s [OK] classic_GAPDH...0s [OK] -classic_WNT1...0s [OK] +classic_WNT1...1s [OK] classic_MYH6...0s [OK] heli_WNT9B...0s [OK] heli_TBX18...0s [OK] @@ -625,11 +661,11 @@ heli_SFRP3...0s [OK] heli_IFT20...0s [OK] heli_DVL1...0s [OK] -heli_IFT88...0s [OK] +heli_IFT88...1s [OK] heli_FZD2...0s [OK] heli_GAPDH...0s [OK] -heli_WNT1...1s [OK] -heli_MYH6...0s [OK] +heli_WNT1...0s [OK] +heli_MYH6...1s [OK] long_WNT9B...0s [OK] long_TBX18...0s [OK] long_RYK...0s [OK] @@ -647,7 +683,7 @@ optimal_TBX18...0s [OK] optimal_RYK...0s [OK] optimal_WNT2...0s [OK] -optimal_ROCK2...0s [OK] +optimal_ROCK2...1s [OK] optimal_SFRP3...0s [OK] optimal_IFT20...0s [OK] optimal_DVL1...0s [OK] @@ -671,7 +707,7 @@ only_mv_MYH6...0s [OK] no_dmso_WNT9B...0s [OK] no_dmso_TBX18...0s [OK] -no_dmso_RYK...0s [OK] +no_dmso_RYK...1s [OK] no_dmso_WNT2...0s [OK] no_dmso_ROCK2...0s [OK] no_dmso_SFRP3...0s [OK] @@ -683,9 +719,9 @@ no_dmso_WNT1...0s [OK] no_dmso_MYH6...0s [OK] -Tests in a3test.pl ran for 1 s (0.0166666666666667 min) +Tests in a3test.pl ran for 7 s (0.116666666666667 min) -DONE Tue Feb 24 00:27:49 2026 Passed all tests - [OK] +DONE Tue Jan 21 18:24:48 2025 Passed all tests - [OK] echo; echo; echo 'TESTING primer3_core'; echo; perl p3test.pl @@ -702,7 +738,7 @@ p3test.pl: testing ../src/primer3_core -START, Tue Feb 24 00:27:49 2026 +START, Tue Jan 21 18:24:48 2025 testing fatal errors... ./primer_global_err/annealing_temp_salt @@ -814,95 +850,95 @@ [OK] primer_must_use_th...0s [OK] primer_sec_struct_dpal...0s [OK] -primer_task_th...4s [OK] +primer_task_th...3s [OK] primer_thal_args...1s [OK] -primer_thal_max_seq_error...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...1s [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] +primer_boundary1_formatted...1s [OK] primer3_v1_1_4_default_settings...0s [OK] primer3web_v0_4_0_default_settings...0s [OK] -primer3web_v3_0_0_default_settings...2s [OK] +primer3web_v3_0_0_default_settings...3s [OK] primer3web_v4_0_0_default_settings...0s [OK] primer_internal...0s [OK] primer_internal1...0s [OK] -primer_internal_formatted...0s [OK] -primer_internal1_formatted...1s [OK] +primer_internal_formatted...1s [OK] +primer_internal1_formatted...0s [OK] primer_ok_regions...0s [OK] primer_ok_regions_formatted...0s [OK] -primer_ok_regions2...15s [OK] +primer_ok_regions2...26s [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...1s [OK] primer_task_formatted...0s [OK] primer_renewed_tasks...0s [OK] primer_dmso_formamide...1s [OK] primer_new_tasks...0s [OK] -primer_new_tasks_formatted...0s [OK] +primer_new_tasks_formatted...1s [OK] primer_internal_position...1s [OK] primer_annealing_temp...0s [OK] -primer_windows_newlines...1s [OK] -primer_must_overlap_point...1s [OK] +primer_windows_newlines...3s [OK] +primer_must_overlap_point...2s [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...0s [OK] primer_check...0s [OK] -primer_must_use...0s [OK] +primer_must_use...1s [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...5s [OK] +primer...3s [OK] primer_list_files...[OK] primer1...0s [OK] primer1_list_files...[OK] primer_mispriming...1s [OK] primer_mispriming_formatted...1s [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...1s [OK] +primer_mispriming_boundary2_formatted...0s [OK] primer_mispriming_long_lib...0s [OK] -primer_rat...4s [OK] -primer_human...3s [OK] -long_seq...0s [OK] -primer_position_penalty...2s [OK] -primer_position_penalty_formatted...6s [OK] -p3-tmpl-mispriming...1s [OK] +primer_rat...1s [OK] +primer_human...2s [OK] +long_seq...1s [OK] +primer_position_penalty...1s [OK] +primer_position_penalty_formatted...2s [OK] +p3-tmpl-mispriming...0s [OK] primer_poly_x...0s [OK] primer_three_prime_distance...0s [OK] -primer_obj_fn...3s [OK] +primer_obj_fn...5s [OK] p3_3_prime_n...0s [OK] -primer_masker...7s [OK] -primer_masker_formatted...7s [OK] +primer_masker...6s [OK] +primer_masker_formatted...5s [OK] primer_overhang...0s [OK] primer_overhang_th...27s [OK] -primer_mispriming_th...18s [OK] -th-w-other-tasks...27s [OK] +primer_mispriming_th...22s [OK] +th-w-other-tasks...28s [OK] th-w-other-tasks_list_files...[OK] -primer_new_tasks_th...40s [OK] -primer_sec_struct_thal...36s [OK] -primer_thermod_align...91s [OK] -primer_thermod_align_formatted...82s [OK] -primer1_th...228s [OK] +primer_new_tasks_th...42s [OK] +primer_sec_struct_thal...34s [OK] +primer_thermod_align...110s [OK] +primer_thermod_align_formatted...111s [OK] +primer1_th...274s [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 Tue Feb 24 00:38:10 2026...323s [OK] +starting primer_lib_amb_codes at Tue Jan 21 18:36:55 2025...217s [OK] Tests in p3test.pl ran for 944 s (15.7333333333333 min) -DONE Tue Feb 24 00:43:33 2026 Passed all tests - [OK] +DONE Tue Jan 21 18:40:32 2025 Passed all tests - [OK] echo; echo; echo "Testing completed. You must check the test output for the string FAILED"; echo; echo; @@ -914,7 +950,7 @@ 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 -j42 clean + cd test && make -j20 clean make[2]: Entering directory '/build/reproducible-path/primer3-2.6.1/test' echo; echo; echo 'CLEAN UP TEST DIRECTORIES'; echo; echo; @@ -961,7 +997,7 @@ 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 -j42 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 + cd src && make -j20 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" @@ -1015,12 +1051,14 @@ 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/3256846/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3256846/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/638090 and its subdirectories -I: Current time: Mon Feb 23 12:45:25 -12 2026 -I: pbuilder-time-stamp: 1771893925 +I: removing directory /srv/workspace/pbuilder/3256846 and its subdirectories +I: Current time: Wed Jan 22 08:43:58 +14 2025 +I: pbuilder-time-stamp: 1737485038 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/primer3_2.6.1-5.diff: 75.9% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/primer3_2.6.1-5.diff.gz b2/build.log: 81.5% -- replaced with stdout Compressing the 1st log... b1/build.log: 82.1% -- replaced with stdout Tue Jan 21 18:44:01 UTC 2025 I: diffoscope 285 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_primer3_unstable_amd64_1737485041 + touch /var/log/reproducible-builds/diffoscope_stamp_primer3_unstable_amd64_1737485041 + RESULT=0 + systemd-run '--description=diffoscope on primer3/2.6.1-5 in unstable/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_8-45948 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7 --run-session -c jenkins-reproducible-unstable-diffoscope-cb2ac31e-19c3-4e5a-bf7c-2f8810736b4a -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7/dbd-tmp-MRd6aFe ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7/primer3_2.6.1-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7/primer3_2.6.1-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7/primer3_2.6.1-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7/b1/primer3_2.6.1-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7/b2/primer3_2.6.1-5_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_8-45948.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7/primer3_2.6.1-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7/primer3_2.6.1-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7/primer3_2.6.1-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7/b1/primer3_2.6.1-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.zFxAXyg7/b2/primer3_2.6.1-5_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.637s) 0.637s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.289s) 0.289s 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: 942ms CPU time consumed: 942ms _ _____ _ __ _ __(_)_ __ ___ ___ _ _|___ / | '_ \| '__| | '_ ` _ \ / _ \ '__||_ \ | |_) | | | | | | | | | __/ | ___) | | .__/|_| |_|_| |_| |_|\___|_| |____/ |_| Tue Jan 21 18:44:02 UTC 2025 I: diffoscope 285 found no differences in the changes files, and a .buildinfo file also exists. Tue Jan 21 18:44:02 UTC 2025 I: primer3 from unstable built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-01-21 18:44:03] INFO: Starting at 2025-01-21 18:44:03.168855 [2025-01-21 18:44:03] INFO: Generating the pages of 1 package(s) [2025-01-21 18:44:03] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/primer3 didn't produce a buildlog, even though it has been built. [2025-01-21 18:44:03] INFO: Finished at 2025-01-21 18:44:03.751204, took: 0:00:00.582359 Tue Jan 21 18:44:03 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/primer3.html Tue Jan 21 18:44:03 UTC 2025 I: Submitting .buildinfo files to external archives: Tue Jan 21 18:44:03 UTC 2025 I: Submitting 8.0K b1/primer3_2.6.1-5_amd64.buildinfo.asc https://buildinfo.debian.net/59253a5319c76988e39275434ea040498526fcf9/primer3_2.6.1-5_all Tue Jan 21 18:44:04 UTC 2025 I: Submitting 8.0K b2/primer3_2.6.1-5_amd64.buildinfo.asc https://buildinfo.debian.net/43e5affbd4b959241af967877f872f72d90a8ee2/primer3_2.6.1-5_all Tue Jan 21 18:44:05 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Jan 21 18:44:05 UTC 2025 I: Done submitting .buildinfo files. Tue Jan 21 18:44:05 UTC 2025 I: Removing signed primer3_2.6.1-5_amd64.buildinfo.asc files: removed './b1/primer3_2.6.1-5_amd64.buildinfo.asc' removed './b2/primer3_2.6.1-5_amd64.buildinfo.asc' 1737485045 amd64 unstable primer3 Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/primer3_2.6.1-5.rbuild.log: 79.0% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/primer3_2.6.1-5.rbuild.log.gz [2025-01-21 18:44:05] INFO: Starting at 2025-01-21 18:44:05.747901 [2025-01-21 18:44:05] INFO: Generating the pages of 1 package(s) [2025-01-21 18:44:06] INFO: Finished at 2025-01-21 18:44:06.171224, took: 0:00:00.423333 All cleanup done. Tue Jan 21 18:44:06 UTC 2025 - total duration: 0h 42m 24s. Tue Jan 21 18:44:06 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-EKlfyBVp, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 42min 27.766s CPU time consumed: 8.049s