Running as unit: rb-build-arm64_7-102637.service; invocation ID: 6e1857d895424c16bf64e9086fac6f53 ==================================================================================== Fri Oct 31 13:17:25 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_7) on jenkins, called using "codethink04-arm64 codethink03-arm64" as arguments. Fri Oct 31 13:17:25 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-wvM0dljR" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Oct 31 13:17:25 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Fri Oct 31 13:17:25 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-JRGB9L' Fri Oct 31 13:17:26 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Fri Oct 31 13:17:26 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-wIm3pG' ok, let's check if prodigal is building anywhere yet… ok, prodigal is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of prodigal in unstable on arm64 on jenkins now. 1st build will be done on codethink04-arm64.debian.net. 2nd build will be done on codethink03-arm64.debian.net. ============================================================================= Fri Oct 31 13:17:36 UTC 2025 I: starting to build prodigal/unstable/arm64 on jenkins on '2025-10-31 13:17' Fri Oct 31 13:17:36 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_7/102637/console.log 1761916656 arm64 unstable prodigal Fri Oct 31 13:17:36 UTC 2025 I: Downloading source for unstable/prodigal=1:2.6.3-6 --2025-10-31 13:17:37-- http://deb.debian.org/debian/pool/main/p/prodigal/prodigal_2.6.3-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1992 (1.9K) [text/prs.lines.tag] Saving to: ‘prodigal_2.6.3-6.dsc’ 0K . 100% 222M=0s 2025-10-31 13:17:37 (222 MB/s) - ‘prodigal_2.6.3-6.dsc’ saved [1992/1992] --2025-10-31 13:17:37-- http://deb.debian.org/debian/pool/main/p/prodigal/prodigal_2.6.3-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1992 (1.9K) [text/prs.lines.tag] Saving to: ‘prodigal_2.6.3-6.dsc’ 0K . 100% 222M=0s 2025-10-31 13:17:37 (222 MB/s) - ‘prodigal_2.6.3-6.dsc’ saved [1992/1992] Fri Oct 31 13:17:37 UTC 2025 I: prodigal_2.6.3-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: prodigal Binary: prodigal Architecture: any Version: 1:2.6.3-6 Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou , Andreas Tille Homepage: http://prodigal.ornl.gov/ Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/prodigal Vcs-Git: https://salsa.debian.org/med-team/prodigal.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: prodigal deb science optional arch=any Checksums-Sha1: 1259e999193cd0c095935baebfb8bcb0233e850f 610934 prodigal_2.6.3.orig.tar.gz 281a30ce91f8775880a5d92d210506e6522921b0 49304 prodigal_2.6.3-6.debian.tar.xz Checksums-Sha256: 89094ad4bff5a8a8732d899f31cec350f5a4c27bcbdd12663f87c9d1f0ec599f 610934 prodigal_2.6.3.orig.tar.gz e47e360e0d4a97a361ed1cb6c294072a9d847f2a28a88e7d406122b4fa9c8583 49304 prodigal_2.6.3-6.debian.tar.xz Files: 5181809fdb740e9a675cfdbb6c038466 610934 prodigal_2.6.3.orig.tar.gz 2da877285635f03bf298eff790734a8e 49304 prodigal_2.6.3-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmOPQJ0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGPxQ/9GZ8yzKQncHykka5SpuzYVNHcnzUcJfrt uYbBAAKjEn9UiRdo+Cu3HliWVVIDbS3LFNmbIuND1kXpyt9GQl15/5pD3MnqfsAB nog9dYhKoNo6LqjlLGx/avmlcTuJzH7lVFPPDzanaPFYd6ueTfPdkgYBS+JirleM RgmD4xx4sPltoC9660KaNz0U6BOAhU+sY9/SErhUHezSp0D8e+FKowCqVdpazItb 9uxDTUyksgUgwgi/fYD6fhLYZJRSgbCjxGQoc4eOmIYzvgDMPzF+qBrPUMCvdZpc rX6Oup4wPciBpPKlWDpotMoefdlZqiAK2bKeZOidAvIX8P43kjgx9lmguc6ahKTU hFZOtUT3nYYUm8DTf1PJz3y+2CnIPlsn6YlKGNVmimDXJmBxsdn2sQ25ag9npLMu FvEnN0AliLVB6yk+PO4fU8OUr9codpsRZUEcC7rhxxDnb3Tzne6H01pI87SEovyr CxvzPH8uf/LDhZqFQrUl6D0xPoL/boR2cTuIq4J59CBUmkCRCOyStHO26xCK4D8W vz6kKIvFBrGcGNg8Bte64mJrs4hJPeo46x3KtiGZB/whi6HuMSnduElsX7UCWOkq sT7qRO/W7MbwUXtlubbbcD8AEBnX6rVnGJKCxRRg5aPHNGUstvjinNk55w9LjTf3 7d//QfRp1tQ= =QE7B -----END PGP SIGNATURE----- Fri Oct 31 13:17:37 UTC 2025 I: Checking whether the package is not for us Fri Oct 31 13:17:37 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Fri Oct 31 13:17:37 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Fri Oct 31 13:17:37 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Fri Oct 31 13:17:37 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-gcF9jD' ==================================================================================== Fri Oct 31 13:17:38 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "1 prodigal unstable /srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l 1:2.6.3-6" as arguments. Fri Oct 31 13:17:38 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-gK49quTk" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Oct 31 13:17:38 UTC 2025 I: Downloading source for unstable/prodigal=1:2.6.3-6 Reading package lists... NOTICE: 'prodigal' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/prodigal.git Please use: git clone https://salsa.debian.org/med-team/prodigal.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 662 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main prodigal 1:2.6.3-6 (dsc) [1992 B] Get:2 http://deb.debian.org/debian unstable/main prodigal 1:2.6.3-6 (tar) [611 kB] Get:3 http://deb.debian.org/debian unstable/main prodigal 1:2.6.3-6 (diff) [49.3 kB] Fetched 662 kB in 0s (5597 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'prodigal' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/prodigal.git Please use: git clone https://salsa.debian.org/med-team/prodigal.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 662 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main prodigal 1:2.6.3-6 (dsc) [1992 B] Get:2 http://deb.debian.org/debian unstable/main prodigal 1:2.6.3-6 (tar) [611 kB] Get:3 http://deb.debian.org/debian unstable/main prodigal 1:2.6.3-6 (diff) [49.3 kB] Fetched 662 kB in 0s (5597 kB/s) Download complete and in download only mode ============================================================================= Building prodigal in unstable on arm64 on codethink04-arm64 now. Date: Fri Oct 31 13:17:38 GMT 2025 Date UTC: Fri Oct 31 13:17:38 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Oct 31 01:17:38 -12 2025 I: pbuilder-time-stamp: 1761916658 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 [prodigal_2.6.3-6.dsc] I: copying [./prodigal_2.6.3.orig.tar.gz] I: copying [./prodigal_2.6.3-6.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./prodigal_2.6.3-6.dsc: no acceptable signature found dpkg-source: info: extracting prodigal in prodigal-2.6.3 dpkg-source: info: unpacking prodigal_2.6.3.orig.tar.gz dpkg-source: info: unpacking prodigal_2.6.3-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_hardcoded_O3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2763741/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='c29a8e7f09c543db9f402a31961b007a' 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='2763741' 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.U5RvVm1l/pbuilderrc_AVYx --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.U5RvVm1l/b1 --logfile b1/build.log prodigal_2.6.3-6.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2763741/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19964 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} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 11.0 MB of archives. After unpacking 44.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41.2-4 [97.3 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.20-2 [315 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.18.1-2 [877 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-7 [540 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.194-1 [184 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.16-2 [100 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libxml2-16 arm64 2.15.1+dfsg-0.3 [591 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.28 [941 kB] Fetched 11.0 MB in 0s (83.5 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 ... 19964 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_arm64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.2-4_arm64.deb ... Unpacking bsdextrautils (2.41.2-4) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.20-2_arm64.deb ... Unpacking m4 (1.4.20-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.18.1-2_all.deb ... Unpacking automake (1:1.18.1-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.28_all.deb ... Unpacking libdebhelper-perl (13.28) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-7_all.deb ... Unpacking libtool (2.5.4-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.194-1_arm64.deb ... Unpacking libelf1t64:arm64 (0.194-1) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.16-2_arm64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../23-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2-16:arm64. Preparing to unpack .../24-libxml2-16_2.15.1+dfsg-0.3_arm64.deb ... Unpacking libxml2-16:arm64 (2.15.1+dfsg-0.3) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2+b1_arm64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.28_all.deb ... Unpacking debhelper (13.28) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41.2-4) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:arm64 (2.15.1+dfsg-0.3) ... Setting up libdebhelper-perl (13.28) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-2) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.194-1) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:arm64 (0.0.8-2) ... Setting up automake (1:1.18.1-2) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.28) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/prodigal-2.6.3/ && 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 > ../prodigal_2.6.3-6_source.changes dpkg-buildpackage: info: source package prodigal dpkg-buildpackage: info: source version 1:2.6.3-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 distclean make[1]: Entering directory '/build/reproducible-path/prodigal-2.6.3' rm -f bitmap.o dprog.o gene.o main.o metagenomic.o node.o sequence.o training.o rm -f prodigal make[1]: Leaving directory '/build/reproducible-path/prodigal-2.6.3' debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/prodigal-2.6.3' dh_clean rm -f prodigal.1 make[1]: Leaving directory '/build/reproducible-path/prodigal-2.6.3' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/prodigal-2.6.3' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o bitmap.o bitmap.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o dprog.o dprog.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o gene.o gene.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o main.o main.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o metagenomic.o metagenomic.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o node.o node.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o sequence.o sequence.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o training.o training.c gene.c: In function 'record_gene_data': gene.c:303:9: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 303 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 304 | genes[i].gene_data, sd_string[nod[ndx].rbs[1]], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 305 | sd_spacer[nod[ndx].rbs[1]]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:298:9: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 298 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 299 | genes[i].gene_data, sd_string[nod[ndx].rbs[0]], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 300 | sd_spacer[nod[ndx].rbs[0]]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:309:12: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 309 | else sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%dbp", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 310 | genes[i].gene_data, qt, nod[ndx].mot.spacer); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:307:9: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 307 | sprintf(genes[i].gene_data, "%srbs_motif=None;rbs_spacer=None", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 308 | genes[i].gene_data); | ~~~~~~~~~~~~~~~~~~~ gene.c:290:9: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 290 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 291 | genes[i].gene_data, sd_string[nod[ndx].rbs[1]], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 292 | sd_spacer[nod[ndx].rbs[1]]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:286:9: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 286 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 | genes[i].gene_data, sd_string[nod[ndx].rbs[0]], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | sd_spacer[nod[ndx].rbs[0]]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:312:5: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 312 | sprintf(genes[i].gene_data, "%s;gc_cont=%.3f", genes[i].gene_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 313 | nod[ndx].gc_cont); | ~~~~~~~~~~~~~~~~~ gene.c:322:5: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 322 | sprintf(genes[i].score_data, "%stscore=%.2f;", genes[i].score_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 323 | nod[ndx].tscore); | ~~~~~~~~~~~~~~~~ gene.c:322:5: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] gene.c: In function 'print_genes': gene.c:347:26: warning: 'model="' directive writing 7 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 347 | sprintf(run_data, "%smodel=\"%s\";", run_data, mdesc); | ^~~~~~~~ gene.c:347:5: note: 'sprintf' output 10 or more bytes (assuming 10009) into a destination of size 10000 347 | sprintf(run_data, "%smodel=\"%s\";", run_data, mdesc); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:347:5: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] gene.c:335:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 335 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ gene.c:343:26: warning: 'model="Ab initio";' directive writing 18 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 343 | sprintf(run_data, "%smodel=\"Ab initio\";", run_data); | ^~~~~~~~~~~~~~~~~~~~ gene.c:343:5: note: 'sprintf' output between 19 and 10018 bytes into a destination of size 10000 343 | sprintf(run_data, "%smodel=\"Ab initio\";", run_data); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:343:5: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] gene.c:335:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 335 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ gene.c:349:24: warning: 'gc_cont=' directive writing 8 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 349 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~ gene.c:349:21: note: assuming directive output of 4 bytes 349 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:349:3: note: 'sprintf' output between 37 and 10366 bytes into a destination of size 10000 349 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 350 | tinf->gc*100.0, tinf->trans_table, tinf->uses_sd); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:349:3: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] gene.c:335:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 335 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ node.c: In function 'write_start_file': node.c:1426:26: warning: 'model="' directive writing 7 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 1426 | sprintf(run_data, "%smodel=\"%s\";", run_data, mdesc); | ^~~~~~~~ node.c:1426:5: note: 'sprintf' output 10 or more bytes (assuming 10009) into a destination of size 10000 1426 | sprintf(run_data, "%smodel=\"%s\";", run_data, mdesc); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ node.c:1426:5: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] node.c:1414:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 1414 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ node.c:1422:26: warning: 'model="Ab initio";' directive writing 18 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 1422 | sprintf(run_data, "%smodel=\"Ab initio\";", run_data); | ^~~~~~~~~~~~~~~~~~~~ node.c:1422:5: note: 'sprintf' output between 19 and 10018 bytes into a destination of size 10000 1422 | sprintf(run_data, "%smodel=\"Ab initio\";", run_data); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ node.c:1422:5: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] node.c:1414:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 1414 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ node.c:1428:24: warning: 'gc_cont=' directive writing 8 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 1428 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~ node.c:1428:21: note: assuming directive output of 4 bytes 1428 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ node.c:1428:3: note: 'sprintf' output between 37 and 10366 bytes into a destination of size 10000 1428 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1429 | tinf->gc*100.0, tinf->trans_table, tinf->uses_sd); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ node.c:1428:3: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] node.c:1414:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 1414 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -o prodigal bitmap.o dprog.o gene.o main.o metagenomic.o node.o sequence.o training.o -lm -Wl,-z,relro -Wl,-z,now make[1]: Leaving directory '/build/reproducible-path/prodigal-2.6.3' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/prodigal-2.6.3' echo "Do not try to install to /usr/local" Do not try to install to /usr/local make[1]: Leaving directory '/build/reproducible-path/prodigal-2.6.3' dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'prodigal-dbgsym' in '../prodigal-dbgsym_2.6.3-6_arm64.deb'. dpkg-deb: building package 'prodigal' in '../prodigal_2.6.3-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../prodigal_2.6.3-6_arm64.buildinfo dpkg-genchanges --build=binary -O../prodigal_2.6.3-6_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2763741 and its subdirectories I: Current time: Fri Oct 31 01:23:42 -12 2025 I: pbuilder-time-stamp: 1761917022 Fri Oct 31 13:23:42 UTC 2025 I: Signing ./b1/prodigal_2.6.3-6_arm64.buildinfo as prodigal_2.6.3-6_arm64.buildinfo.asc Fri Oct 31 13:23:42 UTC 2025 I: Signed ./b1/prodigal_2.6.3-6_arm64.buildinfo as ./b1/prodigal_2.6.3-6_arm64.buildinfo.asc Fri Oct 31 13:23:42 UTC 2025 - build #1 for prodigal/unstable/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Fri Oct 31 13:23:42 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-gK49quTk, removing. /srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Oct 31 13:23 b1 drwxrwxr-x 2 jenkins jenkins 4096 Oct 31 13:17 b2 -rw-rw-r-- 1 jenkins jenkins 1992 Dec 6 2022 prodigal_2.6.3-6.dsc -rw------- 1 jenkins jenkins 3111 Oct 31 13:17 rbuildlog.TzQqLK1 /srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l/b1: total 800 -rw-r--r-- 1 jenkins jenkins 29823 Oct 31 13:23 build.log -rw-r--r-- 1 jenkins jenkins 98732 Oct 31 13:23 prodigal-dbgsym_2.6.3-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 49304 Oct 31 13:23 prodigal_2.6.3-6.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1992 Oct 31 13:23 prodigal_2.6.3-6.dsc -rw-r--r-- 1 jenkins jenkins 4743 Oct 31 13:23 prodigal_2.6.3-6_arm64.buildinfo -rw-rw-r-- 1 jenkins jenkins 5625 Oct 31 13:23 prodigal_2.6.3-6_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1369 Oct 31 13:23 prodigal_2.6.3-6_arm64.changes -rw-r--r-- 1 jenkins jenkins 598216 Oct 31 13:23 prodigal_2.6.3-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 1223 Oct 31 13:23 prodigal_2.6.3-6_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l/b2: total 0 Fri Oct 31 13:23:43 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Oct 31 01:17:38 -12 2025 I: pbuilder-time-stamp: 1761916658 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 [prodigal_2.6.3-6.dsc] I: copying [./prodigal_2.6.3.orig.tar.gz] I: copying [./prodigal_2.6.3-6.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./prodigal_2.6.3-6.dsc: no acceptable signature found dpkg-source: info: extracting prodigal in prodigal-2.6.3 dpkg-source: info: unpacking prodigal_2.6.3.orig.tar.gz dpkg-source: info: unpacking prodigal_2.6.3-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_hardcoded_O3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2763741/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='c29a8e7f09c543db9f402a31961b007a' 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='2763741' 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.U5RvVm1l/pbuilderrc_AVYx --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.U5RvVm1l/b1 --logfile b1/build.log prodigal_2.6.3-6.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2763741/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19964 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} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 11.0 MB of archives. After unpacking 44.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41.2-4 [97.3 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.20-2 [315 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.18.1-2 [877 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-7 [540 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.194-1 [184 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.16-2 [100 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libxml2-16 arm64 2.15.1+dfsg-0.3 [591 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.28 [941 kB] Fetched 11.0 MB in 0s (83.5 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 ... 19964 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. 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Setting up automake (1:1.18.1-2) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.28) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/prodigal-2.6.3/ && 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 > ../prodigal_2.6.3-6_source.changes dpkg-buildpackage: info: source package prodigal dpkg-buildpackage: info: source version 1:2.6.3-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 distclean make[1]: Entering directory '/build/reproducible-path/prodigal-2.6.3' rm -f bitmap.o dprog.o gene.o main.o metagenomic.o node.o sequence.o training.o rm -f prodigal make[1]: Leaving directory '/build/reproducible-path/prodigal-2.6.3' debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/prodigal-2.6.3' dh_clean rm -f prodigal.1 make[1]: Leaving directory '/build/reproducible-path/prodigal-2.6.3' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/prodigal-2.6.3' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o bitmap.o bitmap.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o dprog.o dprog.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o gene.o gene.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o main.o main.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o metagenomic.o metagenomic.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o node.o node.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o sequence.o sequence.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o training.o training.c gene.c: In function 'record_gene_data': gene.c:303:9: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 303 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 304 | genes[i].gene_data, sd_string[nod[ndx].rbs[1]], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 305 | sd_spacer[nod[ndx].rbs[1]]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:298:9: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 298 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 299 | genes[i].gene_data, sd_string[nod[ndx].rbs[0]], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 300 | sd_spacer[nod[ndx].rbs[0]]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:309:12: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 309 | else sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%dbp", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 310 | genes[i].gene_data, qt, nod[ndx].mot.spacer); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:307:9: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 307 | sprintf(genes[i].gene_data, "%srbs_motif=None;rbs_spacer=None", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 308 | genes[i].gene_data); | ~~~~~~~~~~~~~~~~~~~ gene.c:290:9: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 290 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 291 | genes[i].gene_data, sd_string[nod[ndx].rbs[1]], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 292 | sd_spacer[nod[ndx].rbs[1]]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:286:9: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 286 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 | genes[i].gene_data, sd_string[nod[ndx].rbs[0]], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | sd_spacer[nod[ndx].rbs[0]]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:312:5: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 312 | sprintf(genes[i].gene_data, "%s;gc_cont=%.3f", genes[i].gene_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 313 | nod[ndx].gc_cont); | ~~~~~~~~~~~~~~~~~ gene.c:322:5: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 322 | sprintf(genes[i].score_data, "%stscore=%.2f;", genes[i].score_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 323 | nod[ndx].tscore); | ~~~~~~~~~~~~~~~~ gene.c:322:5: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] gene.c: In function 'print_genes': gene.c:347:26: warning: 'model="' directive writing 7 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 347 | sprintf(run_data, "%smodel=\"%s\";", run_data, mdesc); | ^~~~~~~~ gene.c:347:5: note: 'sprintf' output 10 or more bytes (assuming 10009) into a destination of size 10000 347 | sprintf(run_data, "%smodel=\"%s\";", run_data, mdesc); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:347:5: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] gene.c:335:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 335 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ gene.c:343:26: warning: 'model="Ab initio";' directive writing 18 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 343 | sprintf(run_data, "%smodel=\"Ab initio\";", run_data); | ^~~~~~~~~~~~~~~~~~~~ gene.c:343:5: note: 'sprintf' output between 19 and 10018 bytes into a destination of size 10000 343 | sprintf(run_data, "%smodel=\"Ab initio\";", run_data); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:343:5: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] gene.c:335:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 335 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ gene.c:349:24: warning: 'gc_cont=' directive writing 8 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 349 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~ gene.c:349:21: note: assuming directive output of 4 bytes 349 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:349:3: note: 'sprintf' output between 37 and 10366 bytes into a destination of size 10000 349 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 350 | tinf->gc*100.0, tinf->trans_table, tinf->uses_sd); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:349:3: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] gene.c:335:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 335 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ node.c: In function 'write_start_file': node.c:1426:26: warning: 'model="' directive writing 7 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 1426 | sprintf(run_data, "%smodel=\"%s\";", run_data, mdesc); | ^~~~~~~~ node.c:1426:5: note: 'sprintf' output 10 or more bytes (assuming 10009) into a destination of size 10000 1426 | sprintf(run_data, "%smodel=\"%s\";", run_data, mdesc); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ node.c:1426:5: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] node.c:1414:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 1414 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ node.c:1422:26: warning: 'model="Ab initio";' directive writing 18 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 1422 | sprintf(run_data, "%smodel=\"Ab initio\";", run_data); | ^~~~~~~~~~~~~~~~~~~~ node.c:1422:5: note: 'sprintf' output between 19 and 10018 bytes into a destination of size 10000 1422 | sprintf(run_data, "%smodel=\"Ab initio\";", run_data); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ node.c:1422:5: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] node.c:1414:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 1414 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ node.c:1428:24: warning: 'gc_cont=' directive writing 8 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 1428 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~ node.c:1428:21: note: assuming directive output of 4 bytes 1428 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ node.c:1428:3: note: 'sprintf' output between 37 and 10366 bytes into a destination of size 10000 1428 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1429 | tinf->gc*100.0, tinf->trans_table, tinf->uses_sd); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ node.c:1428:3: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] node.c:1414:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 1414 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -o prodigal bitmap.o dprog.o gene.o main.o metagenomic.o node.o sequence.o training.o -lm -Wl,-z,relro -Wl,-z,now make[1]: Leaving directory '/build/reproducible-path/prodigal-2.6.3' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/prodigal-2.6.3' echo "Do not try to install to /usr/local" Do not try to install to /usr/local make[1]: Leaving directory '/build/reproducible-path/prodigal-2.6.3' dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'prodigal-dbgsym' in '../prodigal-dbgsym_2.6.3-6_arm64.deb'. dpkg-deb: building package 'prodigal' in '../prodigal_2.6.3-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../prodigal_2.6.3-6_arm64.buildinfo dpkg-genchanges --build=binary -O../prodigal_2.6.3-6_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2763741 and its subdirectories I: Current time: Fri Oct 31 01:23:42 -12 2025 I: pbuilder-time-stamp: 1761917022 Fri Oct 31 13:23:44 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Fri Oct 31 13:23:44 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Fri Oct 31 13:23:44 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Fri Oct 31 13:23:44 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-4B3WVx' ==================================================================================== Thu Dec 3 19:46:45 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "2 prodigal unstable /srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l 1:2.6.3-6" as arguments. Thu Dec 3 19:46:45 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-Hyc9X3cm" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Dec 3 19:46:45 UTC 2026 I: Downloading source for unstable/prodigal=1:2.6.3-6 Reading package lists... NOTICE: 'prodigal' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/prodigal.git Please use: git clone https://salsa.debian.org/med-team/prodigal.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 662 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main prodigal 1:2.6.3-6 (dsc) [1992 B] Get:2 http://deb.debian.org/debian unstable/main prodigal 1:2.6.3-6 (tar) [611 kB] Get:3 http://deb.debian.org/debian unstable/main prodigal 1:2.6.3-6 (diff) [49.3 kB] Fetched 662 kB in 0s (29.1 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'prodigal' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/prodigal.git Please use: git clone https://salsa.debian.org/med-team/prodigal.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 662 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main prodigal 1:2.6.3-6 (dsc) [1992 B] Get:2 http://deb.debian.org/debian unstable/main prodigal 1:2.6.3-6 (tar) [611 kB] Get:3 http://deb.debian.org/debian unstable/main prodigal 1:2.6.3-6 (diff) [49.3 kB] Fetched 662 kB in 0s (29.1 MB/s) Download complete and in download only mode ============================================================================= Re-Building prodigal in unstable on arm64 on codethink03-arm64 now. Date: Thu Dec 3 19:46:45 GMT 2026 Date UTC: Thu Dec 3 19:46:45 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l/pbuilderrc_Xlsk + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' prodigal = debian-installer -o prodigal = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' prodigal = u-boot ']' + case "${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.U5RvVm1l/pbuilderrc_Xlsk --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.U5RvVm1l/b2 --logfile b2/build.log prodigal_2.6.3-6.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Dec 4 09:46:45 +14 2026 I: pbuilder-time-stamp: 1796327205 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 [prodigal_2.6.3-6.dsc] I: copying [./prodigal_2.6.3.orig.tar.gz] I: copying [./prodigal_2.6.3-6.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./prodigal_2.6.3-6.dsc: no acceptable signature found dpkg-source: info: extracting prodigal in prodigal-2.6.3 dpkg-source: info: unpacking prodigal_2.6.3.orig.tar.gz dpkg-source: info: unpacking prodigal_2.6.3-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_hardcoded_O3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2817160/tmp/hooks/D01_modify_environment starting debug: Running on codethink03-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Dec 3 19:46 /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/2817160/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2817160/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.3.3(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=a53c6be96e8c437ebdde2ccd6bf472f4 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2817160 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.U5RvVm1l/pbuilderrc_Xlsk --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.U5RvVm1l/b2 --logfile b2/build.log prodigal_2.6.3-6.dsc' SUDO_GID=109 SUDO_HOME=/var/lib/jenkins SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2817160/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19964 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} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 11.0 MB of archives. After unpacking 44.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41.2-4 [97.3 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.20-2 [315 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.18.1-2 [877 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-7 [540 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.194-1 [184 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.16-2 [100 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libxml2-16 arm64 2.15.1+dfsg-0.3 [591 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.28 [941 kB] Fetched 11.0 MB in 0s (74.2 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 ... 19964 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_arm64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.2-4_arm64.deb ... Unpacking bsdextrautils (2.41.2-4) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.20-2_arm64.deb ... Unpacking m4 (1.4.20-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.18.1-2_all.deb ... Unpacking automake (1:1.18.1-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.28_all.deb ... Unpacking libdebhelper-perl (13.28) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-7_all.deb ... Unpacking libtool (2.5.4-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.194-1_arm64.deb ... Unpacking libelf1t64:arm64 (0.194-1) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.16-2_arm64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../23-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2-16:arm64. Preparing to unpack .../24-libxml2-16_2.15.1+dfsg-0.3_arm64.deb ... Unpacking libxml2-16:arm64 (2.15.1+dfsg-0.3) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2+b1_arm64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.28_all.deb ... Unpacking debhelper (13.28) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41.2-4) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:arm64 (2.15.1+dfsg-0.3) ... Setting up libdebhelper-perl (13.28) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-2) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.194-1) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:arm64 (0.0.8-2) ... Setting up automake (1:1.18.1-2) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.28) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2817160/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/2817160/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/prodigal-2.6.3/ && 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 > ../prodigal_2.6.3-6_source.changes dpkg-buildpackage: info: source package prodigal dpkg-buildpackage: info: source version 1:2.6.3-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 distclean make[1]: Entering directory '/build/reproducible-path/prodigal-2.6.3' rm -f bitmap.o dprog.o gene.o main.o metagenomic.o node.o sequence.o training.o rm -f prodigal make[1]: Leaving directory '/build/reproducible-path/prodigal-2.6.3' debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/prodigal-2.6.3' dh_clean rm -f prodigal.1 make[1]: Leaving directory '/build/reproducible-path/prodigal-2.6.3' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/prodigal-2.6.3' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o bitmap.o bitmap.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o dprog.o dprog.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o gene.o gene.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o main.o main.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o metagenomic.o metagenomic.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o node.o node.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o sequence.o sequence.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -c -o training.o training.c gene.c: In function 'record_gene_data': gene.c:303:9: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 303 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 304 | genes[i].gene_data, sd_string[nod[ndx].rbs[1]], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 305 | sd_spacer[nod[ndx].rbs[1]]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:298:9: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 298 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 299 | genes[i].gene_data, sd_string[nod[ndx].rbs[0]], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 300 | sd_spacer[nod[ndx].rbs[0]]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:309:12: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 309 | else sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%dbp", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 310 | genes[i].gene_data, qt, nod[ndx].mot.spacer); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:307:9: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 307 | sprintf(genes[i].gene_data, "%srbs_motif=None;rbs_spacer=None", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 308 | genes[i].gene_data); | ~~~~~~~~~~~~~~~~~~~ gene.c:290:9: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 290 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 291 | genes[i].gene_data, sd_string[nod[ndx].rbs[1]], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 292 | sd_spacer[nod[ndx].rbs[1]]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:286:9: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 286 | sprintf(genes[i].gene_data, "%srbs_motif=%s;rbs_spacer=%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 | genes[i].gene_data, sd_string[nod[ndx].rbs[0]], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | sd_spacer[nod[ndx].rbs[0]]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:312:5: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 312 | sprintf(genes[i].gene_data, "%s;gc_cont=%.3f", genes[i].gene_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 313 | nod[ndx].gc_cont); | ~~~~~~~~~~~~~~~~~ gene.c:322:5: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] 322 | sprintf(genes[i].score_data, "%stscore=%.2f;", genes[i].score_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 323 | nod[ndx].tscore); | ~~~~~~~~~~~~~~~~ gene.c:322:5: warning: 'sprintf' argument 3 overlaps destination object '' [-Wrestrict] gene.c: In function 'print_genes': gene.c:347:26: warning: 'model="' directive writing 7 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 347 | sprintf(run_data, "%smodel=\"%s\";", run_data, mdesc); | ^~~~~~~~ gene.c:347:5: note: 'sprintf' output 10 or more bytes (assuming 10009) into a destination of size 10000 347 | sprintf(run_data, "%smodel=\"%s\";", run_data, mdesc); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:347:5: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] gene.c:335:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 335 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ gene.c:343:26: warning: 'model="Ab initio";' directive writing 18 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 343 | sprintf(run_data, "%smodel=\"Ab initio\";", run_data); | ^~~~~~~~~~~~~~~~~~~~ gene.c:343:5: note: 'sprintf' output between 19 and 10018 bytes into a destination of size 10000 343 | sprintf(run_data, "%smodel=\"Ab initio\";", run_data); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:343:5: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] gene.c:335:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 335 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ gene.c:349:24: warning: 'gc_cont=' directive writing 8 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 349 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~ gene.c:349:21: note: assuming directive output of 4 bytes 349 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:349:3: note: 'sprintf' output between 37 and 10366 bytes into a destination of size 10000 349 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 350 | tinf->gc*100.0, tinf->trans_table, tinf->uses_sd); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.c:349:3: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] gene.c:335:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 335 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ node.c: In function 'write_start_file': node.c:1426:26: warning: 'model="' directive writing 7 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 1426 | sprintf(run_data, "%smodel=\"%s\";", run_data, mdesc); | ^~~~~~~~ node.c:1426:5: note: 'sprintf' output 10 or more bytes (assuming 10009) into a destination of size 10000 1426 | sprintf(run_data, "%smodel=\"%s\";", run_data, mdesc); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ node.c:1426:5: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] node.c:1414:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 1414 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ node.c:1422:26: warning: 'model="Ab initio";' directive writing 18 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 1422 | sprintf(run_data, "%smodel=\"Ab initio\";", run_data); | ^~~~~~~~~~~~~~~~~~~~ node.c:1422:5: note: 'sprintf' output between 19 and 10018 bytes into a destination of size 10000 1422 | sprintf(run_data, "%smodel=\"Ab initio\";", run_data); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ node.c:1422:5: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] node.c:1414:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 1414 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ node.c:1428:24: warning: 'gc_cont=' directive writing 8 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 1428 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~ node.c:1428:21: note: assuming directive output of 4 bytes 1428 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ node.c:1428:3: note: 'sprintf' output between 37 and 10366 bytes into a destination of size 10000 1428 | sprintf(run_data, "%sgc_cont=%.2f;transl_table=%d;uses_sd=%d", run_data, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1429 | tinf->gc*100.0, tinf->trans_table, tinf->uses_sd); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ node.c:1428:3: warning: 'sprintf' argument 3 overlaps destination object 'run_data' [-Wrestrict] node.c:1414:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 1414 | char seq_data[MAX_LINE*2], run_data[MAX_LINE]; | ^~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prodigal-2.6.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -pedantic -Wall -o prodigal bitmap.o dprog.o gene.o main.o metagenomic.o node.o sequence.o training.o -lm -Wl,-z,relro -Wl,-z,now make[1]: Leaving directory '/build/reproducible-path/prodigal-2.6.3' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/prodigal-2.6.3' echo "Do not try to install to /usr/local" Do not try to install to /usr/local make[1]: Leaving directory '/build/reproducible-path/prodigal-2.6.3' dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'prodigal' in '../prodigal_2.6.3-6_arm64.deb'. dpkg-deb: building package 'prodigal-dbgsym' in '../prodigal-dbgsym_2.6.3-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../prodigal_2.6.3-6_arm64.buildinfo dpkg-genchanges --build=binary -O../prodigal_2.6.3-6_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2817160/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2817160/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/2817160 and its subdirectories I: Current time: Fri Dec 4 09:52:48 +14 2026 I: pbuilder-time-stamp: 1796327568 + false + set +x Thu Dec 3 19:52:48 UTC 2026 I: Signing ./b2/prodigal_2.6.3-6_arm64.buildinfo as prodigal_2.6.3-6_arm64.buildinfo.asc Thu Dec 3 19:52:48 UTC 2026 I: Signed ./b2/prodigal_2.6.3-6_arm64.buildinfo as ./b2/prodigal_2.6.3-6_arm64.buildinfo.asc Thu Dec 3 19:52:48 UTC 2026 - build #2 for prodigal/unstable/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Thu Dec 3 19:52:48 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-Hyc9X3cm, removing. /srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l: total 48 drwxrwxr-x 2 jenkins jenkins 4096 Oct 31 13:23 b1 drwxrwxr-x 2 jenkins jenkins 4096 Oct 31 13:29 b2 -rw-rw-r-- 1 jenkins jenkins 1992 Dec 6 2022 prodigal_2.6.3-6.dsc -rw------- 1 jenkins jenkins 33235 Oct 31 13:23 rbuildlog.TzQqLK1 /srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l/b1: total 812 -rw-r--r-- 1 jenkins jenkins 29823 Oct 31 13:23 build.log -rw-r--r-- 1 jenkins jenkins 98732 Oct 31 13:23 prodigal-dbgsym_2.6.3-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 49304 Oct 31 13:23 prodigal_2.6.3-6.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1992 Oct 31 13:23 prodigal_2.6.3-6.dsc -rw-r--r-- 1 jenkins jenkins 4743 Oct 31 13:23 prodigal_2.6.3-6_arm64.buildinfo -rw-rw-r-- 1 jenkins jenkins 5625 Oct 31 13:23 prodigal_2.6.3-6_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1369 Oct 31 13:23 prodigal_2.6.3-6_arm64.changes -rw-r--r-- 1 jenkins jenkins 598216 Oct 31 13:23 prodigal_2.6.3-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 1223 Oct 31 13:23 prodigal_2.6.3-6_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l/b2: total 800 -rw-rw-r-- 1 jenkins jenkins 31764 Oct 31 13:29 build.log -rw-r--r-- 1 jenkins jenkins 98732 Oct 31 13:29 prodigal-dbgsym_2.6.3-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 49304 Oct 31 13:29 prodigal_2.6.3-6.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1992 Oct 31 13:29 prodigal_2.6.3-6.dsc -rw-rw-r-- 1 jenkins jenkins 4743 Oct 31 13:29 prodigal_2.6.3-6_arm64.buildinfo -rw-rw-r-- 1 jenkins jenkins 5625 Oct 31 13:29 prodigal_2.6.3-6_arm64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 1369 Oct 31 13:29 prodigal_2.6.3-6_arm64.changes -rw-r--r-- 1 jenkins jenkins 598216 Oct 31 13:29 prodigal_2.6.3-6_arm64.deb -rw-rw-r-- 1 jenkins jenkins 1223 Oct 31 13:29 prodigal_2.6.3-6_source.changes Fri Oct 31 13:29:49 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Fri Oct 31 13:29:50 UTC 2025 I: prodigal_2.6.3-6_arm64.changes: Format: 1.8 Date: Tue, 06 Dec 2022 14:00:03 +0100 Source: prodigal Binary: prodigal prodigal-dbgsym Architecture: arm64 Version: 1:2.6.3-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: prodigal - Microbial (bacterial and archaeal) gene finding program Changes: prodigal (1:2.6.3-6) unstable; urgency=medium . * Fix watch file * Standards-Version: 4.6.1 (routine-update) Checksums-Sha1: bc8d03a98cd4a6157d4c4382abda1a7274dc33f9 98732 prodigal-dbgsym_2.6.3-6_arm64.deb 025db5f5c774e8b7ca20a07d410464167e2c49aa 4743 prodigal_2.6.3-6_arm64.buildinfo 5c0cf828cbd516f87ea52035b67f2939cb4c0e34 598216 prodigal_2.6.3-6_arm64.deb Checksums-Sha256: 28b7f25eee372186f20baa6be45019c6daa2eb621d3b3704bef29ae832e707f2 98732 prodigal-dbgsym_2.6.3-6_arm64.deb 6e84e567536db242b63174169690411b1e25b5764e9dd92bd4b5ce794800cfaa 4743 prodigal_2.6.3-6_arm64.buildinfo b96b43d48ebe7aee1f6d1c6bec2936805c550a3a72d62fcab365596263cfb71b 598216 prodigal_2.6.3-6_arm64.deb Files: 9388304fd7bd15fe6072152242c2f937 98732 debug optional prodigal-dbgsym_2.6.3-6_arm64.deb 25c9f18362d9256d22641c838a7b9415 4743 science optional prodigal_2.6.3-6_arm64.buildinfo aad8377ac3085e78cf73635aa50c7d0d 598216 science optional prodigal_2.6.3-6_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/prodigal_2.6.3-6.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/prodigal_2.6.3-6.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/prodigal_2.6.3-6.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/prodigal_2.6.3-6.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/arm64/prodigal_2.6.3-6_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/prodigal_2.6.3-6.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-10-31 13:23:43.384779503 +0000 +++ b2/build.log 2025-10-31 13:29:49.553237146 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Oct 31 01:17:38 -12 2025 -I: pbuilder-time-stamp: 1761916658 +I: Current time: Fri Dec 4 09:46:45 +14 2026 +I: pbuilder-time-stamp: 1796327205 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -24,53 +24,85 @@ dpkg-source: info: applying no_hardcoded_O3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2763741/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2817160/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 3 19:46 /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/2817160/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2817160/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='c29a8e7f09c543db9f402a31961b007a' - 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='2763741' - PS1='# ' - PS2='> ' + INVOCATION_ID=a53c6be96e8c437ebdde2ccd6bf472f4 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2817160 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.U5RvVm1l/pbuilderrc_AVYx --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.U5RvVm1l/b1 --logfile b1/build.log prodigal_2.6.3-6.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l/pbuilderrc_Xlsk --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.U5RvVm1l/b2 --logfile b2/build.log prodigal_2.6.3-6.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2763741/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2817160/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -135,7 +167,7 @@ Get: 27 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.28 [941 kB] -Fetched 11.0 MB in 0s (83.5 MB/s) +Fetched 11.0 MB in 0s (74.2 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 ... 19964 files and directories currently installed.) @@ -266,7 +298,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/prodigal-2.6.3/ && 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 > ../prodigal_2.6.3-6_source.changes +I: user script /srv/workspace/pbuilder/2817160/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2817160/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/prodigal-2.6.3/ && 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 > ../prodigal_2.6.3-6_source.changes dpkg-buildpackage: info: source package prodigal dpkg-buildpackage: info: source version 1:2.6.3-6 dpkg-buildpackage: info: source distribution unstable @@ -456,8 +492,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'prodigal-dbgsym' in '../prodigal-dbgsym_2.6.3-6_arm64.deb'. dpkg-deb: building package 'prodigal' in '../prodigal_2.6.3-6_arm64.deb'. +dpkg-deb: building package 'prodigal-dbgsym' in '../prodigal-dbgsym_2.6.3-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../prodigal_2.6.3-6_arm64.buildinfo dpkg-genchanges --build=binary -O../prodigal_2.6.3-6_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -465,12 +501,14 @@ 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/2817160/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2817160/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/2763741 and its subdirectories -I: Current time: Fri Oct 31 01:23:42 -12 2025 -I: pbuilder-time-stamp: 1761917022 +I: removing directory /srv/workspace/pbuilder/2817160 and its subdirectories +I: Current time: Fri Dec 4 09:52:48 +14 2026 +I: pbuilder-time-stamp: 1796327568 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/prodigal_2.6.3-6.diff: 67.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/prodigal_2.6.3-6.diff.gz b2/build.log: 79.4% -- replaced with stdout Compressing the 1st log... b1/build.log: 80.3% -- replaced with stdout Fri Oct 31 13:29:50 UTC 2025 I: diffoscope 306 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_prodigal_unstable_arm64_1761917390 + touch /var/log/reproducible-builds/diffoscope_stamp_prodigal_unstable_arm64_1761917390 + RESULT=0 + systemd-run '--description=diffoscope on prodigal/1:2.6.3-6 in unstable/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_7-102637 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l --run-session -c jenkins-reproducible-unstable-diffoscope-f0cbbc5f-9396-46a2-96a8-83b07b844037 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l/dbd-tmp-A2MEpEl ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l/prodigal_2.6.3-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l/prodigal_2.6.3-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l/prodigal_2.6.3-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l/b1/prodigal_2.6.3-6_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l/b2/prodigal_2.6.3-6_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_7-102637.service; invocation ID: 5000329db46543c5b31bc026ac79cf7f # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l/prodigal_2.6.3-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l/prodigal_2.6.3-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l/prodigal_2.6.3-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l/b1/prodigal_2.6.3-6_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.U5RvVm1l/b2/prodigal_2.6.3-6_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 198ms CPU time consumed: 171ms Memory peak: 17.7M (swap: 0B) _ _ _ _ __ _ __ ___ __| (_) __ _ __ _| | | '_ \| '__/ _ \ / _` | |/ _` |/ _` | | | |_) | | | (_) | (_| | | (_| | (_| | | | .__/|_| \___/ \__,_|_|\__, |\__,_|_| |_| |___/ Fri Oct 31 13:29:51 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Fri Oct 31 13:29:51 UTC 2025 I: prodigal from unstable built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-10-31 13:29:51] INFO: Starting at 2025-10-31 13:29:51.702318 [2025-10-31 13:29:51] INFO: Generating the pages of 1 package(s) [2025-10-31 13:29:51] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/prodigal didn't produce a buildlog, even though it has been built. [2025-10-31 13:29:51] INFO: Finished at 2025-10-31 13:29:51.978706, took: 0:00:00.276391 Fri Oct 31 13:29:52 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/prodigal.html Fri Oct 31 13:29:52 UTC 2025 I: Removing signed prodigal_2.6.3-6_arm64.buildinfo.asc files: removed './b1/prodigal_2.6.3-6_arm64.buildinfo.asc' removed './b2/prodigal_2.6.3-6_arm64.buildinfo.asc' 1761917392 arm64 unstable prodigal Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/prodigal_2.6.3-6.rbuild.log: 76.2% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/prodigal_2.6.3-6.rbuild.log.gz [2025-10-31 13:29:52] INFO: Starting at 2025-10-31 13:29:52.296662 [2025-10-31 13:29:52] INFO: Generating the pages of 1 package(s) [2025-10-31 13:29:52] INFO: Finished at 2025-10-31 13:29:52.567804, took: 0:00:00.271146 All cleanup done. Fri Oct 31 13:29:52 UTC 2025 - total duration: 0h 12m 26s. Fri Oct 31 13:29:52 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-wvM0dljR, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 12min 26.967s CPU time consumed: 3.072s Memory peak: 42.1M (swap: 0B)