Running as unit: rb-build-amd64_8-72493.service; invocation ID: 7a792dcc932e4c3ea68bb6ea5c638233 ==================================================================================== Sun Sep 14 12:53:52 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_8) on jenkins, called using "ionos15-amd64 ionos11-amd64" as arguments. Sun Sep 14 12:53:52 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-7EoUhXsB" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sun Sep 14 12:53:52 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Sun Sep 14 12:53:52 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-wxiZbt' Sun Sep 14 12:53:52 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Sun Sep 14 12:53:52 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-UGXOnW' ok, let's check if soapdenovo2 is building anywhere yet… ok, soapdenovo2 is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of soapdenovo2 in unstable on amd64 on jenkins now. 1st build will be done on ionos15-amd64.debian.net. 2nd build will be done on ionos11-amd64.debian.net. ============================================================================= Sun Sep 14 12:54:00 UTC 2025 I: starting to build soapdenovo2/unstable/amd64 on jenkins on '2025-09-14 12:53' Sun Sep 14 12:54:00 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_8/72493/console.log 1757854440 amd64 unstable soapdenovo2 Sun Sep 14 12:54:00 UTC 2025 I: Downloading source for unstable/soapdenovo2=242+dfsg-4 --2025-09-14 12:54:00-- http://deb.debian.org/debian/pool/main/s/soapdenovo2/soapdenovo2_242%2bdfsg-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2283 (2.2K) [text/prs.lines.tag] Saving to: ‘soapdenovo2_242+dfsg-4.dsc’ 0K .. 100% 268M=0s 2025-09-14 12:54:00 (268 MB/s) - ‘soapdenovo2_242+dfsg-4.dsc’ saved [2283/2283] --2025-09-14 12:54:00-- http://deb.debian.org/debian/pool/main/s/soapdenovo2/soapdenovo2_242%2bdfsg-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2283 (2.2K) [text/prs.lines.tag] Saving to: ‘soapdenovo2_242+dfsg-4.dsc’ 0K .. 100% 268M=0s 2025-09-14 12:54:00 (268 MB/s) - ‘soapdenovo2_242+dfsg-4.dsc’ saved [2283/2283] Sun Sep 14 12:54:00 UTC 2025 I: soapdenovo2_242+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: soapdenovo2 Binary: soapdenovo2 Architecture: any-amd64 any-ppc64 any-ia64 Version: 242+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou , Andreas Tille Homepage: http://soap.genomics.org.cn/soapdenovo.html Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/soapdenovo2 Vcs-Git: https://salsa.debian.org/med-team/soapdenovo2.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbam-dev, libaio-dev, rename Package-List: soapdenovo2 deb science optional arch=any-amd64,any-ppc64,any-ia64 Checksums-Sha1: c817de22b6e7cea70a4be17c869ab04973963eab 251060 soapdenovo2_242+dfsg.orig.tar.xz 19bbccf1e81957e8dafc95eea2bdf4254750c7df 489588 soapdenovo2_242+dfsg-4.debian.tar.xz Checksums-Sha256: ff787d4227c9862347663f7426c71b026559720c501033c96190f8aad26549a1 251060 soapdenovo2_242+dfsg.orig.tar.xz 2155b1f51446f343bd1d62799e00f10f2f0b5e8cf31c54658e120116c70d40ab 489588 soapdenovo2_242+dfsg-4.debian.tar.xz Files: d09be53b4104c67050aa3757c49b19d1 251060 soapdenovo2_242+dfsg.orig.tar.xz 67fd3383838d2cc934858bc77c2ed828 489588 soapdenovo2_242+dfsg-4.debian.tar.xz Dgit: 680d24855e51ee50b4bd5a69c96f9a765aeabd79 debian archive/debian/242+dfsg-4 https://git.dgit.debian.org/soapdenovo2 -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAma48QAUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoPBQ/9GyBYUSr5GCsTzNcT1gG2s9lQMPSn gJ7zoFGUJGWpDaJYDZFbcVzPC1IgAPROvtamrJhsZHZPE8gq4A1ARZiPPHeW4HWZ 7Apisq7apMLMgY5z/NBO8LRHGALN0eHJfPUxDnBIQIVG4UCtVvb6c8hgIKYBjFCR S79JT/Y7UtYiJaUCG3bfDPuiKolLMeOpRSKOUCcWNvJ4Nkg2zQekmkRZBRxslIQ7 EhRmpiddd+qfsrBaSmuBdyUVbqVWquvAg2BpSxCsU1u0NAdnT9NdKY0qTIQPjwGo xHRf90qGjC/LlfQz5KX5m14ZGqmq5komBwJ/8/Q6AyO+tqEJX2Jogijtr5KZD3y2 H90AcbJ1MJxc5yCpJlDkZQrwM2DYJcu67Vkedl1ah0W1QnqX/4otReeJEOlYQqaH KSsNJBnUv5H92s1Q37mRfUZ5fCspTQPb6pkyhA0kiIxhKLDGVnpzB/cDLauajVeI qmFpQkCCQV/5oZdyPa9Hy/+b79F8OowDL32xXNsxddwLy/MGww4i0REoHidud7Jv 34HKG5SfAWSmwM6IAakF0kMu3xXO/TH8sFpOiDVQLpo0P6Z9npTy0u3jrNiFo3y2 HSzT3bA+U0DSknWF0t/FuSB5t/OZOsG9HdIbARuK2m+O8EDgusynI1fBwr0b8sMw s6jF2Yoan+QfY2g= =WMO7 -----END PGP SIGNATURE----- Sun Sep 14 12:54:00 UTC 2025 I: Checking whether the package is not for us Sun Sep 14 12:54:00 UTC 2025 I: Starting 1st build on remote node ionos15-amd64.debian.net. Sun Sep 14 12:54:00 UTC 2025 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Sun Sep 14 12:54:00 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Sun Sep 14 12:54:00 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-Vol9Gh' ==================================================================================== Sat Oct 17 19:17:00 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "1 soapdenovo2 unstable /srv/reproducible-results/rbuild-debian/r-b-build.9oKkropQ 242+dfsg-4" as arguments. Sat Oct 17 19:17:00 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-GR00H1A4" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Oct 17 19:17:01 UTC 2026 I: Downloading source for unstable/soapdenovo2=242+dfsg-4 Reading package lists... NOTICE: 'soapdenovo2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/soapdenovo2.git Please use: git clone https://salsa.debian.org/med-team/soapdenovo2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 743 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main soapdenovo2 242+dfsg-4 (dsc) [2283 B] Get:2 http://deb.debian.org/debian unstable/main soapdenovo2 242+dfsg-4 (tar) [251 kB] Get:3 http://deb.debian.org/debian unstable/main soapdenovo2 242+dfsg-4 (diff) [490 kB] Fetched 743 kB in 0s (13.0 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'soapdenovo2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/soapdenovo2.git Please use: git clone https://salsa.debian.org/med-team/soapdenovo2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 743 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main soapdenovo2 242+dfsg-4 (dsc) [2283 B] Get:2 http://deb.debian.org/debian unstable/main soapdenovo2 242+dfsg-4 (tar) [251 kB] Get:3 http://deb.debian.org/debian unstable/main soapdenovo2 242+dfsg-4 (diff) [490 kB] Fetched 743 kB in 0s (13.0 MB/s) Download complete and in download only mode ============================================================================= Building soapdenovo2 in unstable on amd64 on ionos15-amd64 now. Date: Sat Oct 17 19:17:01 UTC 2026 Date UTC: Sat Oct 17 19:17:01 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Sat Oct 17 07:17:01 -12 2026 I: pbuilder-time-stamp: 1792264621 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 [soapdenovo2_242+dfsg-4.dsc] I: copying [./soapdenovo2_242+dfsg.orig.tar.xz] I: copying [./soapdenovo2_242+dfsg-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./soapdenovo2_242+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting soapdenovo2 in soapdenovo2-242+dfsg dpkg-source: info: unpacking soapdenovo2_242+dfsg.orig.tar.xz dpkg-source: info: unpacking soapdenovo2_242+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_libsam dpkg-source: info: applying fix_compilation dpkg-source: info: applying fix_usage_name dpkg-source: info: applying add_hardening dpkg-source: info: applying use_debian_zlib dpkg-source: info: applying reproducible dpkg-source: info: applying gcc-10.patch dpkg-source: info: applying gcc-14.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1627924/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='ce7403dc168f4dc6b1f13c8abe357d65' 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='1627924' 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.9oKkropQ/pbuilderrc_gGjm --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.9oKkropQ/b1 --logfile b1/build.log soapdenovo2_242+dfsg-4.dsc' SUDO_GID='111' SUDO_HOME='/var/lib/jenkins' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1627924/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libbam-dev, libaio-dev, rename dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbam-dev; however: Package libbam-dev is not installed. pbuilder-satisfydepends-dummy depends on libaio-dev; however: Package libaio-dev is not installed. pbuilder-satisfydepends-dummy depends on rename; however: Package rename 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} libaio-dev{a} libaio1t64{a} libarchive-zip-perl{a} libbam-dev{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} rename{a} sensible-utils{a} zlib1g-dev{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, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 12.3 MB of archives. After unpacking 44.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libaio1t64 amd64 0.3.113-8+b1 [14.9 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libaio-dev amd64 0.3.113-8+b1 [31.4 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libbam-dev amd64 0.1.19+dfsg-6 [118 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 rename all 2.02-1 [21.8 kB] Fetched 12.3 MB in 3s (4045 kB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.193-3_amd64.deb ... Unpacking libelf1t64:amd64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../24-libxml2-16_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.26_all.deb ... Unpacking debhelper (13.26) ... Selecting previously unselected package libaio1t64:amd64. Preparing to unpack .../29-libaio1t64_0.3.113-8+b1_amd64.deb ... Unpacking libaio1t64:amd64 (0.3.113-8+b1) ... Selecting previously unselected package libaio-dev:amd64. Preparing to unpack .../30-libaio-dev_0.3.113-8+b1_amd64.deb ... Unpacking libaio-dev:amd64 (0.3.113-8+b1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../31-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package libbam-dev. Preparing to unpack .../32-libbam-dev_0.1.19+dfsg-6_amd64.deb ... Unpacking libbam-dev (0.1.19+dfsg-6) ... Selecting previously unselected package rename. Preparing to unpack .../33-rename_2.02-1_all.deb ... Unpacking rename (2.02-1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up bsdextrautils (2.41.1-3) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up rename (2.02-1) ... update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.16-2) ... Setting up libaio1t64:amd64 (0.3.113-8+b1) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up libaio-dev:amd64 (0.3.113-8+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libbam-dev (0.1.19+dfsg-6) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.26) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/soapdenovo2-242+dfsg/ && 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 > ../soapdenovo2_242+dfsg-4_source.changes dpkg-buildpackage: info: source package soapdenovo2 dpkg-buildpackage: info: source version 242+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --no-parallel dh_auto_clean -O--no-parallel make -j1 clean pregraph_sparse_63mer.v1.0.3 cleaning done. SOAPdenovo-63mer cleaning done. SOAPdenovo-fusion cleaning done. dh_autoreconf_clean -O--no-parallel debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/soapdenovo2-242+dfsg' cd standardPregraph && make 63mer=1 clean && make 127mer=1 clean make[2]: Entering directory '/build/reproducible-path/soapdenovo2-242+dfsg/standardPregraph' SOAPdenovo-63mer cleaning done. make[2]: Leaving directory '/build/reproducible-path/soapdenovo2-242+dfsg/standardPregraph' make[2]: Entering directory '/build/reproducible-path/soapdenovo2-242+dfsg/standardPregraph' SOAPdenovo-127mer cleaning done. make[2]: Leaving directory '/build/reproducible-path/soapdenovo2-242+dfsg/standardPregraph' cd sparsePregraph && make clean make[2]: Entering directory '/build/reproducible-path/soapdenovo2-242+dfsg/sparsePregraph' pregraph_sparse_63mer.v1.0.3 cleaning done. make[2]: Leaving directory '/build/reproducible-path/soapdenovo2-242+dfsg/sparsePregraph' dh_clean make[1]: Leaving directory '/build/reproducible-path/soapdenovo2-242+dfsg' debian/rules binary dh binary --no-parallel dh_update_autotools_config -O--no-parallel dh_autoreconf -O--no-parallel dh_auto_configure -O--no-parallel dh_auto_build -O--no-parallel make -j1 "INSTALL=install --strip-program=true" pregraph_sparse_63mer.v1.0.3 cleaning done. Compiling build_graph.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling build_edge.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling multi_threads.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling build_preArc.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling pregraph_sparse.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling io_func.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling global.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling convert_soapdenovo.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ pregraph_sparse_63mer.v1.0.3 objects generated. SOAPdenovo-63mer cleaning done. Compiling arc.c... Compiling attachPEinfo.c... Compiling bubble.c... Compiling check.c... Compiling compactEdge.c... Compiling concatenateEdge.c... Compiling connect.c... Compiling contig.c... Compiling cutTipPreGraph.c... Compiling cutTip_graph.c... Compiling darray.c... Compiling dfib.c... Compiling dfibHeap.c... Compiling fib.c... Compiling fibHeap.c... Compiling hashFunction.c... Compiling kmer.c... Compiling lib.c... Compiling loadGraph.c... Compiling loadPath.c... Compiling loadPreGraph.c... Compiling localAsm.c... Compiling main.c... Compiling map.c... Compiling mem_manager.c... Compiling newhash.c... Compiling node2edge.c... Compiling orderContig.c... orderContig.c:1965:13: error: conflicting types for 'debugging2'; have 'void(unsigned int)' 1965 | static void debugging2 ( unsigned int ctg ) | ^~~~~~~~~~ orderContig.c:86:13: note: previous declaration of 'debugging2' with type 'void(void)' 86 | static void debugging2(); | ^~~~~~~~~~ Error in command: gcc -c -O3 -fomit-frame-pointer -w -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo2-242+dfsg/standardPregraph=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DBDATE="Aug 11 2024" -DBTIME="17:08:09" -DMER63 -m64 -Iinc -I/usr/include/samtools orderContig.c Compiling output_contig.c... Compiling output_pregraph.c... Compiling output_scaffold.c... Compiling pregraph.c... Compiling prlHashCtg.c... Compiling prlHashReads.c... Compiling prlRead2Ctg.c... Compiling prlRead2path.c... Compiling prlReadFillGap.c... Compiling read2scaf.c... Compiling readInterval.c... Compiling stack.c... Compiling readseq1by1.c... Compiling scaffold.c... Compiling searchPath.c... Compiling seq.c... Compiling splitReps.c... Compiling cutTip_graph2.c... Compiling linearEdge.c... Compiling kmerhash.c... Compiling read2edge.c... Compiling iterate.c... SOAPdenovo-63mer objects generated. /usr/bin/ld: standardPregraph/scaffold.o: in function `call_scaffold': ././scaffold.c:71:(.text+0x7e8): undefined reference to `checkFiles4Scaff' /usr/bin/ld: ././scaffold.c:93:(.text+0x85f): undefined reference to `ScafStat' /usr/bin/ld: ././scaffold.c:81:(.text+0x970): undefined reference to `PE2Links' /usr/bin/ld: ././scaffold.c:86:(.text+0x9ce): undefined reference to `Links2Scaf' /usr/bin/ld: ././scaffold.c:89:(.text+0xa0c): undefined reference to `scaffolding' collect2: error: ld returned 1 exit status make[1]: *** [Makefile:62: SOAPdenovo-63mer] Error 1 dh_auto_build: error: make -j1 "INSTALL=install --strip-program=true" returned exit code 2 make: *** [debian/rules:14: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/1627924 and its subdirectories Starting cleanup. All cleanup done. Sat Oct 17 19:18:32 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-GR00H1A4, removing. /srv/reproducible-results/rbuild-debian/r-b-build.9oKkropQ: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Sep 14 12:55 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 14 12:54 b2 -rw------- 1 jenkins jenkins 3429 Sep 14 12:54 rbuildlog.XIYiZAG -rw-rw-r-- 1 jenkins jenkins 2283 Aug 11 2024 soapdenovo2_242+dfsg-4.dsc /srv/reproducible-results/rbuild-debian/r-b-build.9oKkropQ/b1: total 28 -rw-r--r-- 1 jenkins jenkins 26262 Sep 14 12:55 build.log /srv/reproducible-results/rbuild-debian/r-b-build.9oKkropQ/b2: total 0 Sun Sep 14 12:55:33 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Oct 17 07:17:01 -12 2026 I: pbuilder-time-stamp: 1792264621 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 [soapdenovo2_242+dfsg-4.dsc] I: copying [./soapdenovo2_242+dfsg.orig.tar.xz] I: copying [./soapdenovo2_242+dfsg-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./soapdenovo2_242+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting soapdenovo2 in soapdenovo2-242+dfsg dpkg-source: info: unpacking soapdenovo2_242+dfsg.orig.tar.xz dpkg-source: info: unpacking soapdenovo2_242+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_libsam dpkg-source: info: applying fix_compilation dpkg-source: info: applying fix_usage_name dpkg-source: info: applying add_hardening dpkg-source: info: applying use_debian_zlib dpkg-source: info: applying reproducible dpkg-source: info: applying gcc-10.patch dpkg-source: info: applying gcc-14.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1627924/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='ce7403dc168f4dc6b1f13c8abe357d65' 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='1627924' 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.9oKkropQ/pbuilderrc_gGjm --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.9oKkropQ/b1 --logfile b1/build.log soapdenovo2_242+dfsg-4.dsc' SUDO_GID='111' SUDO_HOME='/var/lib/jenkins' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1627924/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libbam-dev, libaio-dev, rename dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbam-dev; however: Package libbam-dev is not installed. pbuilder-satisfydepends-dummy depends on libaio-dev; however: Package libaio-dev is not installed. pbuilder-satisfydepends-dummy depends on rename; however: Package rename 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} libaio-dev{a} libaio1t64{a} libarchive-zip-perl{a} libbam-dev{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} rename{a} sensible-utils{a} zlib1g-dev{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, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 12.3 MB of archives. After unpacking 44.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libaio1t64 amd64 0.3.113-8+b1 [14.9 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libaio-dev amd64 0.3.113-8+b1 [31.4 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libbam-dev amd64 0.1.19+dfsg-6 [118 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 rename all 2.02-1 [21.8 kB] Fetched 12.3 MB in 3s (4045 kB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. 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Preparing to unpack .../33-rename_2.02-1_all.deb ... Unpacking rename (2.02-1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up bsdextrautils (2.41.1-3) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up rename (2.02-1) ... update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.16-2) ... Setting up libaio1t64:amd64 (0.3.113-8+b1) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up libaio-dev:amd64 (0.3.113-8+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libbam-dev (0.1.19+dfsg-6) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.26) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/soapdenovo2-242+dfsg/ && 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 > ../soapdenovo2_242+dfsg-4_source.changes dpkg-buildpackage: info: source package soapdenovo2 dpkg-buildpackage: info: source version 242+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --no-parallel dh_auto_clean -O--no-parallel make -j1 clean pregraph_sparse_63mer.v1.0.3 cleaning done. SOAPdenovo-63mer cleaning done. SOAPdenovo-fusion cleaning done. dh_autoreconf_clean -O--no-parallel debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/soapdenovo2-242+dfsg' cd standardPregraph && make 63mer=1 clean && make 127mer=1 clean make[2]: Entering directory '/build/reproducible-path/soapdenovo2-242+dfsg/standardPregraph' SOAPdenovo-63mer cleaning done. make[2]: Leaving directory '/build/reproducible-path/soapdenovo2-242+dfsg/standardPregraph' make[2]: Entering directory '/build/reproducible-path/soapdenovo2-242+dfsg/standardPregraph' SOAPdenovo-127mer cleaning done. make[2]: Leaving directory '/build/reproducible-path/soapdenovo2-242+dfsg/standardPregraph' cd sparsePregraph && make clean make[2]: Entering directory '/build/reproducible-path/soapdenovo2-242+dfsg/sparsePregraph' pregraph_sparse_63mer.v1.0.3 cleaning done. make[2]: Leaving directory '/build/reproducible-path/soapdenovo2-242+dfsg/sparsePregraph' dh_clean make[1]: Leaving directory '/build/reproducible-path/soapdenovo2-242+dfsg' debian/rules binary dh binary --no-parallel dh_update_autotools_config -O--no-parallel dh_autoreconf -O--no-parallel dh_auto_configure -O--no-parallel dh_auto_build -O--no-parallel make -j1 "INSTALL=install --strip-program=true" pregraph_sparse_63mer.v1.0.3 cleaning done. Compiling build_graph.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling build_edge.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling multi_threads.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling build_preArc.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling pregraph_sparse.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling io_func.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling global.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ Compiling convert_soapdenovo.cpp... cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ pregraph_sparse_63mer.v1.0.3 objects generated. SOAPdenovo-63mer cleaning done. Compiling arc.c... Compiling attachPEinfo.c... Compiling bubble.c... Compiling check.c... Compiling compactEdge.c... Compiling concatenateEdge.c... Compiling connect.c... Compiling contig.c... Compiling cutTipPreGraph.c... Compiling cutTip_graph.c... Compiling darray.c... Compiling dfib.c... Compiling dfibHeap.c... Compiling fib.c... Compiling fibHeap.c... Compiling hashFunction.c... Compiling kmer.c... Compiling lib.c... Compiling loadGraph.c... Compiling loadPath.c... Compiling loadPreGraph.c... Compiling localAsm.c... Compiling main.c... Compiling map.c... Compiling mem_manager.c... Compiling newhash.c... Compiling node2edge.c... Compiling orderContig.c... orderContig.c:1965:13: error: conflicting types for 'debugging2'; have 'void(unsigned int)' 1965 | static void debugging2 ( unsigned int ctg ) | ^~~~~~~~~~ orderContig.c:86:13: note: previous declaration of 'debugging2' with type 'void(void)' 86 | static void debugging2(); | ^~~~~~~~~~ Error in command: gcc -c -O3 -fomit-frame-pointer -w -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapdenovo2-242+dfsg/standardPregraph=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DBDATE="Aug 11 2024" -DBTIME="17:08:09" -DMER63 -m64 -Iinc -I/usr/include/samtools orderContig.c Compiling output_contig.c... Compiling output_pregraph.c... Compiling output_scaffold.c... Compiling pregraph.c... Compiling prlHashCtg.c... Compiling prlHashReads.c... Compiling prlRead2Ctg.c... Compiling prlRead2path.c... Compiling prlReadFillGap.c... Compiling read2scaf.c... Compiling readInterval.c... Compiling stack.c... Compiling readseq1by1.c... Compiling scaffold.c... Compiling searchPath.c... Compiling seq.c... Compiling splitReps.c... Compiling cutTip_graph2.c... Compiling linearEdge.c... Compiling kmerhash.c... Compiling read2edge.c... Compiling iterate.c... SOAPdenovo-63mer objects generated. /usr/bin/ld: standardPregraph/scaffold.o: in function `call_scaffold': ././scaffold.c:71:(.text+0x7e8): undefined reference to `checkFiles4Scaff' /usr/bin/ld: ././scaffold.c:93:(.text+0x85f): undefined reference to `ScafStat' /usr/bin/ld: ././scaffold.c:81:(.text+0x970): undefined reference to `PE2Links' /usr/bin/ld: ././scaffold.c:86:(.text+0x9ce): undefined reference to `Links2Scaf' /usr/bin/ld: ././scaffold.c:89:(.text+0xa0c): undefined reference to `scaffolding' collect2: error: ld returned 1 exit status make[1]: *** [Makefile:62: SOAPdenovo-63mer] Error 1 dh_auto_build: error: make -j1 "INSTALL=install --strip-program=true" returned exit code 2 make: *** [debian/rules:14: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/1627924 and its subdirectories soapdenovo2 failed to build from source. removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/soapdenovo2_242+dfsg-4.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/soapdenovo2_242+dfsg-4.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/soapdenovo2_242+dfsg-4.build1.log.gz' Sun Sep 14 12:55:34 UTC 2025 W: No second build log, what happened? Compressing the 1st log... b1/build.log: 77.8% -- replaced with stdout INSERT 0 1 INSERT 0 1 DELETE 1 [2025-09-14 12:55:34] INFO: Starting at 2025-09-14 12:55:34.626264 [2025-09-14 12:55:34] INFO: Generating the pages of 1 package(s) [2025-09-14 12:55:34] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/soapdenovo2 didn't produce a buildlog, even though it has been built. [2025-09-14 12:55:34] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/soapdenovo2_242+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/soapdenovo2_242+dfsg-4.diff.gz is missing [2025-09-14 12:55:34] CRITICAL: https://tests.reproducible-builds.org/debian/forky/arm64/soapdenovo2 didn't produce a buildlog, even though it has been built. [2025-09-14 12:55:34] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/soapdenovo2_242+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/soapdenovo2_242+dfsg-4.diff.gz is missing [2025-09-14 12:55:34] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/arm64/soapdenovo2_242+dfsg-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/arm64/soapdenovo2_242+dfsg-3.diff.gz is missing [2025-09-14 12:55:34] INFO: Finished at 2025-09-14 12:55:34.886161, took: 0:00:00.259900 Sun Sep 14 12:55:34 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/soapdenovo2.html Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/soapdenovo2_242+dfsg-4.rbuild.log: 74.5% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/soapdenovo2_242+dfsg-4.rbuild.log.gz [2025-09-14 12:55:35] INFO: Starting at 2025-09-14 12:55:35.190401 [2025-09-14 12:55:35] INFO: Generating the pages of 1 package(s) [2025-09-14 12:55:35] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/soapdenovo2_242+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/soapdenovo2_242+dfsg-4.diff.gz is missing [2025-09-14 12:55:35] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/soapdenovo2_242+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/soapdenovo2_242+dfsg-4.diff.gz is missing [2025-09-14 12:55:35] CRITICAL: https://tests.reproducible-builds.org/debian/forky/arm64/soapdenovo2 didn't produce a buildlog, even though it has been built. [2025-09-14 12:55:35] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/soapdenovo2_242+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/soapdenovo2_242+dfsg-4.diff.gz is missing [2025-09-14 12:55:35] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/arm64/soapdenovo2_242+dfsg-3.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/arm64/soapdenovo2_242+dfsg-3.diff.gz is missing [2025-09-14 12:55:35] INFO: Finished at 2025-09-14 12:55:35.449795, took: 0:00:00.259396 All cleanup done. Sun Sep 14 12:55:35 UTC 2025 - total duration: 0h 1m 42s. Sun Sep 14 12:55:35 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-7EoUhXsB, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 1min 43.399s CPU time consumed: 2.414s Memory peak: 40.5M (swap: 0B)