Mon Oct 27 10:17:10 UTC 2025 I: starting to build soapdenovo2/forky/amd64 on jenkins on '2025-10-27 10:16' Mon Oct 27 10:17:10 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_34/87744/console.log Mon Oct 27 10:17:10 UTC 2025 I: Downloading source for forky/soapdenovo2=242+dfsg-5 --2025-10-27 10:17:10-- http://deb.debian.org/debian/pool/main/s/soapdenovo2/soapdenovo2_242%2bdfsg-5.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-5.dsc’ 0K .. 100% 272M=0s 2025-10-27 10:17:10 (272 MB/s) - ‘soapdenovo2_242+dfsg-5.dsc’ saved [2283/2283] Mon Oct 27 10:17:10 UTC 2025 I: soapdenovo2_242+dfsg-5.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-5 Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou , Andreas Tille Homepage: http://soap.genomics.org.cn/soapdenovo.html Standards-Version: 4.7.2 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 09e73b0db7ccec22a1ace65b2b2ebb588b5d88d5 490384 soapdenovo2_242+dfsg-5.debian.tar.xz Checksums-Sha256: ff787d4227c9862347663f7426c71b026559720c501033c96190f8aad26549a1 251060 soapdenovo2_242+dfsg.orig.tar.xz 9527bbf9471bb5249fdbcb899e7a61e8c57c903f3075512da0b8e22afbf0aa86 490384 soapdenovo2_242+dfsg-5.debian.tar.xz Files: d09be53b4104c67050aa3757c49b19d1 251060 soapdenovo2_242+dfsg.orig.tar.xz e27036d80543de3c7dd051c29938293c 490384 soapdenovo2_242+dfsg-5.debian.tar.xz Dgit: 338707029a08f9b87be15cd8b7b7972c735e5d42 debian archive/debian/242+dfsg-5 https://git.dgit.debian.org/soapdenovo2 -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmj7vdwUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdp/0BAAylOypLd7w1PkeE7nUSSKNeVU7gH7 HCIGg2VJTGsvOdwAYfqdq1ABIgvhDr0yoNUijiD5LM3zUEuZBCfRe0zSpsN6MMm/ ASB9h4I9f0FWF+Z49+4iUpKvrnndE5BBQSkE0RBwcW2bJdhTL/rGBw8MjstjCN2V sCHGCsNVdfuRi5BtXQOgRemSdoLZCBbvtw5L9HTmqtB6fMzSWlqCcbyhO603bcQT AWfBI1Ob7ycIt9qVQgY3dzfQjmr1xIdExSOaD3LELBeCDxggyeRVRVDXdmI90m6+ dLtAZaV116i616rG1bUJUrHUItDxP8O52F+9ehmefXm7ECF/t8RZOnqZ88J4p7rc N+es2gNIvgE+L+6Xwh/dQiOiVXfbFYIPRLr/GsBPES2BybS1Q76YszmyX3UL+X+B a7dZUimEgiKepmw59Gp999o38HEpZBqjbOivWGJzl2oalJodDg91fVsxkvkjOHD2 ua7asKU0+c3PtZQXIxFD9VSkzEwefPCaul3ivvuOiIegnaE4uOnvaggjBcHuY/Vj /r+3taVwyXqFpMUkW24Ra1QmKGBQ6jyfo+kOY9E51oJEopszxQ4hOwqvC/vzShXe F1wohvb1KLtR0+EleU9/osL2+Vst43aThTy4vpcDwdPaBpwh77Tev8OrEmGC1u9N UTAnKytRUMtsOZ4= =+2k2 -----END PGP SIGNATURE----- Mon Oct 27 10:17:10 UTC 2025 I: Checking whether the package is not for us Mon Oct 27 10:17:10 UTC 2025 I: Starting 1st build on remote node infom02-amd64.debian.net. Mon Oct 27 10:17:10 UTC 2025 I: Preparing to do remote build '1' on infom02-amd64.debian.net. Mon Oct 27 10:19:33 UTC 2025 I: Deleting $TMPDIR on infom02-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Nov 29 04:40:12 -12 2026 I: pbuilder-time-stamp: 1795970412 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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-5.dsc] I: copying [./soapdenovo2_242+dfsg.orig.tar.xz] I: copying [./soapdenovo2_242+dfsg-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./soapdenovo2_242+dfsg-5.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-5.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 dpkg-source: info: applying gcc-15.patch dpkg-source: info: applying fix-deps.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2724712/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=16 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='5c7993a41b5a4d1580bc331945fb231e' 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='2724712' 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.B9V81bgT/pbuilderrc_L7Ue --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.B9V81bgT/b1 --logfile b1/build.log soapdenovo2_242+dfsg-5.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' I: uname -a Linux infom02-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) 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/2724712/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 ... 19900 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 12.4 MB of archives. After unpacking 44.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.2-1 [95.2 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-2 [325 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 automake all 1:1.18.1-2 [877 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.28 [92.4 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 22 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.6+dfsg-0.1 [651 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 debhelper all 13.28 [941 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 libaio1t64 amd64 0.3.113-8+b1 [14.9 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 libaio-dev amd64 0.3.113-8+b1 [31.4 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 libbam-dev amd64 0.1.19+dfsg-6 [118 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 rename all 2.02-1 [21.8 kB] Fetched 12.4 MB in 0s (53.6 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 ... 19900 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_2.41.2-1_amd64.deb ... Unpacking bsdextrautils (2.41.2-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.20-2_amd64.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_2.5.4-5_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_2.14.6+dfsg-0.1_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.6+dfsg-0.1) ... 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_13.28_all.deb ... Unpacking debhelper (13.28) ... 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 (2.41.2-1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.6+dfsg-0.1) ... Setting up libdebhelper-perl (13.28) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-2) ... 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 (1:1.18.1-2) ... 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 (2.5.4-5) ... 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 (13.28) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.37.1.2-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 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-5_source.changes dpkg-buildpackage: info: source package soapdenovo2 dpkg-buildpackage: info: source version 242+dfsg-5 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. SOAPdenovo-63mer 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. 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... 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. pregraph_sparse_127mer.v1.0.3 cleaning done. SOAPdenovo-127mer 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_127mer.v1.0.3 objects generated. 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... 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-127mer objects generated. Compiling searchPath.c... Compiling scaffold.c... Compiling check.c... Compiling seq.c... Compiling bundle.c... Compiling potential.c... Compiling loadGraph.c... Compiling mem_manager.c... Compiling attachPEinfo.c... Compiling newhash.c... Compiling output_scaffold.c... Compiling orderContig.c... Compiling connect.c... Compiling hashFunction.c... Compiling readseq1by1.c... Compiling fib.c... Compiling fibHeap.c... Compiling stack.c... Compiling kmer.c... Compiling prepare.c... Compiling prlHashCtg.c... Compiling prlRead2Ctg.c... Compiling map.c... Compiling localAsm.c... Compiling lib.c... Compiling darray.c... Compiling prlReadFillGap.c... Compiling read2scaf.c... Compiling main.c... Making SOAPdenovo-fusion... SOAPdenovo-fusion compilation done. dh_auto_test -O--no-parallel create-stamp debian/debhelper-build-stamp dh_testroot -O--no-parallel dh_prep -O--no-parallel dh_auto_install --destdir=debian/soapdenovo2/ -O--no-parallel debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/soapdenovo2-242+dfsg' dh_install cd debian/soapdenovo2/usr/bin/;rename 's/SOAPdenovo/soapdenovo2/' SOAP* make[1]: Leaving directory '/build/reproducible-path/soapdenovo2-242+dfsg' dh_installdocs -O--no-parallel dh_installchangelogs -O--no-parallel dh_installman -O--no-parallel dh_installsystemduser -O--no-parallel dh_perl -O--no-parallel dh_link -O--no-parallel dh_strip_nondeterminism -O--no-parallel dh_compress -O--no-parallel dh_fixperms -O--no-parallel dh_missing -O--no-parallel dh_dwz -a -O--no-parallel dh_strip -a -O--no-parallel dh_makeshlibs -a -O--no-parallel dh_shlibdeps -a -O--no-parallel dh_installdeb -O--no-parallel dh_gencontrol -O--no-parallel dh_md5sums -O--no-parallel dh_builddeb -O--no-parallel dpkg-deb: building package 'soapdenovo2' in '../soapdenovo2_242+dfsg-5_amd64.deb'. dpkg-deb: building package 'soapdenovo2-dbgsym' in '../soapdenovo2-dbgsym_242+dfsg-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../soapdenovo2_242+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../soapdenovo2_242+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2724712 and its subdirectories I: Current time: Sun Nov 29 04:42:33 -12 2026 I: pbuilder-time-stamp: 1795970553 Mon Oct 27 10:19:34 UTC 2025 I: 1st build successful. Starting 2nd build on remote node infom01-amd64.debian.net. Mon Oct 27 10:19:34 UTC 2025 I: Preparing to do remote build '2' on infom01-amd64.debian.net. Mon Oct 27 10:22:56 UTC 2025 I: Deleting $TMPDIR on infom01-amd64.debian.net. Mon Oct 27 10:22:56 UTC 2025 I: soapdenovo2_242+dfsg-5_amd64.changes: Format: 1.8 Date: Fri, 24 Oct 2025 19:53:20 +0200 Source: soapdenovo2 Binary: soapdenovo2 soapdenovo2-dbgsym Architecture: amd64 Version: 242+dfsg-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: soapdenovo2 - short-read assembly method to build de novo draft assembly Closes: 1097909 1105578 Changes: soapdenovo2 (242+dfsg-5) unstable; urgency=medium . * Team upload. * gcc-15.patch: new: fix build failure with gcc-15. (Closes: #1097909) * fix-deps.patch: new: stabilise make rules ordering. (Closes: #1105578) * reproducible patch: normalise Last-Update timestamp. * d/watch: bump to watch file version 5. * d/u/metadata: locate upstream repository. * d/control: drop redundant Rules-Requires-Root: no. * d/control: declare compliance to standards version 4.7.2. Checksums-Sha1: e50d00e3d9e78e7e63688728eed93b6c790b3e7c 1427312 soapdenovo2-dbgsym_242+dfsg-5_amd64.deb 3c169dea6c849203e65d7c727fe5dc183d6bec5e 5039 soapdenovo2_242+dfsg-5_amd64.buildinfo 96f967f38e1b40b2473474302ff9e40f6b53c83e 927440 soapdenovo2_242+dfsg-5_amd64.deb Checksums-Sha256: ca671746683abec7a14e8659c5a151ba9642844848226dd5259875a0b5ad38ac 1427312 soapdenovo2-dbgsym_242+dfsg-5_amd64.deb 0bb5588cccecaee62e096327b1013fe6f3bfa95e04d5621450c7b744191e364f 5039 soapdenovo2_242+dfsg-5_amd64.buildinfo b071428cdfb8d9b4b9664bf861c138eb9440501b1928a6cb08f880104689d794 927440 soapdenovo2_242+dfsg-5_amd64.deb Files: 1ea9cd4987f3b66e4ccc121948a84346 1427312 debug optional soapdenovo2-dbgsym_242+dfsg-5_amd64.deb e30309febb67f70e450af349563f5629 5039 science optional soapdenovo2_242+dfsg-5_amd64.buildinfo 927717e196d33c683b12194492bb2d4c 927440 science optional soapdenovo2_242+dfsg-5_amd64.deb Mon Oct 27 10:22:57 UTC 2025 I: diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_34-87744.service; invocation ID: c3a5deb28d0349878da5a1eca1020a74 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.B9V81bgT/soapdenovo2_242+dfsg-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.B9V81bgT/soapdenovo2_242+dfsg-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.B9V81bgT/soapdenovo2_242+dfsg-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.B9V81bgT/b1/soapdenovo2_242+dfsg-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.B9V81bgT/b2/soapdenovo2_242+dfsg-5_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call 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: 196ms CPU time consumed: 171ms Memory peak: 18M (swap: 0B) Mon Oct 27 10:22:58 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Mon Oct 27 10:22:58 UTC 2025 I: soapdenovo2 from forky built successfully and reproducibly on amd64. Mon Oct 27 10:22:58 UTC 2025 I: Removing signed soapdenovo2_242+dfsg-5_amd64.buildinfo.asc files: removed './b1/soapdenovo2_242+dfsg-5_amd64.buildinfo.asc' removed './b2/soapdenovo2_242+dfsg-5_amd64.buildinfo.asc'