Sat Nov 23 12:39:15 UTC 2024 I: starting to build soapdenovo2/unstable/amd64 on jenkins on '2024-11-23 12:39' Sat Nov 23 12:39:15 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_11/36567/console.log Sat Nov 23 12:39:15 UTC 2024 I: Downloading source for unstable/soapdenovo2=242+dfsg-4 --2024-11-23 12:39:15-- 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% 252M=0s 2024-11-23 12:39:15 (252 MB/s) - ‘soapdenovo2_242+dfsg-4.dsc’ saved [2283/2283] Sat Nov 23 12:39:15 UTC 2024 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----- Sat Nov 23 12:39:15 UTC 2024 I: Checking whether the package is not for us Sat Nov 23 12:39:15 UTC 2024 I: Starting 1st build on remote node ionos1-amd64.debian.net. Sat Nov 23 12:39:15 UTC 2024 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Sat Nov 23 12:42:53 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Nov 23 00:39:18 -12 2024 I: pbuilder-time-stamp: 1732365558 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 gpgv: Signature made Sun Aug 11 17:12:32 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./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/1139673/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=20 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='88a1686448d54553ada6280f7224d428' 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='1139673' 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.DP3zA5dX/pbuilderrc_GGYj --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.DP3zA5dX/b1 --logfile b1/build.log soapdenovo2_242+dfsg-4.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1139673/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 ... 19966 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} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libxml2{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 20.9 MB of archives. After unpacking 77.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 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 13.20 [915 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 20.9 MB in 1s (34.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19966 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_amd64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../23-libicu72_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... 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 libicu72:amd64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... 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 (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up libaio1t64:amd64 (0.3.113-8+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up libaio-dev:amd64 (0.3.113-8+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libbam-dev (0.1.19+dfsg-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/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 make[1]: Entering directory '/build/reproducible-path/soapdenovo2-242+dfsg' pregraph_sparse_63mer.v1.0.3 cleaning done. SOAPdenovo-63mer cleaning done. SOAPdenovo-fusion cleaning done. make[1]: Leaving directory '/build/reproducible-path/soapdenovo2-242+dfsg' 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" make[1]: Entering directory '/build/reproducible-path/soapdenovo2-242+dfsg' 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... 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. 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. SOAPdenovo-127mer 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... 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. make[1]: Leaving directory '/build/reproducible-path/soapdenovo2-242+dfsg' 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-4_amd64.deb'. dpkg-deb: building package 'soapdenovo2-dbgsym' in '../soapdenovo2-dbgsym_242+dfsg-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../soapdenovo2_242+dfsg-4_amd64.buildinfo dpkg-genchanges --build=binary -O../soapdenovo2_242+dfsg-4_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/1139673 and its subdirectories I: Current time: Sat Nov 23 00:42:53 -12 2024 I: pbuilder-time-stamp: 1732365773 Sat Nov 23 12:42:54 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Sat Nov 23 12:42:54 UTC 2024 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Sat Nov 23 12:44:49 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Sat Nov 23 12:44:49 UTC 2024 I: soapdenovo2_242+dfsg-4_amd64.changes: Format: 1.8 Date: Sun, 11 Aug 2024 19:08:09 +0200 Source: soapdenovo2 Binary: soapdenovo2 soapdenovo2-dbgsym Architecture: amd64 Version: 242+dfsg-4 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: 1075524 Changes: soapdenovo2 (242+dfsg-4) unstable; urgency=medium . * Team upload. * gcc-14.patch: new: fix a lot of issues caught by gcc 14. (Closes: #1075524) * d/control: declare compliance to standards version 4.7.0. * d/salsa-ci.yml: skip test build on i386. This architecture is not declared supported by soapdenovo2. Checksums-Sha1: e254933f358f988abbffb07d556e45dd83683441 1430044 soapdenovo2-dbgsym_242+dfsg-4_amd64.deb 15342e57cb4c871ef35ae86581944c412ef45c2e 5165 soapdenovo2_242+dfsg-4_amd64.buildinfo 39580e49908a9f208271377274d64d88bf55c5fe 926168 soapdenovo2_242+dfsg-4_amd64.deb Checksums-Sha256: 6ca5bb4541354cb2259243cfa9e6f40b0a68d8d9c7ae277997c700d7aee3c0d7 1430044 soapdenovo2-dbgsym_242+dfsg-4_amd64.deb aa37f980cedf6060e2a0df33553e92037b9e52ada7813675efcd5d045c20a62d 5165 soapdenovo2_242+dfsg-4_amd64.buildinfo ae515947926ebe0e9d6232bd67024023234574f484eb6715e28f03f793211fb7 926168 soapdenovo2_242+dfsg-4_amd64.deb Files: 01af263b0a267905e81f723ed1055b89 1430044 debug optional soapdenovo2-dbgsym_242+dfsg-4_amd64.deb a55054b49450915c6468e6769291e23b 5165 science optional soapdenovo2_242+dfsg-4_amd64.buildinfo e66835002d0b8ccfd908ccecc00ce96c 926168 science optional soapdenovo2_242+dfsg-4_amd64.deb Sat Nov 23 12:44:50 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_11-36567.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.DP3zA5dX/soapdenovo2_242+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.DP3zA5dX/soapdenovo2_242+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.DP3zA5dX/soapdenovo2_242+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.DP3zA5dX/b1/soapdenovo2_242+dfsg-4_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.DP3zA5dX/b2/soapdenovo2_242+dfsg-4_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.363s) 0.363s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.036s) 0.036s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 699ms CPU time consumed: 698ms Sat Nov 23 12:44:51 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Sat Nov 23 12:44:51 UTC 2024 I: soapdenovo2 from unstable built successfully and reproducibly on amd64. Sat Nov 23 12:44:53 UTC 2024 I: Submitting .buildinfo files to external archives: Sat Nov 23 12:44:53 UTC 2024 I: Submitting 8.0K b1/soapdenovo2_242+dfsg-4_amd64.buildinfo.asc Sat Nov 23 12:44:53 UTC 2024 I: Submitting 8.0K b2/soapdenovo2_242+dfsg-4_amd64.buildinfo.asc Sat Nov 23 12:44:54 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Nov 23 12:44:54 UTC 2024 I: Done submitting .buildinfo files. Sat Nov 23 12:44:54 UTC 2024 I: Removing signed soapdenovo2_242+dfsg-4_amd64.buildinfo.asc files: removed './b1/soapdenovo2_242+dfsg-4_amd64.buildinfo.asc' removed './b2/soapdenovo2_242+dfsg-4_amd64.buildinfo.asc'