Tue May 7 10:46:38 UTC 2024 I: starting to build sspace/unstable/amd64 on jenkins on '2024-05-07 10:46' Tue May 7 10:46:38 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_36/10764/console.log Tue May 7 10:46:38 UTC 2024 I: Downloading source for unstable/sspace=2.1.1+dfsg-7 --2024-05-07 10:46:39-- http://deb.debian.org/debian/pool/main/s/sspace/sspace_2.1.1%2bdfsg-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2037 (2.0K) [text/prs.lines.tag] Saving to: ‘sspace_2.1.1+dfsg-7.dsc’ 0K . 100% 292M=0s 2024-05-07 10:46:39 (292 MB/s) - ‘sspace_2.1.1+dfsg-7.dsc’ saved [2037/2037] Tue May 7 10:46:39 UTC 2024 I: sspace_2.1.1+dfsg-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: sspace Binary: sspace Architecture: all Version: 2.1.1+dfsg-7 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Sascha Steinbiss Homepage: https://github.com/nsoranzo/sspace_basic Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/sspace Vcs-Git: https://salsa.debian.org/med-team/sspace.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), recode, python3, asciidoctor, bowtie Package-List: sspace deb science optional arch=all Checksums-Sha1: 0911ac377d0cdfa0611cd27df211a850cddf648a 1234924 sspace_2.1.1+dfsg.orig.tar.xz 133e45da64647d8d13e45d8445fc0a942e5e4876 501040 sspace_2.1.1+dfsg-7.debian.tar.xz Checksums-Sha256: 5bbb1cfd1e68af66fd31ab3d9720c450a9acf9a2a4bf9bde7e8e54a859b04aa1 1234924 sspace_2.1.1+dfsg.orig.tar.xz 8eb1eab0c3e3293c0817c9aa34fc038ac5daa60ec0452a79b219a55e2a42c8ab 501040 sspace_2.1.1+dfsg-7.debian.tar.xz Files: 2dc72080013bc674ff8a1fb5190381f2 1234924 sspace_2.1.1+dfsg.orig.tar.xz 08838d5d2dfaf699793a4007a7955722 501040 sspace_2.1.1+dfsg-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAmNWkQsACgkQ6NN64vCf SHLuwA//VZYFlKxAh4pVodWLzPGtK0GCAlZ3T9Yj5IFSLId3uzcO+5u8nryUu0bF j+PqOczQFWZgLW8ZuH4vs7IIAb+vJNeSle0EdU9CrHFp2fdRQhB2KH2ePGAeA3xn eUs6DE5KwuEHYTqXQptqMX3dWDqxCe3joNsdLEDVYkACuCK9vv5H50lGk486D7rj iPUVzy/wq9wmL9Hw3V8ewV2S+s/kl/SX6eTZtaFGJCWtJgQW9BZGXkj27PI74+Pb DLh/OaynDI59Pm4nvLGwSYyyGPivljb+rHmYfLPkGcYEA38+CI4QmYp5jgLRTp67 +peTpUrGmMsEEQCiVgCT0oK1ARcq2qpMtIkudzQezlUTHWLWjBPIb+qZvdd3gfIi P+VWJREoNBtIoIOzb/8hnAP3g5B+IRQYnY+oZFFKhl6GfYbu7RuQWU/EP108pfb0 s8Djo1vNJ2YHhpi3WYGBQAWef7mDWhcKNwjzAK6N2bQqL4Cl4lKY+PAnP+/8tCg7 LHy1Hq4x+He+4vw4yQH/Af4s1IfnwQlgFrK/9BUXEk7ylvA0eEbvL2K19l/a0vmw JqXFjVh+8c64ZP6bsZQSfwC/kjcCvk2L4JFNhTYfI/rRwzuDj3xiq/emtl+7g8hc iF6DBMIQRd2wpgW26ESmC0bh5HgqmHf6W/0nzWOVRtKFSbeR0EU= =8htq -----END PGP SIGNATURE----- Tue May 7 10:46:39 UTC 2024 I: Checking whether the package is not for us Tue May 7 10:46:39 UTC 2024 I: Starting 1st build on remote node infom02-amd64.debian.net. Tue May 7 10:46:39 UTC 2024 I: Preparing to do remote build '1' on infom02-amd64.debian.net. Tue May 7 10:48:03 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jun 9 05:09:41 -12 2025 I: pbuilder-time-stamp: 1749488981 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 [sspace_2.1.1+dfsg-7.dsc] I: copying [./sspace_2.1.1+dfsg.orig.tar.xz] I: copying [./sspace_2.1.1+dfsg-7.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Oct 24 13:20:11 2022 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./sspace_2.1.1+dfsg-7.dsc: no acceptable signature found dpkg-source: info: extracting sspace in sspace-2.1.1+dfsg dpkg-source: info: unpacking sspace_2.1.1+dfsg.orig.tar.xz dpkg-source: info: unpacking sspace_2.1.1+dfsg-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying shebangs.patch dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1573247/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=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='a5d521f916d14cb7803aaffe144aab16' 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='1573247' 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.niWR3PKU/pbuilderrc_NB66 --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.niWR3PKU/b1 --logfile b1/build.log sspace_2.1.1+dfsg-7.dsc' SUDO_GID='109' 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 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 8 14:05 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1573247/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), recode, python3, asciidoctor, bowtie dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19699 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 recode; however: Package recode is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on asciidoctor; however: Package asciidoctor is not installed. pbuilder-satisfydepends-dummy depends on bowtie; however: Package bowtie 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: asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bowtie{a} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libdebhelper-perl{a} libedit2{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librecode0{a} libruby{a} libruby3.1t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} rake{a} readline-common{a} recode{a} ruby{a} ruby-asciidoctor{a} ruby-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-lato libarchive-cpio-perl libgpm2 libjs-jquery libltdl-dev libmail-sendmail-perl lynx wget zip 0 packages upgraded, 65 newly installed, 0 to remove and 0 not upgraded. Need to get 35.9 MB of archives. After unpacking 141 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 rubygems-integration all 1.18 [6704 B] Get: 27 http://deb.debian.org/debian unstable/main amd64 rake all 13.2.1-1 [65.2 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 ruby-sdbm amd64 1.0.0-5+b4 [15.4 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.4+20240414-1 [104 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libruby3.1t64 amd64 3.1.2-8.3 [5399 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 ruby3.1 amd64 3.1.2-8.3 [664 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libruby amd64 1:3.1+nmu1 [4664 B] Get: 39 http://deb.debian.org/debian unstable/main amd64 ruby-rubygems all 3.4.20-1 [309 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 ruby amd64 1:3.1+nmu1 [5584 B] Get: 41 http://deb.debian.org/debian unstable/main amd64 ruby-asciidoctor all 2.0.20-1 [212 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 asciidoctor all 2.0.20-1 [87.7 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 bowtie amd64 1.3.1-3 [1627 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 56 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 librecode0 amd64 3.6-26 [530 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 recode amd64 3.6-26 [186 kB] Fetched 35.9 MB in 2s (21.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (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 ... 19699 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (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 ... 20015 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (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 ... 21007 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package sensible-utils. 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Universal Time is now: Mon Jun 9 17:10:44 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up recode (3.6-26) ... Setting up libncurses6:amd64 (6.4+20240414-1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up ruby-webrick (1.8.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up readline-common (8.2-4) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... 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 (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libedit2:amd64 (3.1-20230828-1+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libreadline8t64:amd64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up bowtie (1.3.1-3) ... Setting up rake (13.2.1-1) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b4) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up libruby3.1t64:amd64 (3.1.2-8.3) ... Setting up ruby3.1 (3.1.2-8.3) ... Setting up libruby:amd64 (1:3.1+nmu1) ... Setting up ruby (1:3.1+nmu1) ... Setting up ruby-asciidoctor (2.0.20-1) ... Setting up asciidoctor (2.0.20-1) ... Processing triggers for libc-bin (2.38-8) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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/sspace-2.1.1+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 > ../sspace_2.1.1+dfsg-7_source.changes dpkg-buildpackage: info: source package sspace dpkg-buildpackage: info: source version 2.1.1+dfsg-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/sspace-2.1.1+dfsg' dh_auto_clean rm -f debian/sspace.1 make[1]: Leaving directory '/build/reproducible-path/sspace-2.1.1+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/sspace-2.1.1+dfsg' debian/tests/example-tests /build/reproducible-path/sspace-2.1.1+dfsg/SSPACE_Basic.pl Your inserted inputs on [SSPACE_Basic v2.1] at Mon Jun 9 05:10:54 2025: Required inputs: -l = libraries.txt -s = contigs_abyss.fasta -b = standard_output Optional inputs: -x = 0 -z = 0 -k = 5 -a = 0.7 -n = 15 -T = 1 -p = 0 =>Mon Jun 9 05:10:54 2025: Reading, filtering and converting input sequences of library file initiated Reading read-pairs lib1.1 @ 0 ------------------------------------------------------------ =>Mon Jun 9 05:10:54 2025: Storing contigs to format for scaffolding 100 200 300 400 500 LIBRARY lib1 ------------------------------------------------------------ =>Mon Jun 9 05:10:54 2025: Reading contig file =>Mon Jun 9 05:10:54 2025: Building Bowtie index for contigs =>Mon Jun 9 05:10:54 2025: Mapping reads to contigs. Reading bowtie output and pairing contigs Setting the index via positional argument will be deprecated in a future release. Please use -x option instead. # reads processed: 19924 # reads with at least one alignment: 1879 (9.43%) # reads that failed to align: 18045 (90.57%) Reported 1879 alignments =>Mon Jun 9 05:10:54 2025: Building scaffolds file 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 =>Mon Jun 9 05:10:54 2025: Merging contigs and creating FASTA file of scaffolds 100 200 300 400 500 ------------------------------------------------------------ =>Mon Jun 9 05:10:54 2025: Creating summary file ************************************************** Process run succesfully on Mon Jun 9 05:10:54 2025 in 0 minutes and 0 seconds make[1]: Leaving directory '/build/reproducible-path/sspace-2.1.1+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/sspace/ debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/sspace-2.1.1+dfsg' dh_install find debian -name "*.pl" -exec recode ibmpc.. \{\} \; recode: debian/sspace/usr/share/sspace/tools/estimate_insert_size.pl failed: Ambiguous output in step `CR-LF..data' recode: debian/sspace/usr/share/sspace/tools/sam_bam2tab.pl failed: Ambiguous output in step `CR-LF..data' recode: debian/sspace/usr/share/sspace/tools/fq_all2std.pl failed: Ambiguous output in step `CR-LF..data' recode: debian/sspace/usr/share/sspace/tools/qseq2fasta.pl failed: Ambiguous output in step `CR-LF..data' recode: debian/sspace/usr/share/sspace/tools/qseq2fastq.pl failed: Ambiguous output in step `CR-LF..data' recode: debian/sspace/usr/share/sspace/SSPACE_Basic.pl failed: Ambiguous output in step `CR-LF..data' recode: debian/sspace/usr/share/sspace/bin/PairingAndScaffolding.pl failed: Ambiguous output in step `CR-LF..data' recode: debian/sspace/usr/share/sspace/bin/readLibFiles.pl failed: Ambiguous output in step `CR-LF..data' recode: debian/sspace/usr/share/sspace/bin/ExtendOrFormatContigs.pl failed: Ambiguous output in step `CR-LF..data' recode: debian/sspace/usr/share/sspace/SSPACE_Basic_v2.0.pl failed: Ambiguous output in step `CR-LF..data' chmod -x debian/sspace/usr/share/sspace/tools/TRIMMING_PAIRED_READS.README \ debian/sspace/usr/share/sspace/tools/TQS.readme \ debian/sspace/usr/share/sspace/dotlib/DotLib.pm for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/reproducible-path/sspace-2.1.1+dfsg' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/sspace-2.1.1+dfsg' dh_installexamples chmod -x debian/sspace/usr/share/doc/sspace/examples/libraries.txt make[1]: Leaving directory '/build/reproducible-path/sspace-2.1.1+dfsg' debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/sspace-2.1.1+dfsg' asciidoctor -a docdate='' -b manpage debian/sspace.1.adoc dh_installman make[1]: Leaving directory '/build/reproducible-path/sspace-2.1.1+dfsg' dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/sspace-2.1.1+dfsg' dh_fixperms find debian -name contigs_abyss.fasta -exec chmod -x \{\} \; make[1]: Leaving directory '/build/reproducible-path/sspace-2.1.1+dfsg' dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'sspace' in '../sspace_2.1.1+dfsg-7_all.deb'. dpkg-genbuildinfo --build=binary -O../sspace_2.1.1+dfsg-7_amd64.buildinfo dpkg-genchanges --build=binary -O../sspace_2.1.1+dfsg-7_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/1573247 and its subdirectories I: Current time: Mon Jun 9 05:11:02 -12 2025 I: pbuilder-time-stamp: 1749489062 Tue May 7 10:48:03 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom01-amd64.debian.net. Tue May 7 10:48:03 UTC 2024 I: Preparing to do remote build '2' on infom01-amd64.debian.net. Tue May 7 10:49:36 UTC 2024 I: Deleting $TMPDIR on infom01-amd64.debian.net. Tue May 7 10:49:37 UTC 2024 I: sspace_2.1.1+dfsg-7_amd64.changes: Format: 1.8 Date: Mon, 24 Oct 2022 15:08:39 +0200 Source: sspace Binary: sspace Architecture: all Version: 2.1.1+dfsg-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: sspace - scaffolding pre-assembled contigs after extension Changes: sspace (2.1.1+dfsg-7) unstable; urgency=medium . * Bump Standards-Version. * Update email and dates in d/copyright. * Fix watchfile. Checksums-Sha1: be306a281a977fad2defba84212f7b4cb33998d0 1237164 sspace_2.1.1+dfsg-7_all.deb c174f9c0e83b45cf54e438b6df19821fbef5f9e9 5901 sspace_2.1.1+dfsg-7_amd64.buildinfo Checksums-Sha256: 67099611dc77602a5bc8e96b7b214e3ea38ef49e67608efe273d85cf9e7ef6ee 1237164 sspace_2.1.1+dfsg-7_all.deb 7eefd566dfd2284288fd5af01b259924db096a726cef68a4656ec44a6105f73e 5901 sspace_2.1.1+dfsg-7_amd64.buildinfo Files: 3e894e64220dbd274ac802cd04334944 1237164 science optional sspace_2.1.1+dfsg-7_all.deb 3b92156cc8432785548b8f4b7507d436 5901 science optional sspace_2.1.1+dfsg-7_amd64.buildinfo Tue May 7 10:49:38 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_36-10764.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.niWR3PKU/sspace_2.1.1+dfsg-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.niWR3PKU/sspace_2.1.1+dfsg-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.niWR3PKU/sspace_2.1.1+dfsg-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.niWR3PKU/b1/sspace_2.1.1+dfsg-7_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.niWR3PKU/b2/sspace_2.1.1+dfsg-7_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: 0.398s) 0.398s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.030s) 0.030s 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: 741ms CPU time consumed: 736ms Tue May 7 10:49:39 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Tue May 7 10:49:39 UTC 2024 I: sspace from unstable built successfully and reproducibly on amd64. Tue May 7 10:49:41 UTC 2024 I: Submitting .buildinfo files to external archives: Tue May 7 10:49:41 UTC 2024 I: Submitting 8.0K b1/sspace_2.1.1+dfsg-7_amd64.buildinfo.asc Tue May 7 10:49:43 UTC 2024 I: Submitting 8.0K b2/sspace_2.1.1+dfsg-7_amd64.buildinfo.asc Tue May 7 10:49:43 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue May 7 10:49:43 UTC 2024 I: Done submitting .buildinfo files. Tue May 7 10:49:43 UTC 2024 I: Removing signed sspace_2.1.1+dfsg-7_amd64.buildinfo.asc files: removed './b1/sspace_2.1.1+dfsg-7_amd64.buildinfo.asc' removed './b2/sspace_2.1.1+dfsg-7_amd64.buildinfo.asc'