Fri Aug 4 21:58:04 UTC 2023 I: starting to build sspace/bullseye/amd64 on jenkins on '2023-08-04 21:57' Fri Aug 4 21:58:04 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_27/4228/console.log Fri Aug 4 21:58:04 UTC 2023 I: Downloading source for bullseye/sspace=2.1.1+dfsg-5 --2023-08-04 21:58:04-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/sspace/sspace_2.1.1%2bdfsg-5.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1692 (1.7K) [text/prs.lines.tag] Saving to: ‘sspace_2.1.1+dfsg-5.dsc’ 0K . 100% 171M=0s 2023-08-04 21:58:04 (171 MB/s) - ‘sspace_2.1.1+dfsg-5.dsc’ saved [1692/1692] Fri Aug 4 21:58:04 UTC 2023 I: sspace_2.1.1+dfsg-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: sspace Binary: sspace Architecture: all Version: 2.1.1+dfsg-5 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Sascha Steinbiss Homepage: https://github.com/nsoranzo/sspace_basic Standards-Version: 4.4.1 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 (= 12), recode, python3, asciidoctor, bowtie Package-List: sspace deb science optional arch=all Checksums-Sha1: 0911ac377d0cdfa0611cd27df211a850cddf648a 1234924 sspace_2.1.1+dfsg.orig.tar.xz c31f0568773fe235792a83d298349830dabac48f 498272 sspace_2.1.1+dfsg-5.debian.tar.xz Checksums-Sha256: 5bbb1cfd1e68af66fd31ab3d9720c450a9acf9a2a4bf9bde7e8e54a859b04aa1 1234924 sspace_2.1.1+dfsg.orig.tar.xz 6ae57893e2c76a02ad0c1944a5d58a8fe87dcba1a783fb55845ad90a4bdd9b62 498272 sspace_2.1.1+dfsg-5.debian.tar.xz Files: 2dc72080013bc674ff8a1fb5190381f2 1234924 sspace_2.1.1+dfsg.orig.tar.xz 186069c1b6a8354ffa44be166a8114d2 498272 sspace_2.1.1+dfsg-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEEhFH5F4Fy5+Lcc/eVUfhKj+zKfgkFAl4Pj1kACgkQUfhKj+zK fgldaQgAolVyXUUeI5RF6OjS5JhzIJQMcvW4r41Z6LJj51BpIfwY+K94/fjjfNwe Oh1J+qXAIO6rhxpNVpzJkirOi6/vQQIiqrGqFp4H16brumvysF7DS9+8MLYoXCJO DN7VaoYWSB+7lr7PbG1A8bbeX9mgM55I5uxRuL64mawyYj1gLhzrUdy91pUbjdNf SAdub1fego/bo0Hzqavx0MVKDfQ9BqQr3s1PtYJ6Ouny2fDMvMVMfEoPUiXkYYXz E0GsyWn3Mgsh79T3GKLJm5pvaW0HXk6MS5vGoGMyRgFi07Hp3mcDsIcwbcKZbGtP d7IAPTXtwJRgxpwJiONBpUs1xzG1Ww== =E/Mb -----END PGP SIGNATURE----- Fri Aug 4 21:58:04 UTC 2023 I: Checking whether the package is not for us Fri Aug 4 21:58:04 UTC 2023 I: Starting 1st build on remote node ionos1-amd64.debian.net. Fri Aug 4 21:58:04 UTC 2023 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Fri Aug 4 21:59:01 UTC 2023 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Aug 4 09:58:07 -12 2023 I: pbuilder-time-stamp: 1691186287 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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-5.dsc] I: copying [./sspace_2.1.1+dfsg.orig.tar.xz] I: copying [./sspace_2.1.1+dfsg-5.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.iWA_165L/trustedkeys.kbx': General error gpgv: Signature made Fri Jan 3 07:00:41 2020 -12 gpgv: using RSA key 8451F9178172E7E2DC73F79551F84A8FECCA7E09 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./sspace_2.1.1+dfsg-5.dsc 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-5.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: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/69673/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' 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,-fixfilepath parallel=15 ' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='4cc20ce7b34e4067a697095cf166592d' 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='69673' 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.nLjr3Hy1/pbuilderrc_daPF --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.nLjr3Hy1/b1 --logfile b1/build.log sspace_2.1.1+dfsg-5.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://78.137.99.97:3128' I: uname -a Linux ionos1-amd64 6.1.0-10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.38-2 (2023-07-27) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98048 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 20 2022 more -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount -rwxr-xr-x 1 root root 18664 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 6 21:24 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jan 20 2022 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 20 2022 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/69673/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 (= 12), 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 ... 19707 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 (= 12); 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} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmpdec3{a} libpipeline1{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librecode0{a} libruby2.7{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} openssl{a} po-debconf{a} python3{a} python3-minimal{a} python3.9{a} python3.9-minimal{a} rake{a} readline-common{a} recode{a} ruby{a} ruby-asciidoctor{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-rubygems{a} ruby-test-unit{a} ruby-xmlrpc{a} ruby2.7{a} rubygems-integration{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-lato libarchive-cpio-perl 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 33.2 MB of archives. After unpacking 123 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1n-0+deb11u4 [853 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 rubygems-integration all 1.18 [6704 B] Get: 26 http://deb.debian.org/debian bullseye/main amd64 rake all 13.0.3-1 [84.7 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 ruby-minitest all 5.13.0-1 [57.3 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 ruby-power-assert all 1.1.7-2 [11.5 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 ruby-test-unit all 3.3.9-1 [86.1 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libedit2 amd64 3.1-20191231-2+b1 [96.7 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libruby2.7 amd64 2.7.4-1+deb11u1 [4202 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 ruby2.7 amd64 2.7.4-1+deb11u1 [747 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 ruby-rubygems all 3.2.5-2 [281 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 ruby amd64 1:2.7+2 [11.7 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 ruby-asciidoctor all 2.0.12-2 [206 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 asciidoctor all 2.0.12-2 [83.9 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 bowtie amd64 1.3.0+dfsg1-1 [1638 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 librecode0 amd64 3.6-24 [531 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 recode amd64 3.6-24 [188 kB] Fetched 33.2 MB in 1s (40.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19707 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8+deb11u1_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. 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Setting up ruby-minitest (5.13.0-1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up ruby-test-unit (3.3.9-1) ... Setting up recode (3.6-24) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up libmd0:amd64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up openssl (1.1.1n-0+deb11u4) ... Setting up libbsd0:amd64 (0.11.3-1) ... Setting up libelf1:amd64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libedit2:amd64 (3.1-20191231-2+b1) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up python3.9 (3.9.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up bowtie (1.3.0+dfsg1-1) ... Setting up ruby2.7 (2.7.4-1+deb11u1) ... Setting up ruby-rubygems (3.2.5-2) ... Setting up ruby (1:2.7+2) ... Setting up ruby-asciidoctor (2.0.12-2) ... Setting up rake (13.0.3-1) ... Setting up asciidoctor (2.0.12-2) ... Setting up libruby2.7:amd64 (2.7.4-1+deb11u1) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... Processing triggers for ca-certificates (20210119) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/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-5_source.changes dpkg-buildpackage: info: source package sspace dpkg-buildpackage: info: source version 2.1.1+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/sspace-2.1.1+dfsg' dh_auto_clean rm -f debian/sspace.1 make[1]: Leaving directory '/build/sspace-2.1.1+dfsg' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_test make[1]: Entering directory '/build/sspace-2.1.1+dfsg' debian/tests/example-tests /build/sspace-2.1.1+dfsg/SSPACE_Basic.pl Your inserted inputs on [SSPACE_Basic v2.1] at Fri Aug 4 09:58:47 2023: 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 =>Fri Aug 4 09:58:47 2023: Reading, filtering and converting input sequences of library file initiated Reading read-pairs lib1.1 @ 0 ------------------------------------------------------------ =>Fri Aug 4 09:58:47 2023: Storing contigs to format for scaffolding 100 200 300 400 500 LIBRARY lib1 ------------------------------------------------------------ =>Fri Aug 4 09:58:47 2023: Reading contig file =>Fri Aug 4 09:58:47 2023: Building Bowtie index for contigs =>Fri Aug 4 09:58:48 2023: 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 =>Fri Aug 4 09:58:48 2023: 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 =>Fri Aug 4 09:58:48 2023: Merging contigs and creating FASTA file of scaffolds 100 200 300 400 500 ------------------------------------------------------------ =>Fri Aug 4 09:58:48 2023: Creating summary file ************************************************** Process run succesfully on Fri Aug 4 09:58:48 2023 in 0 minutes and 1 seconds make[1]: Leaving directory '/build/sspace-2.1.1+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep debian/rules override_dh_install make[1]: Entering directory '/build/sspace-2.1.1+dfsg' dh_install find debian -name "*.pl" -exec recode ibmpc.. \{\} \; 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/sam_bam2tab.pl failed: Ambiguous output in step `CR-LF..data' 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/qseq2fastq.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/bin/readLibFiles.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/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' recode: debian/sspace/usr/share/sspace/SSPACE_Basic.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/sspace-2.1.1+dfsg' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/sspace-2.1.1+dfsg' dh_installexamples chmod -x debian/sspace/usr/share/doc/sspace/examples/libraries.txt make[1]: Leaving directory '/build/sspace-2.1.1+dfsg' debian/rules override_dh_installman make[1]: Entering directory '/build/sspace-2.1.1+dfsg' asciidoctor -a docdate='' -b manpage debian/sspace.1.adoc dh_installman make[1]: Leaving directory '/build/sspace-2.1.1+dfsg' dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/sspace-2.1.1+dfsg' dh_fixperms find debian -name contigs_abyss.fasta -exec chmod -x \{\} \; make[1]: Leaving directory '/build/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-5_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../sspace_2.1.1+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/69673 and its subdirectories I: Current time: Fri Aug 4 09:59:00 -12 2023 I: pbuilder-time-stamp: 1691186340 Fri Aug 4 21:59:01 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Fri Aug 4 21:59:01 UTC 2023 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Fri Aug 4 21:59:46 UTC 2023 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Fri Aug 4 21:59:47 UTC 2023 I: sspace_2.1.1+dfsg-5_amd64.changes: Format: 1.8 Date: Fri, 03 Jan 2020 19:59:38 +0100 Source: sspace Binary: sspace Architecture: all Version: 2.1.1+dfsg-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: sspace - scaffolding pre-assembled contigs after extension Closes: 938565 Changes: sspace (2.1.1+dfsg-5) unstable; urgency=medium . [ Andreas Tille ] * Use 2to3 to port to Python3 Closes: #938565 * debhelper-compat 12 * Remove trailing whitespace in debian/changelog * Fix permission of fasta file . [ Sascha Steinbiss ] * Bump Standards-Version. Checksums-Sha1: 0fc2016ef3d4d688007866e23a25cb647e2e3cfa 1236952 sspace_2.1.1+dfsg-5_all.deb 536c7fbfe37d4515aa6ce9491f25c042576da9de 6019 sspace_2.1.1+dfsg-5_amd64.buildinfo Checksums-Sha256: 009025261383d10318f90c80d3f497ce562f7e5688e44358f98feb14fb56bea0 1236952 sspace_2.1.1+dfsg-5_all.deb 2858fc0dc01b7b80e739c077023228bc504f805c2ec092319de4cd0941dd3033 6019 sspace_2.1.1+dfsg-5_amd64.buildinfo Files: 47ed941f3d930e0410c8b100cf15b4ac 1236952 science optional sspace_2.1.1+dfsg-5_all.deb 131b0c9be9ac3a224142d36bc7892555 6019 science optional sspace_2.1.1+dfsg-5_amd64.buildinfo Fri Aug 4 21:59:48 UTC 2023 I: diffoscope 243 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.nLjr3Hy1/sspace_2.1.1+dfsg-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.nLjr3Hy1/sspace_2.1.1+dfsg-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.nLjr3Hy1/sspace_2.1.1+dfsg-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.nLjr3Hy1/b1/sspace_2.1.1+dfsg-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.nLjr3Hy1/b2/sspace_2.1.1+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 abc.DotChangesFile ## main (total time: 0.241s) 0.241s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.026s) 0.026s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Fri Aug 4 21:59:48 UTC 2023 I: diffoscope 243 found no differences in the changes files, and a .buildinfo file also exists. Fri Aug 4 21:59:48 UTC 2023 I: sspace from bullseye built successfully and reproducibly on amd64. Fri Aug 4 21:59:50 UTC 2023 I: Submitting .buildinfo files to external archives: Fri Aug 4 21:59:50 UTC 2023 I: Submitting 8.0K b1/sspace_2.1.1+dfsg-5_amd64.buildinfo.asc Fri Aug 4 21:59:52 UTC 2023 I: Submitting 8.0K b2/sspace_2.1.1+dfsg-5_amd64.buildinfo.asc Fri Aug 4 21:59:52 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Aug 4 21:59:52 UTC 2023 I: Done submitting .buildinfo files. Fri Aug 4 21:59:52 UTC 2023 I: Removing signed sspace_2.1.1+dfsg-5_amd64.buildinfo.asc files: removed './b1/sspace_2.1.1+dfsg-5_amd64.buildinfo.asc' removed './b2/sspace_2.1.1+dfsg-5_amd64.buildinfo.asc'