Mon Aug 16 14:42:08 UTC 2021 I: starting to build sspace/bullseye/arm64 on jenkins on '2021-08-16 14:42' Mon Aug 16 14:42:08 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_23/25923/console.log Mon Aug 16 14:42:08 UTC 2021 I: Downloading source for bullseye/sspace=2.1.1+dfsg-5 --2021-08-16 14:42:08-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/sspace/sspace_2.1.1+dfsg-5.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1692 (1.7K) Saving to: ‘sspace_2.1.1+dfsg-5.dsc’ 0K . 100% 169M=0s 2021-08-16 14:42:08 (169 MB/s) - ‘sspace_2.1.1+dfsg-5.dsc’ saved [1692/1692] Mon Aug 16 14:42:08 UTC 2021 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----- Mon Aug 16 14:42:08 UTC 2021 I: Checking whether the package is not for us Mon Aug 16 14:42:08 UTC 2021 I: Starting 1st build on remote node codethink14-arm64.debian.net. Mon Aug 16 14:42:08 UTC 2021 I: Preparing to do remote build '1' on codethink14-arm64.debian.net. Mon Aug 16 14:43:29 UTC 2021 I: Deleting $TMPDIR on codethink14-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Aug 16 02:42:11 -12 2021 I: pbuilder-time-stamp: 1629124931 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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.J3r9rAGO/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/10170/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='10170' 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/tmp.CBtXEH9MdY/pbuilderrc_VItx --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.CBtXEH9MdY/b1 --logfile b1/build.log sspace_2.1.1+dfsg-5.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink14-arm64 4.15.0-153-generic #160-Ubuntu SMP Thu Jul 29 07:06:07 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Aug 4 08:25 bash -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 34808 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 34808 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 14264 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 39832 Sep 22 2020 cat -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash -rwxr-xr-x 1 root root 101384 Sep 22 2020 date -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd -rwxr-xr-x 1 root root 89824 Sep 22 2020 df -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir -rwxr-xr-x 1 root root 76152 Jul 28 07:09 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 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 64856 Jul 28 07:09 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe -rwxr-xr-x 1 root root 93744 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln -rwxr-xr-x 1 root root 52720 Feb 7 2020 login -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls -rwxr-xr-x 1 root root 161960 Jul 28 07:09 lsblk -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 51368 Jul 28 07:09 more -rwsr-xr-x 1 root root 51360 Jul 28 07:09 mount -rwxr-xr-x 1 root root 14496 Jul 28 07:09 mountpoint -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 15 21:27 sh -> dash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Jul 28 07:09 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 16 21:55 tar -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch -rwxr-xr-x 1 root root 31512 Sep 22 2020 true -rwxr-xr-x 1 root root 14264 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 30880 Jul 28 07:09 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 Jul 28 07:09 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew I: user script /srv/workspace/pbuilder/10170/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: arm64 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 ... 19646 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 32.1 MB of archives. After unpacking 121 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-8 [142 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-minimal arm64 3.9.2-1 [797 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 python3.9-minimal arm64 3.9.2-1 [1884 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libmpdec3 arm64 2.5.1-1 [84.4 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-stdlib arm64 3.9.2-1 [1658 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 python3.9 arm64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 python3 arm64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 openssl arm64 1.1.1k-1 [829 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 ca-certificates all 20210119 [158 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 rubygems-integration all 1.18 [6704 B] Get: 26 http://deb.debian.org/debian bullseye/main arm64 rake all 13.0.3-1 [84.7 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 ruby-minitest all 5.13.0-1 [57.3 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 ruby-power-assert all 1.1.7-2 [11.5 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 ruby-test-unit all 3.3.9-1 [86.1 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 libmd0 arm64 1.0.3-3 [27.9 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 libbsd0 arm64 0.11.3-1 [106 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libedit2 arm64 3.1-20191231-2+b1 [92.1 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 libyaml-0-2 arm64 0.2.2-1 [45.1 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libruby2.7 arm64 2.7.4-1 [4031 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 ruby2.7 arm64 2.7.4-1 [747 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 ruby-rubygems all 3.2.5-2 [281 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 ruby arm64 1:2.7+2 [11.7 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 ruby-asciidoctor all 2.0.12-2 [206 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 asciidoctor all 2.0.12-2 [83.9 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 bowtie arm64 1.3.0+dfsg1-1 [1262 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 58 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 59 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 60 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 61 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 62 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 63 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 64 http://deb.debian.org/debian bullseye/main arm64 librecode0 arm64 3.6-24 [509 kB] Get: 65 http://deb.debian.org/debian bullseye/main arm64 recode arm64 3.6-24 [188 kB] Fetched 32.1 MB in 1s (27.6 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 ... 19646 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8_arm64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../1-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_arm64.deb ... 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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 ... 20934 files and directories currently installed.) Preparing to unpack .../00-python3_3.9.2-3_arm64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package openssl. 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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:arm64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up libmd0:arm64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libmpdec3:arm64 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up openssl (1.1.1k-1) ... Setting up libbsd0:arm64 (0.11.3-1) ... Setting up libelf1:arm64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.7) ... 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:arm64 (3.1-20191231-2+b1) ... Setting up libreadline8:arm64 (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:arm64 (3.9.2-1) ... Setting up libpython3-stdlib:arm64 (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) ... 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:arm64 (2.7.4-1) ... Processing triggers for libc-bin (2.31-13) ... 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 arm64 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 Mon Aug 16 02:43:03 2021: 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 Aug 16 02:43:03 2021: Reading, filtering and converting input sequences of library file initiated Reading read-pairs lib1.1 @ 0 ------------------------------------------------------------ =>Mon Aug 16 02:43:03 2021: Storing contigs to format for scaffolding 100 200 300 400 500 LIBRARY lib1 ------------------------------------------------------------ =>Mon Aug 16 02:43:03 2021: Reading contig file =>Mon Aug 16 02:43:03 2021: Building Bowtie index for contigs =>Mon Aug 16 02:43:05 2021: 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 Aug 16 02:43:05 2021: 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 Aug 16 02:43:05 2021: Merging contigs and creating FASTA file of scaffolds 100 200 300 400 500 ------------------------------------------------------------ =>Mon Aug 16 02:43:05 2021: Creating summary file ************************************************** Process run succesfully on Mon Aug 16 02:43:05 2021 in 0 minutes and 2 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/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/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/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_arm64.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/10170 and its subdirectories I: Current time: Mon Aug 16 02:43:27 -12 2021 I: pbuilder-time-stamp: 1629125007 Mon Aug 16 14:43:30 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink13-arm64.debian.net. Mon Aug 16 14:43:30 UTC 2021 I: Preparing to do remote build '2' on codethink13-arm64.debian.net. Mon Aug 16 14:44:24 UTC 2021 I: Deleting $TMPDIR on codethink13-arm64.debian.net. Mon Aug 16 14:44:25 UTC 2021 I: sspace_2.1.1+dfsg-5_arm64.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 55174316b484fda91200b34c42dde86bf091c90d 5578 sspace_2.1.1+dfsg-5_arm64.buildinfo Checksums-Sha256: 009025261383d10318f90c80d3f497ce562f7e5688e44358f98feb14fb56bea0 1236952 sspace_2.1.1+dfsg-5_all.deb ef2f5617f081ffa7595df735c593e8d07d4365996506fd8fcee513f0bf1ab61b 5578 sspace_2.1.1+dfsg-5_arm64.buildinfo Files: 47ed941f3d930e0410c8b100cf15b4ac 1236952 science optional sspace_2.1.1+dfsg-5_all.deb acb4c57249b6b85913bc887c382209a8 5578 science optional sspace_2.1.1+dfsg-5_arm64.buildinfo Mon Aug 16 14:44:26 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.CBtXEH9MdY/sspace_2.1.1+dfsg-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.CBtXEH9MdY/sspace_2.1.1+dfsg-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.CBtXEH9MdY/sspace_2.1.1+dfsg-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.CBtXEH9MdY/b1/sspace_2.1.1+dfsg-5_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.CBtXEH9MdY/b2/sspace_2.1.1+dfsg-5_arm64.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: 0.267s) 0.267s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.027s) 0.026s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Mon Aug 16 14:44:28 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Mon Aug 16 14:44:28 UTC 2021 I: sspace from bullseye built successfully and reproducibly on arm64. Mon Aug 16 14:44:29 UTC 2021 I: Submitting .buildinfo files to external archives: Mon Aug 16 14:44:29 UTC 2021 I: Submitting 8.0K b1/sspace_2.1.1+dfsg-5_arm64.buildinfo.asc Mon Aug 16 14:44:31 UTC 2021 I: Submitting 8.0K b2/sspace_2.1.1+dfsg-5_arm64.buildinfo.asc Mon Aug 16 14:44:33 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Aug 16 14:44:33 UTC 2021 I: Done submitting .buildinfo files. Mon Aug 16 14:44:33 UTC 2021 I: Removing signed sspace_2.1.1+dfsg-5_arm64.buildinfo.asc files: removed './b1/sspace_2.1.1+dfsg-5_arm64.buildinfo.asc' removed './b2/sspace_2.1.1+dfsg-5_arm64.buildinfo.asc'