Fri Aug 14 20:47:38 UTC 2020 I: starting to build sspace/buster/arm64 on jenkins on '2020-08-14 20:47' Fri Aug 14 20:47:38 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_24/12/console.log Fri Aug 14 20:47:38 UTC 2020 I: Downloading source for buster/sspace=2.1.1+dfsg-4 --2020-08-14 20:47:38-- http://deb.debian.org/debian/pool/main/s/sspace/sspace_2.1.1+dfsg-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2056 (2.0K) Saving to: ‘sspace_2.1.1+dfsg-4.dsc’ 0K .. 100% 220M=0s 2020-08-14 20:47:38 (220 MB/s) - ‘sspace_2.1.1+dfsg-4.dsc’ saved [2056/2056] Fri Aug 14 20:47:38 UTC 2020 I: sspace_2.1.1+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: sspace Binary: sspace Architecture: all Version: 2.1.1+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Sascha Steinbiss Homepage: https://github.com/nsoranzo/sspace_basic Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/sspace Vcs-Git: https://salsa.debian.org/med-team/sspace.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11~), recode, python, asciidoctor, bowtie Package-List: sspace deb science optional arch=all Checksums-Sha1: 0911ac377d0cdfa0611cd27df211a850cddf648a 1234924 sspace_2.1.1+dfsg.orig.tar.xz f26cd6f8a85035641637b3faf67d814b9d73aa01 496224 sspace_2.1.1+dfsg-4.debian.tar.xz Checksums-Sha256: 5bbb1cfd1e68af66fd31ab3d9720c450a9acf9a2a4bf9bde7e8e54a859b04aa1 1234924 sspace_2.1.1+dfsg.orig.tar.xz d94b81a857d370899de19aad6f62da6b1740ff881a943ea7cc4bdb41e8210e1a 496224 sspace_2.1.1+dfsg-4.debian.tar.xz Files: 2dc72080013bc674ff8a1fb5190381f2 1234924 sspace_2.1.1+dfsg.orig.tar.xz 3e7c28db12bbde7dd34e1524220d17e9 496224 sspace_2.1.1+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlvJoeURHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtG7BBAAl8AcZA4QxrWElZYZRk7rhHpxUoKyvSH4 gZGW1UjrH3RtvjcyTK6MAG2/KNwvhl2aYdXrryq4crbv66B2a2voEAWi0Hxr8Xad QUmzwvb8VeyArDmTd56cBH560VQZ4Tgp+FzjNvl9EVTLhDzChqcWZy1JmMtDmRUf 8a6D4jSAZIVzMFgLzujxUADwZM+sWTDtJGcCI6XHmmhvnw8Epe3DitWjyZOpMfEh eb5VdOsQ85GJNhKnT9Y6jvoY4VslDPIfNet1zc9qEkWaIHd+4w/O5YefoIrSTWs+ gbsUxiqfjdfDoPOqyVVWc9flzieLsDL9nKKzk6jrdHpQR4n6qCTptI8O3XbL0I5e p8G7n8nXo4Rj2L1vh1ohQD1TlUjEsQiquKyKMTE2hfYv6cNeMMPxDH4j4WOA+MPG tjvh0ithHHEGStAJg00HRstJ86mPpzW11WWRxN8zEZ1JroIxaoedHrA2ZgslerV+ wDJg/lyBN+41YsY6pZSKvDdNHwoYJhqNnlAGkqVzqlmochZTfwNoYtkjB4e4gIRI ey+15srpbIci447hVKfyAkTkK7vU97vs1R843qDZY0sapWTCe0IT1I95/37/ODUd 7Qhr4uyoR0PFWtvyN81cwq8OqQwgS3ksod+1DwBQoyPDhgW9hUse7DZ+VYglWb7r P77dSoABpus= =gaW0 -----END PGP SIGNATURE----- Fri Aug 14 20:47:38 UTC 2020 I: Checking whether the package is not for us Fri Aug 14 20:47:38 UTC 2020 I: Starting 1st build on remote node codethink-sled14-arm64.debian.net. Fri Aug 14 20:47:38 UTC 2020 I: Preparing to do remote build '1' on codethink-sled14-arm64.debian.net. Fri Aug 14 20:48:32 UTC 2020 I: Deleting $TMPDIR on codethink-sled14-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Aug 14 08:47:46 -12 2020 I: pbuilder-time-stamp: 1597438066 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-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-4.dsc] I: copying [./sspace_2.1.1+dfsg.orig.tar.xz] I: copying [./sspace_2.1.1+dfsg-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Thu Oct 18 21:20:37 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./sspace_2.1.1+dfsg-4.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-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying shebangs.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/5616/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 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='5616' 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.ClZrAs9FFD/pbuilderrc_ZX5Q --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.ClZrAs9FFD/b1 --logfile b1/build.log sspace_2.1.1+dfsg-4.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 codethink-sled14-arm64 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:35:21 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14264 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 35576 Feb 28 2019 cat -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash -rwxr-xr-x 1 root root 97136 Feb 28 2019 date -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd -rwxr-xr-x 1 root root 93752 Feb 28 2019 df -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir -rwxr-xr-x 1 root root 75984 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 31368 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 27256 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 174304 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 89656 Jan 5 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln -rwxr-xr-x 1 root root 52544 Jul 26 2018 login -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 9 2019 more -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138736 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35560 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 12 20:27 sh -> dash -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty -rwsr-xr-x 1 root root 59424 Jan 9 2019 su -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch -rwxr-xr-x 1 root root 27256 Feb 28 2019 true -rwxr-xr-x 1 root root 14264 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34824 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/5616/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 (>= 11~), recode, python, 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 ... 19168 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 (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on recode; however: Package recode is not installed. pbuilder-satisfydepends-dummy depends on python; however: Package python 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} bsdmainutils{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} libcroco3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} librecode0{a} libruby2.5{a} libsigsegv2{a} libssl1.1{a} libtbb2{a} libtool{a} libuchardet0{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} mime-support{a} openssl{a} po-debconf{a} python{a} python-minimal{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} rake{a} readline-common{a} recode{a} ruby{a} ruby-asciidoctor{a} ruby-did-you-mean{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-test-unit{a} ruby-xmlrpc{a} ruby2.5{a} rubygems-integration{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-lato libarchive-cpio-perl libglib2.0-data libgpm2 libjs-jquery libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs zip 0 packages upgraded, 68 newly installed, 0 to remove and 0 not upgraded. Need to get 31.7 MB of archives. After unpacking 119 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 libpython2.7-minimal arm64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 python2.7-minimal arm64 2.7.16-2+deb10u1 [1292 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 python2-minimal arm64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 python-minimal arm64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 libssl1.1 arm64 1.1.1d-0+deb10u3 [1382 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 libexpat1 arm64 2.2.6-2+deb10u1 [85.4 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 libreadline7 arm64 7.0-5 [134 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 libpython2.7-stdlib arm64 2.7.16-2+deb10u1 [1890 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 python2.7 arm64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 libpython2-stdlib arm64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 libpython-stdlib arm64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 python2 arm64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 python arm64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 openssl arm64 1.1.1d-0+deb10u3 [823 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 ca-certificates all 20190110 [157 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 rubygems-integration all 1.11+deb10u1 [5212 B] Get: 30 http://deb.debian.org/debian buster/main arm64 rake all 12.3.1-3+deb10u1 [67.1 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 ruby-did-you-mean all 1.2.1-1 [14.4 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 ruby-minitest all 5.11.3-1 [54.8 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 ruby-power-assert all 1.1.1-1 [10.9 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 ruby-test-unit all 3.2.8-1 [72.4 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get: 37 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 libyaml-0-2 arm64 0.2.1-1 [41.4 kB] Get: 39 http://deb.debian.org/debian buster/main arm64 libruby2.5 arm64 2.5.5-3+deb10u2 [3303 kB] Get: 40 http://deb.debian.org/debian buster/main arm64 ruby2.5 arm64 2.5.5-3+deb10u2 [400 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 ruby arm64 1:2.5.1 [11.3 kB] Get: 42 http://deb.debian.org/debian buster/main arm64 ruby-asciidoctor all 1.5.8-1 [188 kB] Get: 43 http://deb.debian.org/debian buster/main arm64 asciidoctor all 1.5.8-1 [75.8 kB] Get: 44 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 45 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 46 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 47 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 48 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 49 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 50 http://deb.debian.org/debian buster/main arm64 libtbb2 arm64 2018~U6-4 [122 kB] Get: 51 http://deb.debian.org/debian buster/main arm64 bowtie arm64 1.2.2+dfsg-4 [1275 kB] Get: 52 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 53 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 54 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 55 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 56 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 57 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 58 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 59 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 60 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 61 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 62 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 63 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 64 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 65 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 66 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 67 http://deb.debian.org/debian buster/main arm64 librecode0 arm64 3.6-23 [495 kB] Get: 68 http://deb.debian.org/debian buster/main arm64 recode arm64 3.6-23 [191 kB] Fetched 31.7 MB in 2s (14.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... 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Selecting previously unselected package python2. (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 ... 20631 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_arm64.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (Reading database ... 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Setting up ruby-minitest (5.11.3-1) ... Setting up autotools-dev (20180224.1) ... Setting up ruby-test-unit (3.2.8-1) ... Setting up recode (3.6-23) ... Setting up libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libsigsegv2:arm64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:arm64 (0.0.6-3) ... Setting up ruby-did-you-mean (1.2.1-1) ... Setting up openssl (1.1.1d-0+deb10u3) ... Setting up libbsd0:arm64 (0.9.1-2) ... Setting up libelf1:arm64 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Setting up libreadline7:arm64 (7.0-5) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libtool (2.4.6-9) ... Setting up m4 (1.4.18-2) ... Setting up libpython2.7-stdlib:arm64 (2.7.16-2+deb10u1) ... Setting up ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 128 added, 0 removed; done. Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:arm64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:arm64 (2.7.16-1) ... Setting up rubygems-integration (1.11+deb10u1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python2 (2.7.16-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython-stdlib:arm64 (2.7.16-1) ... Setting up python (2.7.16-1) ... Setting up bowtie (1.2.2+dfsg-4) ... Setting up po-debconf (1.0.21) ... Setting up rake (12.3.1-3+deb10u1) ... Setting up libruby2.5:arm64 (2.5.5-3+deb10u2) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up ruby2.5 (2.5.5-3+deb10u2) ... Setting up ruby (1:2.5.1) ... Setting up ruby-asciidoctor (1.5.8-1) ... Setting up asciidoctor (1.5.8-1) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for ca-certificates (20190110) ... 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 (1.23-1). 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 dpkg-buildpackage: info: source package sspace dpkg-buildpackage: info: source version 2.1.1+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille 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 Fri Aug 14 08:48:17 2020: 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 14 08:48:17 2020: Reading, filtering and converting input sequences of library file initiated Reading read-pairs lib1.1 @ 0 ------------------------------------------------------------ =>Fri Aug 14 08:48:17 2020: Storing contigs to format for scaffolding 100 200 300 400 500 LIBRARY lib1 ------------------------------------------------------------ =>Fri Aug 14 08:48:17 2020: Reading contig file =>Fri Aug 14 08:48:17 2020: Building Bowtie index for contigs =>Fri Aug 14 08:48:18 2020: Mapping reads to contigs. Reading bowtie output and pairing contigs # reads processed: 19924 # reads with at least one reported alignment: 1879 (9.43%) # reads that failed to align: 18045 (90.57%) Reported 1879 alignments =>Fri Aug 14 08:48:18 2020: 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 14 08:48:18 2020: Merging contigs and creating FASTA file of scaffolds 100 200 300 400 500 ------------------------------------------------------------ =>Fri Aug 14 08:48:18 2020: Creating summary file ************************************************** Process run succesfully on Fri Aug 14 08:48:18 2020 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 dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'sspace' in '../sspace_2.1.1+dfsg-4_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../sspace_2.1.1+dfsg-4_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) 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/5616 and its subdirectories I: Current time: Fri Aug 14 08:48:31 -12 2020 I: pbuilder-time-stamp: 1597438111 Fri Aug 14 20:48:33 UTC 2020 I: 1st build successful. Starting 2nd build on remote node codethink-sled15-arm64.debian.net. Fri Aug 14 20:48:33 UTC 2020 I: Preparing to do remote build '2' on codethink-sled15-arm64.debian.net. Fri Aug 14 20:49:33 UTC 2020 I: Deleting $TMPDIR on codethink-sled15-arm64.debian.net. Fri Aug 14 20:49:35 UTC 2020 I: sspace_2.1.1+dfsg-4_arm64.changes: Format: 1.8 Date: Fri, 19 Oct 2018 11:17:15 +0200 Source: sspace Binary: sspace Architecture: all Version: 2.1.1+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: sspace - scaffolding pre-assembled contigs after extension Changes: sspace (2.1.1+dfsg-4) unstable; urgency=medium . * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 * Secure URI in copyright format * Respect DEB_BUILD_OPTIONS in override_dh_auto_test * Fix perl interpreter Checksums-Sha1: 8e02725929aaaf24273d0e1078afba0ae576a1e9 1339708 sspace_2.1.1+dfsg-4_all.deb 7ed3de3cb3e3d2e9575c2dcc7f72a95736cba98d 5397 sspace_2.1.1+dfsg-4_arm64.buildinfo Checksums-Sha256: b74403a711ec452b6677c8b873b6c7cf44332d62c0528acb3eafb8ce98c033bf 1339708 sspace_2.1.1+dfsg-4_all.deb d61f4985e1a102f39030d7314348b97b22bb661afc3539c16f2f680d7a3bfa04 5397 sspace_2.1.1+dfsg-4_arm64.buildinfo Files: 6f18b43ff10e81dad6aa6a188001dbcf 1339708 science optional sspace_2.1.1+dfsg-4_all.deb 0e359e54a4ed10c5f4ece5ab356ea4ac 5397 science optional sspace_2.1.1+dfsg-4_arm64.buildinfo Fri Aug 14 20:49:36 UTC 2020 I: diffoscope 155 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.ClZrAs9FFD/sspace_2.1.1+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.ClZrAs9FFD/sspace_2.1.1+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.ClZrAs9FFD/sspace_2.1.1+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.ClZrAs9FFD/b1/sspace_2.1.1+dfsg-4_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.ClZrAs9FFD/b2/sspace_2.1.1+dfsg-4_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: 0.272s) 0.272s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.049s) 0.049s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Fri Aug 14 20:49:38 UTC 2020 I: diffoscope 155 found no differences in the changes files, and a .buildinfo file also exists. Fri Aug 14 20:49:38 UTC 2020 I: sspace from buster built successfully and reproducibly on arm64. Fri Aug 14 20:49:41 UTC 2020 I: Submitting .buildinfo files to external archives: Fri Aug 14 20:49:41 UTC 2020 I: Submitting 8.0K b1/sspace_2.1.1+dfsg-4_arm64.buildinfo.asc Fri Aug 14 20:49:42 UTC 2020 I: Submitting 8.0K b2/sspace_2.1.1+dfsg-4_arm64.buildinfo.asc Fri Aug 14 20:49:43 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Aug 14 20:49:43 UTC 2020 I: Done submitting .buildinfo files. Fri Aug 14 20:49:43 UTC 2020 I: Removing signed sspace_2.1.1+dfsg-4_arm64.buildinfo.asc files: removed './b1/sspace_2.1.1+dfsg-4_arm64.buildinfo.asc' removed './b2/sspace_2.1.1+dfsg-4_arm64.buildinfo.asc'