Wed Jun 24 01:17:04 UTC 2020 I: starting to build snpomatic/buster/i386 on jenkins on '2020-06-24 01:16' Wed Jun 24 01:17:04 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_10/8110/console.log Wed Jun 24 01:17:04 UTC 2020 I: Downloading source for buster/snpomatic=1.0-4 --2020-06-24 01:17:04-- http://deb.debian.org/debian/pool/main/s/snpomatic/snpomatic_1.0-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2015 (2.0K) Saving to: ‘snpomatic_1.0-4.dsc’ 0K . 100% 100M=0s 2020-06-24 01:17:04 (100 MB/s) - ‘snpomatic_1.0-4.dsc’ saved [2015/2015] Wed Jun 24 01:17:04 UTC 2020 I: snpomatic_1.0-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: snpomatic Binary: snpomatic Architecture: any Version: 1.0-4 Maintainer: Debian Med Packaging Team Uploaders: Sascha Steinbiss Homepage: https://github.com/magnusmanske/snpomatic Standards-Version: 4.1.4 Vcs-Browser: https://salsa.debian.org/med-team/snpomatic Vcs-Git: https://salsa.debian.org/med-team/snpomatic.git Testsuite: autopkgtest Testsuite-Triggers: samtools Build-Depends: debhelper (>= 11~), asciidoctor, antiword Package-List: snpomatic deb science optional arch=any Checksums-Sha1: ce873229b63a44cf210a7c41ef866642bed72d1f 66546 snpomatic_1.0.orig.tar.gz df14cc26c9f1562bf83a86c8b0a1cc652baf0ed9 9456 snpomatic_1.0-4.debian.tar.xz Checksums-Sha256: b90123226e24edfa5c2ca296f9414b5aa005d3da77ad80b5c576adddbb38a094 66546 snpomatic_1.0.orig.tar.gz 9716e18522f29b255d4073c4ad73955366ae985d5288e968615ec620daa33fb9 9456 snpomatic_1.0-4.debian.tar.xz Files: bac27c60847ad8036faafd7c9a335b5c 66546 snpomatic_1.0.orig.tar.gz 2686c671666bad7fc4727d3d3fc6c91c 9456 snpomatic_1.0-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAls/oBURHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGIAw/7BxZcFw5k2csOpvAbaksW2aOrfKqjNufg pjh+5wSFTiXQy/lmlUtDEXaGlfkEzkoLUePEJrfOR9s4+3vnKBf6ucewOkV4VVmg v8TYHyLjRQ8DF4xDZpAbzPIF7bN/qiwZDyYHvz6xmpJr+v/npQ3zYOiNyTHKh9Gz ewT/RdUR++eO2Q5xopJuVWwKoxpKhFV/ewaLDpgVLm63qeNUNX0j2bGVxbM2VqiT +mhW+eYfLtL+KbcWGxO7DVF4iYKShFSzS7V9qMC5tbkhqQyapyczFc0NdE3tAAbR ghMKa3b0d7GSRKs1W50aqqsE/g7wQ7wStYvyPH9WjG/pnCC8ntQLZ7mKuSJK4QWg EtmDLv/yH4Xg6zvNiSdaX3gjfaj+Wf0RkDH0fDi1oaXs9dIotvid0b9i0rd4mj8X k0scfWhImW4YMP08azlbnrIO9EI7qIeUiz3cqXWkxJ21VETRvyZrBjaH0UWRjX9c N4k23HIqcPEYQkMdV6xDJXT1ReR7CYlkakcfr+CLEKDZL74vCdcVM6/0NnMK1Wcb ifTtU0TH7kshccTmiREGVoPHq2rC06ZRO86r8sT/4joVJsh2CpWFtbQQBc/IHxUU Bxzyp0K8KjSF3VbUqWas6ZXIZ3XQcFOGpHwAK30bbECZfzT58aHS27c2YIN5GYXy R4+fFAYpHaA= =XJqW -----END PGP SIGNATURE----- Wed Jun 24 01:17:04 UTC 2020 I: Checking whether the package is not for us Wed Jun 24 01:17:04 UTC 2020 I: Starting 1st build on remote node profitbricks-build6-i386.debian.net. Wed Jun 24 01:17:04 UTC 2020 I: Preparing to do remote build '1' on profitbricks-build6-i386.debian.net. Wed Jun 24 01:17:33 UTC 2020 I: Deleting $TMPDIR on profitbricks-build6-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jul 26 19:40:04 -12 2021 I: pbuilder-time-stamp: 1627371604 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: using eatmydata during job I: Copying source file I: copying [snpomatic_1.0-4.dsc] I: copying [./snpomatic_1.0.orig.tar.gz] I: copying [./snpomatic_1.0-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Jul 6 05:00:05 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 ./snpomatic_1.0-4.dsc dpkg-source: info: extracting snpomatic in snpomatic-1.0 dpkg-source: info: unpacking snpomatic_1.0.orig.tar.gz dpkg-source: info: unpacking snpomatic_1.0-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_ungap dpkg-source: info: applying hardening dpkg-source: info: applying build_all_binaries I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/23632/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=18' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='a779e52d43a944f38eb136d09d358fdb' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='23632' 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.ZHgr5PQQI5/pbuilderrc_noBW --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.ZHgr5PQQI5/b1 --logfile b1/build.log snpomatic_1.0-4.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux profitbricks-build6-i386 4.19.0-9-amd64 #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1302248 Apr 17 2019 bash -rwxr-xr-x 3 root root 38280 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38280 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 38280 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 17768 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 38692 Feb 28 2019 cat -rwxr-xr-x 1 root root 75588 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 63268 Feb 28 2019 chmod -rwxr-xr-x 1 root root 75588 Feb 28 2019 chown -rwxr-xr-x 1 root root 153732 Feb 28 2019 cp -rwxr-xr-x 1 root root 132820 Jan 17 2019 dash -rwxr-xr-x 1 root root 120676 Feb 28 2019 date -rwxr-xr-x 1 root root 92040 Feb 28 2019 dd -rwxr-xr-x 1 root root 100620 Feb 28 2019 df -rwxr-xr-x 1 root root 149736 Feb 28 2019 dir -rwxr-xr-x 1 root root 79412 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 34532 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 34532 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 67700 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 30112 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 206392 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 100952 Jan 5 2019 gzip -rwxr-xr-x 1 root root 21916 Sep 26 2018 hostname -rwxr-xr-x 1 root root 79752 Feb 28 2019 ln -rwxr-xr-x 1 root root 55400 Jul 26 2018 login -rwxr-xr-x 1 root root 149736 Feb 28 2019 ls -rwxr-xr-x 1 root root 112032 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 87972 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 79748 Feb 28 2019 mknod -rwxr-xr-x 1 root root 46916 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 42348 Jan 9 2019 more -rwsr-xr-x 1 root root 50592 Jan 9 2019 mount -rwxr-xr-x 1 root root 13724 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 157832 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 38660 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 46852 Feb 28 2019 readlink -rwxr-xr-x 1 root root 75588 Feb 28 2019 rm -rwxr-xr-x 1 root root 42756 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 22276 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 25 02:47 sh -> dash -rwxr-xr-x 1 root root 34532 Feb 28 2019 sleep -rwxr-xr-x 1 root root 79652 Feb 28 2019 stty -rwsr-xr-x 1 root root 71072 Jan 9 2019 su -rwxr-xr-x 1 root root 34564 Feb 28 2019 sync -rwxr-xr-x 1 root root 504024 Apr 23 2019 tar -rwxr-xr-x 1 root root 13860 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 104292 Feb 28 2019 touch -rwxr-xr-x 1 root root 34532 Feb 28 2019 true -rwxr-xr-x 1 root root 17768 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 30108 Jan 9 2019 umount -rwxr-xr-x 1 root root 34532 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 149736 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34208 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/23632/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: i386 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~), asciidoctor, antiword dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19234 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 asciidoctor; however: Package asciidoctor is not installed. pbuilder-satisfydepends-dummy depends on antiword; however: Package antiword 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: antiword{a} asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{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} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libreadline7{a} libruby2.5{a} libsigsegv2{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} openssl{a} po-debconf{a} rake{a} readline-common{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, 53 newly installed, 0 to remove and 0 not upgraded. Need to get 26.8 MB of archives. After unpacking 95.6 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://deb.debian.org/debian buster/main i386 readline-common all 7.0-5 [70.6 kB] Get: 8 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 9 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 10 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 11 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 12 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 13 http://deb.debian.org/debian buster/main i386 antiword i386 0.37-14 [136 kB] Get: 14 http://deb.debian.org/debian buster/main i386 libssl1.1 i386 1.1.1d-0+deb10u3 [1537 kB] Get: 15 http://deb.debian.org/debian buster/main i386 openssl i386 1.1.1d-0+deb10u3 [853 kB] Get: 16 http://deb.debian.org/debian buster/main i386 ca-certificates all 20190110 [157 kB] Get: 17 http://deb.debian.org/debian buster/main i386 rubygems-integration all 1.11+deb10u1 [5212 B] Get: 18 http://deb.debian.org/debian buster/main i386 rake all 12.3.1-3+deb10u1 [67.1 kB] Get: 19 http://deb.debian.org/debian buster/main i386 ruby-did-you-mean all 1.2.1-1 [14.4 kB] Get: 20 http://deb.debian.org/debian buster/main i386 ruby-minitest all 5.11.3-1 [54.8 kB] Get: 21 http://deb.debian.org/debian buster/main i386 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get: 22 http://deb.debian.org/debian buster/main i386 ruby-power-assert all 1.1.1-1 [10.9 kB] Get: 23 http://deb.debian.org/debian buster/main i386 ruby-test-unit all 3.2.8-1 [72.4 kB] Get: 24 http://deb.debian.org/debian buster/main i386 ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get: 25 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 26 http://deb.debian.org/debian buster/main i386 libreadline7 i386 7.0-5 [156 kB] Get: 27 http://deb.debian.org/debian buster/main i386 libyaml-0-2 i386 0.2.1-1 [49.7 kB] Get: 28 http://deb.debian.org/debian buster/main i386 libruby2.5 i386 2.5.5-3+deb10u1 [3546 kB] Get: 29 http://deb.debian.org/debian buster/main i386 ruby2.5 i386 2.5.5-3+deb10u1 [400 kB] Get: 30 http://deb.debian.org/debian buster/main i386 ruby i386 1:2.5.1 [11.3 kB] Get: 31 http://deb.debian.org/debian buster/main i386 ruby-asciidoctor all 1.5.8-1 [188 kB] Get: 32 http://deb.debian.org/debian buster/main i386 asciidoctor all 1.5.8-1 [75.8 kB] Get: 33 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 34 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 35 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 36 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 37 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 38 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 39 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 40 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 41 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 42 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 43 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 44 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 45 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 46 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 47 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6+deb10u1 [8451 kB] Get: 48 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 49 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 50 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 51 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 52 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 53 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Fetched 26.8 MB in 0s (80.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19234 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../02-libuchardet0_0.0.6-3_i386.deb ... Unpacking libuchardet0:i386 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_i386.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../04-libpipeline1_1.5.1-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_i386.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../06-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../07-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../08-libmagic-mgc_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... 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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/snpomatic-1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package snpomatic dpkg-buildpackage: info: source version 1.0-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/snpomatic-1.0' /usr/bin/make clean make[2]: Entering directory '/build/snpomatic-1.0' rm -f *.o rm -f src/*.o rm -f findknownsnps rm -f variety make[2]: Leaving directory '/build/snpomatic-1.0' rm -rf debian/findknownsnps.1 rm -rf debian/findknownsnps.1.html rm -f mapcontigs reassemble ungap dh_auto_clean -- make -j18 clean make[2]: Entering directory '/build/snpomatic-1.0' rm -f *.o rm -f src/*.o rm -f findknownsnps rm -f variety make[2]: Leaving directory '/build/snpomatic-1.0' make[1]: Leaving directory '/build/snpomatic-1.0' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/snpomatic.substvars debian/files rm -fr -- debian/snpomatic/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j18 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/snpomatic-1.0' g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/findknownsnps.cpp -o src/findknownsnps.o g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/global_functions.cpp -o src/global_functions.o g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosome.cpp -o src/TChromosome.o g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosomalIndices.cpp -o src/TChromosomalIndices.o g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TAlignmentOutput.cpp -o src/TAlignmentOutput.o g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosomeAlign.cpp -o src/TChromosomeAlign.o g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/reassemble.cpp -o src/reassemble.o g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/variety.cpp -o src/variety.o g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/mapcontigs.cpp -o src/mapcontigs.o g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/ungap.cpp -o src/ungap.o src/global_functions.cpp: In function 'void load_all_chromosomes(std::__cxx11::string, std::vector&, bool)': src/global_functions.cpp:116:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/global_functions.cpp: In function 'void incorporate_all_gff(std::__cxx11::string, std::vector&)': src/global_functions.cpp:165:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/global_functions.cpp: In function 'void incorporate_simple_snps(std::__cxx11::string, std::vector&)': src/global_functions.cpp:220:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::run_reads(std::__cxx11::string)': src/TChromosomalIndices.cpp:33:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:37:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::reassemble_reads(FILE*, uint, index2type, index2type)': src/TChromosomalIndices.cpp:126:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:127:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::run_regions(chrvec*, std::__cxx11::string)': src/TChromosomalIndices.cpp:167:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::load_index(std::__cxx11::string)': src/TChromosomalIndices.cpp:409:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread ( &temp , sizeof ( temp ) , 1 , file ) ; // Version ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:410:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread ( &temp , sizeof ( temp ) , 1 , file ) ; // position size ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:415:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread ( &temp , sizeof ( temp ) , 1 , file ) ; // Sub-index size ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:419:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread ( &i.index2 , sizeof ( i.index2 ) , 1 , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:420:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread ( &i.position , sizeof ( i.position ) , 1 , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:421:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread ( &i.chromosome , sizeof ( i.chromosome ) , 1 , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:422:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread ( &i.reverse_complement , sizeof ( i.reverse_complement ) , 1 , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::add_nono_list(std::__cxx11::string)': src/TChromosomeAlign.cpp:93:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosome.cpp: In member function 'void TChromosome::read_chromosome(std::__cxx11::string, std::__cxx11::string)': src/TChromosome.cpp:13:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosome.cpp: In member function 'void TChromosome::incorporate_known_snps_gff(std::__cxx11::string)': src/TChromosome.cpp:54:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::finish_sqlite(int, int, int)': src/TChromosomeAlign.cpp:972:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , sqlite_cache ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::align_solexa_paired(std::__cxx11::string, std::__cxx11::string, uint, uint, uint)': src/TChromosomeAlign.cpp:1070:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1075:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( c1 , READ_CHAR_BUFFER , file2 ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosome.cpp: In member function 'void TChromosome::incorporate_known_snps(std::__cxx11::string)': src/TChromosome.cpp:95:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::align_solexa_fastq(std::__cxx11::string)': src/TChromosomeAlign.cpp:1296:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1306:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1316:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1325:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::align_solexa_fasta(std::__cxx11::string)': src/TChromosomeAlign.cpp:1374:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/reassemble.cpp: In function 'void read_fastq(std::__cxx11::string, std::vector&, int)': src/reassemble.cpp:319:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::align_solexa_fastq_variety(std::__cxx11::string)': src/TChromosomeAlign.cpp:1628:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1637:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1647:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1655:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/findknownsnps.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o findknownsnps g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/reassemble.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o reassemble g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/variety.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o variety g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/mapcontigs.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o mapcontigs g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/ungap.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o ungap make[1]: Leaving directory '/build/snpomatic-1.0' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep rm -f -- debian/snpomatic.substvars rm -fr -- debian/.debhelper/generated/snpomatic/ debian/snpomatic/ debian/tmp/ debian/rules override_dh_auto_install make[1]: Entering directory '/build/snpomatic-1.0' mkdir -p /build/snpomatic-1.0/debian/snpomatic/usr/bin install -p findknownsnps /build/snpomatic-1.0/debian/snpomatic/usr/bin # -- we don't install the others as they seem unmaintained/undocumented #cp reassemble /build/snpomatic-1.0/debian/snpomatic/usr/bin #cp variety /build/snpomatic-1.0/debian/snpomatic/usr/bin #cp mapcontigs /build/snpomatic-1.0/debian/snpomatic/usr/bin #cp ungap /build/snpomatic-1.0/debian/snpomatic/usr/bin make[1]: Leaving directory '/build/snpomatic-1.0' debian/rules override_dh_installdocs make[1]: Entering directory '/build/snpomatic-1.0' antiword doc/Manual.doc > doc/Manual.txt mkdir -p debian/snpomatic/usr/share/doc/snpomatic cp doc/Manual.txt debian/snpomatic/usr/share/doc/snpomatic mkdir -p debian/snpomatic/usr/share/doc-base cp debian/doc-base debian/snpomatic/usr/share/doc-base/snpomatic-doc dh_installdocs -- install -d debian/.debhelper/generated/snpomatic install -p -m0644 debian/copyright debian/snpomatic/usr/share/doc/snpomatic/copyright install -p -m0644 debian/doc-base debian/snpomatic/usr/share/doc-base/snpomatic make[1]: Leaving directory '/build/snpomatic-1.0' dh_installchangelogs install -p -m0644 debian/changelog debian/snpomatic/usr/share/doc/snpomatic/changelog.Debian rm -f debian/snpomatic.debhelper.log debian/rules override_dh_installman make[1]: Entering directory '/build/snpomatic-1.0' asciidoctor -a docdate='' -b manpage debian/findknownsnps.1.adoc dh_installman -- install -d debian/snpomatic/usr/share/man/man1/ install -p -m0644 ./debian/findknownsnps.1 debian/snpomatic/usr/share/man/man1/findknownsnps.1 man -l --recode UTF-8 ./debian/snpomatic/usr/share/man/man1/findknownsnps.1 > debian/snpomatic/usr/share/man/man1/findknownsnps.1.dh-new mv debian/snpomatic/usr/share/man/man1/findknownsnps.1.dh-new debian/snpomatic/usr/share/man/man1/findknownsnps.1 chmod 0644 -- debian/snpomatic/usr/share/man/man1/findknownsnps.1 make[1]: Leaving directory '/build/snpomatic-1.0' dh_perl dh_link dh_strip_nondeterminism dh_compress cd debian/snpomatic chmod a-x usr/share/doc/snpomatic/Manual.txt usr/share/doc/snpomatic/changelog.Debian usr/share/man/man1/findknownsnps.1 gzip -9nf usr/share/doc/snpomatic/Manual.txt usr/share/doc/snpomatic/changelog.Debian usr/share/man/man1/findknownsnps.1 cd '/build/snpomatic-1.0' dh_fixperms find debian/snpomatic -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/snpomatic ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/snpomatic/usr/share/doc -type f -a -true -a ! -regex 'debian/snpomatic/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/snpomatic/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/snpomatic/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/snpomatic -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/snpomatic/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_strip install -d debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/2f objcopy --only-keep-debug --compress-debug-sections debian/snpomatic/usr/bin/findknownsnps debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/2f/e06b85bf70cc2514851de71fddb8739f183532.debug chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/2f/e06b85bf70cc2514851de71fddb8739f183532.debug chown 0:0 -- debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/2f/e06b85bf70cc2514851de71fddb8739f183532.debug strip --remove-section=.comment --remove-section=.note debian/snpomatic/usr/bin/findknownsnps objcopy --add-gnu-debuglink debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/2f/e06b85bf70cc2514851de71fddb8739f183532.debug debian/snpomatic/usr/bin/findknownsnps install -d debian/.debhelper/snpomatic/dbgsym-root/usr/share/doc ln -s snpomatic debian/.debhelper/snpomatic/dbgsym-root/usr/share/doc/snpomatic-dbgsym dh_makeshlibs rm -f debian/snpomatic/DEBIAN/shlibs dh_shlibdeps install -d debian/snpomatic/DEBIAN dpkg-shlibdeps -Tdebian/snpomatic.substvars debian/snpomatic/usr/bin/findknownsnps dh_installdeb dh_gencontrol echo misc:Depends= >> debian/snpomatic.substvars echo misc:Pre-Depends= >> debian/snpomatic.substvars install -d debian/.debhelper/snpomatic/dbgsym-root/DEBIAN dpkg-gencontrol -psnpomatic -ldebian/changelog -Tdebian/snpomatic.substvars -Pdebian/.debhelper/snpomatic/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=snpomatic-dbgsym "-DDepends=snpomatic (= \${binary:Version})" "-DDescription=debug symbols for snpomatic" -DBuild-Ids=2fe06b85bf70cc2514851de71fddb8739f183532 -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/DEBIAN/control chown 0:0 -- debian/.debhelper/snpomatic/dbgsym-root/DEBIAN/control dpkg-gencontrol -psnpomatic -ldebian/changelog -Tdebian/snpomatic.substvars -Pdebian/snpomatic -UMulti-Arch chmod 0644 -- debian/snpomatic/DEBIAN/control chown 0:0 -- debian/snpomatic/DEBIAN/control dh_md5sums cd debian/snpomatic >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/snpomatic/DEBIAN/md5sums chown 0:0 -- debian/snpomatic/DEBIAN/md5sums cd debian/.debhelper/snpomatic/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/snpomatic/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --build debian/snpomatic .. dpkg-deb --build debian/.debhelper/snpomatic/dbgsym-root .. dpkg-deb: building package 'snpomatic' in '../snpomatic_1.0-4_i386.deb'. dpkg-deb: building package 'snpomatic-dbgsym' in '../snpomatic-dbgsym_1.0-4_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../snpomatic_1.0-4_i386.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/23632 and its subdirectories I: Current time: Mon Jul 26 19:40:31 -12 2021 I: pbuilder-time-stamp: 1627371631 Wed Jun 24 01:17:33 UTC 2020 I: 1st build successful. Starting 2nd build on remote node profitbricks-build2-i386.debian.net. Wed Jun 24 01:17:33 UTC 2020 I: Preparing to do remote build '2' on profitbricks-build2-i386.debian.net. Wed Jun 24 01:24:04 UTC 2020 I: Deleting $TMPDIR on profitbricks-build2-i386.debian.net. Wed Jun 24 01:24:05 UTC 2020 I: snpomatic_1.0-4_i386.changes: Format: 1.8 Date: Fri, 06 Jul 2018 18:55:37 +0200 Source: snpomatic Binary: snpomatic snpomatic-dbgsym Architecture: i386 Version: 1.0-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: snpomatic - fast, stringent short-read mapping software Changes: snpomatic (1.0-4) unstable; urgency=medium . * Team upload . [ Steffen Moeller ] * debian/upstream/metadata: Added ref to registry entries . [ Andreas Tille ] * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.4 * Remove unneeded field Testsuite * hardening=+all Checksums-Sha1: 0b3c15abbb49f6b9e040dd8ec4718201c3ed890a 974372 snpomatic-dbgsym_1.0-4_i386.deb f3adcc2c7425459d83171942f4dadb061d4e058f 5158 snpomatic_1.0-4_i386.buildinfo 6126f84dcb268403077fc9f2418fd477a7b58d14 84656 snpomatic_1.0-4_i386.deb Checksums-Sha256: 72b22cd558b002097caf3ea3edb5307c4fb7fc779654d3523203954783ca95ea 974372 snpomatic-dbgsym_1.0-4_i386.deb a01d7340c5ba12488b93e51db4f3783f5309816a8726011220a63a14e46f04f2 5158 snpomatic_1.0-4_i386.buildinfo dd32d93f8583160f0bc70822dd187d71ea0518c09ed811762ed7c686c5c2d6b1 84656 snpomatic_1.0-4_i386.deb Files: ec50325226978ee615ded0732ed5d60b 974372 debug optional snpomatic-dbgsym_1.0-4_i386.deb bae8f8fe0c5a46420a82e844e35c75c5 5158 science optional snpomatic_1.0-4_i386.buildinfo ea753ad906e215913f52b02f2a4c1894 84656 science optional snpomatic_1.0-4_i386.deb Wed Jun 24 01:24:06 UTC 2020 I: diffoscope 148 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.ZHgr5PQQI5/snpomatic_1.0-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.ZHgr5PQQI5/snpomatic_1.0-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.ZHgr5PQQI5/snpomatic_1.0-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.ZHgr5PQQI5/b1/snpomatic_1.0-4_i386.changes /srv/reproducible-results/rbuild-debian/tmp.ZHgr5PQQI5/b2/snpomatic_1.0-4_i386.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: 0.410s) 0.410s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.059s) 0.059s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Wed Jun 24 01:24:08 UTC 2020 I: diffoscope 148 found no differences in the changes files, and a .buildinfo file also exists. Wed Jun 24 01:24:08 UTC 2020 I: snpomatic from buster built successfully and reproducibly on i386. Wed Jun 24 01:24:09 UTC 2020 I: Submitting .buildinfo files to external archives: Wed Jun 24 01:24:09 UTC 2020 I: Submitting 8.0K b1/snpomatic_1.0-4_i386.buildinfo.asc Wed Jun 24 01:24:10 UTC 2020 I: Submitting 8.0K b2/snpomatic_1.0-4_i386.buildinfo.asc Wed Jun 24 01:24:11 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Jun 24 01:24:11 UTC 2020 I: Done submitting .buildinfo files. Wed Jun 24 01:24:11 UTC 2020 I: Removing signed snpomatic_1.0-4_i386.buildinfo.asc files: removed './b1/snpomatic_1.0-4_i386.buildinfo.asc' removed './b2/snpomatic_1.0-4_i386.buildinfo.asc'