Sun Jul 11 13:05:17 UTC 2021 I: starting to build bitseq/buster/amd64 on jenkins on '2021-07-11 13:05' Sun Jul 11 13:05:17 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_27/23291/console.log Sun Jul 11 13:05:17 UTC 2021 I: Downloading source for buster/bitseq=0.7.5+dfsg-4 --2021-07-11 13:05:17-- http://deb.debian.org/debian/pool/main/b/bitseq/bitseq_0.7.5+dfsg-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2039 (2.0K) Saving to: ‘bitseq_0.7.5+dfsg-4.dsc’ 0K . 100% 218M=0s 2021-07-11 13:05:17 (218 MB/s) - ‘bitseq_0.7.5+dfsg-4.dsc’ saved [2039/2039] Sun Jul 11 13:05:17 UTC 2021 I: bitseq_0.7.5+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: bitseq Binary: bitseq Architecture: any Version: 0.7.5+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Tim Booth , Andreas Tille Homepage: https://github.com/BitSeq/BitSeq Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/bitseq Vcs-Git: https://salsa.debian.org/med-team/bitseq.git Build-Depends: debhelper (>= 11~), zlib1g-dev, libbam-dev, libboost-dev, help2man, python, python-numpy Package-List: bitseq deb science optional arch=any Checksums-Sha1: a93fba144039e99acc006846921cb02b61febb47 79132 bitseq_0.7.5+dfsg.orig.tar.xz ec6706a1a61ab437e5e90108bd4a8a0d803adff5 4948 bitseq_0.7.5+dfsg-4.debian.tar.xz Checksums-Sha256: bd48fd14f9687aa4813d5e4f0a8b206616dc7fd9b1060969803f391c9534c04c 79132 bitseq_0.7.5+dfsg.orig.tar.xz bfefc01893198ff320110971ab8483d1baf5c83160ef23df4c6aaa542547c360 4948 bitseq_0.7.5+dfsg-4.debian.tar.xz Files: dbb476c736ab9e1384d55a41dd267336 79132 bitseq_0.7.5+dfsg.orig.tar.xz 47630023339f6a0756162e236aba6ab1 4948 bitseq_0.7.5+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlwc8p8RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGRYBAAmBjRtGypV0WpOnceHBEu7CM/VuILaZMU d5OI1fyLinlVSq5cujNYNZkKbTirPXkrALMtYHrX6mVHjzLRBLYgKPhMmDAUiDqd iXGF9hoyZNAqNGOSkTyOGrxCBqaRZQHwpFyh7V05finfdZnhj4CcGlb9l5sjfdEC jlVudD0BJjv6CXxLGu6+iqtBazyq83DkgstyBOapD5Ao+5HrcUjh494WFNdSD5Si F50X5R9vHco2fJTsnJzBqh5UEoX57FQ/dVbAC8CBtuqP839NWDCJZZp+1/rqTKlk g/PHf4bvpBA6lvi4iRm5+ZvUDLRmHof7LEvBsKwqetNZ//qBhzWYv1+vTgMMGEjs MPTLvSjzA6bMNDmscWiSvFL6vLiZDqysmGvmVQnH5diI+Tf48CnYHMIp6jFZ0kxn Gsm1BiWVyC+CHfFZxtRR1B8coJkZgSAlaWVItSOq54ixc0wV7tNm8CjRDJ/2eplO 8JRCloRer8ojoabgh4NYTb/GI1rTJojYddwlXeSSQiPBf3lJ9EaE0NVYxAn84YBi 99N1p8HOzIeoQCLZC5uAkXelI7JBbR8EiXD6KuJ9NDoElQrFbbekPos2SpVV4xPK KVqwZQ3oT9bar98RljRYSAW5mx1WmpCguby9VuyslC1mSododEXkAYNmCI3myhLP XukowabA6uo= =GByf -----END PGP SIGNATURE----- Sun Jul 11 13:05:17 UTC 2021 I: Checking whether the package is not for us Sun Jul 11 13:05:17 UTC 2021 I: Starting 1st build on remote node ionos1-amd64.debian.net. Sun Jul 11 13:05:17 UTC 2021 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Sun Jul 11 13:06:23 UTC 2021 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jul 11 01:05:19 -12 2021 I: pbuilder-time-stamp: 1626008719 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 [bitseq_0.7.5+dfsg-4.dsc] I: copying [./bitseq_0.7.5+dfsg.orig.tar.xz] I: copying [./bitseq_0.7.5+dfsg-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 Dec 21 02:03:11 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 ./bitseq_0.7.5+dfsg-4.dsc dpkg-source: info: extracting bitseq in bitseq-0.7.5+dfsg dpkg-source: info: unpacking bitseq_0.7.5+dfsg.orig.tar.xz dpkg-source: info: unpacking bitseq_0.7.5+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying link_against_system_samtools.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying fix_clean_target.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying fix_build_options.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4601/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='0305fd1148644d33b6ddbf5b412646d2' 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='4601' 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.2PhDwtzR5e/pbuilderrc_9tMd --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.2PhDwtzR5e/b1 --logfile b1/build.log bitseq_0.7.5+dfsg-4.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos1-amd64 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38984 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 38984 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14328 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 43744 Feb 28 2019 cat -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash -rwxr-xr-x 1 root root 109408 Feb 28 2019 date -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd -rwxr-xr-x 1 root root 93744 Feb 28 2019 df -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir -rwxr-xr-x 1 root root 84288 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 39520 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 35424 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 198976 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 98048 Jan 5 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln -rwxr-xr-x 1 root root 56760 Jul 26 2018 login -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 9 2019 more -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138728 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 39616 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 6 20:24 sh -> dash -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty -rwsr-xr-x 1 root root 63568 Jan 9 2019 su -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch -rwxr-xr-x 1 root root 35424 Feb 28 2019 true -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34896 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/4601/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), zlib1g-dev, libbam-dev, libboost-dev, help2man, python, python-numpy dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 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 zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbam-dev; however: Package libbam-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on python; however: Package python is not installed. pbuilder-satisfydepends-dummy depends on python-numpy; however: Package python-numpy 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: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbam-dev{a} libblas3{a} libboost-dev{a} libboost1.67-dev{a} libbsd0{a} libcroco3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libicu63{a} liblapack3{a} liblocale-gettext-perl{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} libsigsegv2{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{a} po-debconf{a} python{a} python-minimal{a} python-numpy{a} python-pkg-resources{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 59 newly installed, 0 to remove and 0 not upgraded. Need to get 39.1 MB of archives. After unpacking 246 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u6 [1539 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 help2man amd64 1.47.8 [177 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libbam-dev amd64 0.1.19-4 [125 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libboost1.67-dev amd64 1.67.0-13+deb10u1 [8388 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libboost-dev amd64 1.67.0.1 [3864 B] Get: 56 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 python-pkg-resources all 40.8.0-1 [182 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 python-numpy amd64 1:1.16.2-1 [2101 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Fetched 39.1 MB in 1s (64.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. 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Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... 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 ... 20658 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_amd64.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 libblas3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 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:amd64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3+deb10u1) ... 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 liblapack3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:amd64 (2.7.16-1) ... 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:amd64 (2.7.16-1) ... Setting up python (2.7.16-1) ... Setting up python-pkg-resources (40.8.0-1) ... Setting up po-debconf (1.0.21) ... Setting up python-numpy (1:1.16.2-1) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... 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/bitseq-0.7.5+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 bitseq dpkg-buildpackage: info: source version 0.7.5+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 amd64 fakeroot debian/rules clean dh clean dh_auto_clean make -j15 clean make[1]: Entering directory '/build/bitseq-0.7.5+dfsg' rm -f *.o convertSamples estimateDE estimateExpression estimateHyperPar estimateVBExpression extractSamples getFoldChange getGeneExpression getPPLR getVariance getWithinGeneExpression parseAlignment transposeLargeFile make[1]: Leaving directory '/build/bitseq-0.7.5+dfsg' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j15 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bitseq-0.7.5+dfsg' g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c ArgumentParser.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o common.o common.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -ffunction-sections -fdata-sections -c FileHeader.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c misc.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c MyTimer.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TranscriptInfo.o TranscriptInfo.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -ffunction-sections -fdata-sections -c PosteriorSamples.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -c CollapsedSampler.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o GibbsParameters.o GibbsParameters.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -c GibbsSampler.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -c Sampler.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TagAlignments.o TagAlignments.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o transposeFiles.o transposeFiles.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lowess.o lowess.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TranscriptExpression.o TranscriptExpression.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -fopenmp -DSUPPORT_OPENMP -c SimpleSparse.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -fopenmp -DSUPPORT_OPENMP -c VariationalBayes.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -fopenmp -DSUPPORT_OPENMP -c ReadDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TranscriptSequence.o TranscriptSequence.cpp ReadDistribution.cpp: In member function 'bool ReadDistribution::observed(ns_rD::fragmentP)': ReadDistribution.cpp:265:9: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses] (! frag->second->core.flag & BAM_FREVERSE))){ ^~~~~~~~~~~~~~~~~~~~~~~~~ ReadDistribution.cpp: In member function 'bool ReadDistribution::getP(ns_rD::fragmentP, double&, double&)': ReadDistribution.cpp:687:14: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses] (! frag->second->core.flag & BAM_FREVERSE))){ ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections convertSamples.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o TranscriptInfo.o -o convertSamples g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateDE.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o estimateDE g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -fopenmp -DSUPPORT_OPENMP -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o CollapsedSampler.o GibbsParameters.o GibbsSampler.o Sampler.o TagAlignments.o TranscriptInfo.o transposeFiles.o -o estimateExpression g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateHyperPar.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o lowess.o PosteriorSamples.o TranscriptExpression.o -o estimateHyperPar g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -I . -fopenmp -DSUPPORT_OPENMP -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections estimateVBExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o SimpleSparse.o TagAlignments.o TranscriptInfo.o transposeFiles.o VariationalBayes.o -o estimateVBExpression g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections extractSamples.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o extractSamples g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getFoldChange.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o getFoldChange g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getGeneExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o TranscriptInfo.o -o getGeneExpression g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getPPLR.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o getPPLR g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getVariance.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o -o getVariance g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections getWithinGeneExpression.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o PosteriorSamples.o TranscriptInfo.o -o getWithinGeneExpression g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections transposeLargeFile.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o transposeFiles.o -o transposeLargeFile g++ -g -O2 -ffile-prefix-map=/build/bitseq-0.7.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DBS_VERSION=\"0.7.5\" -Wall -O2 -pipe -fopenmp -DSUPPORT_OPENMP -Wl,-z,relro -Wl,-z,now -Wl,-gc-sections -pthread parseAlignment.cpp ArgumentParser.o common.o FileHeader.o misc.o MyTimer.o ReadDistribution.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o -lbam -lz -o parseAlignment make[1]: Leaving directory '/build/bitseq-0.7.5+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/bitseq-0.7.5+dfsg' find -maxdepth 1 -type f -perm /111 -exec dh_install '{}' /usr/bin ';' # Provide scripts with extensions in Debian Med dir and without extension in /usr/bin mkdir -p /build/bitseq-0.7.5+dfsg/debian/bitseq//usr/lib/debian-med/bin rm -f debian/bitseq/usr/bin/releaseDo.sh # internal BitSeq file, not intended for users mv debian/bitseq/usr/bin/*.py debian/bitseq/usr/bin/*.sh /build/bitseq-0.7.5+dfsg/debian/bitseq//usr/lib/debian-med/bin # parseAlignment.py suggests itself not to be used so do not expose this for script in /build/bitseq-0.7.5+dfsg/debian/bitseq//usr/lib/debian-med/bin/* ; do \ bscript=`basename ${script}` ; \ if [ "${bscript}" = "parseAlignment.py" ] ; then continue ; fi ; \ ln -s /usr/lib/debian-med/bin/${bscript} /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//`echo ${bscript} | sed -e 's/\.py$//' -e 's/\.sh$//'` ; \ done make[1]: Leaving directory '/build/bitseq-0.7.5+dfsg' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/bitseq-0.7.5+dfsg' # try to create man pages whereever possible mkdir -p /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1/ help2man --no-info --name='convert or normalize MCMC expression samples' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//convertSamples > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//convertSamples.1 help2man --no-info --name='this bitseq module estimates differential expression from data sets' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//estimateDE > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//estimateDE.1 help2man --no-info --name='estimate expression given precomputed probabilities of (observed) reads'' alignments' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//estimateExpression > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//estimateExpression.1 help2man --no-info --name='estimate expression dependent hyperparameters for bitseq' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//estimateHyperPar > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//estimateHyperPar.1 help2man --no-info --name='estimate expression given precomputed probabilities of (observed) reads'' alignments' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//estimateVBExpression > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//estimateVBExpression.1 help2man --no-info --name='extract MCMC samples of selected transcripts' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//extractSamples > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//extractSamples.1 help2man --no-info --name='computes log_2 Fold Change from MCMC expression samples' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//getFoldChange > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//getFoldChange.1 help2man --no-info --name='compute expression of whole genes' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//getGeneExpression > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//getGeneExpression.1 help2man --no-info --name='compute PPLR from MCMC expression samples' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//getPPLR > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//getPPLR.1 help2man --no-info --name='estimates variance of MCMC samples' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//getVariance > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//getVariance.1 help2man --no-info --name='compute relative expression of transcripts within genes' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//getWithinGeneExpression > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//getWithinGeneExpression.1 help2man --no-info --name='pre\-compute probabilities of (observed) reads'' alignments' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//parseAlignment > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//parseAlignment.1 help2man --no-info --name='helper for bitseq to transpose files lines and columns' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/bin//transposeLargeFile > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//transposeLargeFile.1 help2man --no-info --name='extracts information about transcripts from reference Fasta file' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq//usr/lib/debian-med/bin/extractTranscriptInfo.py > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//extractTranscriptInfo.1 help2man --no-info --name='generate read counts for each input file' \ --version-string="0.7.5+dfsg" --no-discard-stderr \ /build/bitseq-0.7.5+dfsg/debian/bitseq//usr/lib/debian-med/bin/getCounts.py > /build/bitseq-0.7.5+dfsg/debian/bitseq/usr/share/man/man1//getCounts.1 make[1]: Leaving directory '/build/bitseq-0.7.5+dfsg' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'bitseq-dbgsym' in '../bitseq-dbgsym_0.7.5+dfsg-4_amd64.deb'. dpkg-deb: building package 'bitseq' in '../bitseq_0.7.5+dfsg-4_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bitseq_0.7.5+dfsg-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/4601 and its subdirectories I: Current time: Sun Jul 11 01:06:22 -12 2021 I: pbuilder-time-stamp: 1626008782 Sun Jul 11 13:06:23 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Sun Jul 11 13:06:23 UTC 2021 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Sun Jul 11 13:09:21 UTC 2021 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Sun Jul 11 13:09:21 UTC 2021 I: bitseq_0.7.5+dfsg-4_amd64.changes: Format: 1.8 Date: Fri, 21 Dec 2018 14:56:23 +0100 Source: bitseq Binary: bitseq bitseq-dbgsym Architecture: amd64 Version: 0.7.5+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: bitseq - Bayesian Inference of Transcripts from Sequencing Data Changes: bitseq (0.7.5+dfsg-4) unstable; urgency=medium . [ Graham Inggs ] * Link -lbam before -lz to fix build with -Wl,--as-needed . [ Andreas Tille ] * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 * Drop useless get-orig-source target Checksums-Sha1: e26e8a165988f10b2fd5274ff3ad11791a20fc9e 13551452 bitseq-dbgsym_0.7.5+dfsg-4_amd64.deb 59cc4da0f1f6971d51856a57591b1062b085025d 5532 bitseq_0.7.5+dfsg-4_amd64.buildinfo 0cdfe7ec184751f649b2bef90437bfb72813e8be 347904 bitseq_0.7.5+dfsg-4_amd64.deb Checksums-Sha256: 43a35183f70e93037be393021f1a94ffe14551e9e80679fa4c01f95182263a93 13551452 bitseq-dbgsym_0.7.5+dfsg-4_amd64.deb 361726a2540889de8f76b842c71138e5f9f62867a1abbe4009f6080fcae49893 5532 bitseq_0.7.5+dfsg-4_amd64.buildinfo 0b45be20a8b0937d31db3aad9f7d037225abd64d8f135f8a673bb0826766d556 347904 bitseq_0.7.5+dfsg-4_amd64.deb Files: 142fbb20cbf5427d550ca324e74e048d 13551452 debug optional bitseq-dbgsym_0.7.5+dfsg-4_amd64.deb 9fb2fb381903e0169c3f5a5972f61d37 5532 science optional bitseq_0.7.5+dfsg-4_amd64.buildinfo f195643f16e31e69fccce58e6c409118 347904 science optional bitseq_0.7.5+dfsg-4_amd64.deb Sun Jul 11 13:09:22 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.2PhDwtzR5e/bitseq_0.7.5+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.2PhDwtzR5e/bitseq_0.7.5+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.2PhDwtzR5e/bitseq_0.7.5+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.2PhDwtzR5e/b1/bitseq_0.7.5+dfsg-4_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.2PhDwtzR5e/b2/bitseq_0.7.5+dfsg-4_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.442s) 0.442s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.181s) 0.180s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Sun Jul 11 13:09:24 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Sun Jul 11 13:09:24 UTC 2021 I: bitseq from buster built successfully and reproducibly on amd64. Sun Jul 11 13:09:25 UTC 2021 I: Submitting .buildinfo files to external archives: Sun Jul 11 13:09:25 UTC 2021 I: Submitting 8.0K b1/bitseq_0.7.5+dfsg-4_amd64.buildinfo.asc Sun Jul 11 13:09:26 UTC 2021 I: Submitting 8.0K b2/bitseq_0.7.5+dfsg-4_amd64.buildinfo.asc Sun Jul 11 13:09:27 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Jul 11 13:09:27 UTC 2021 I: Done submitting .buildinfo files. Sun Jul 11 13:09:27 UTC 2021 I: Removing signed bitseq_0.7.5+dfsg-4_amd64.buildinfo.asc files: removed './b1/bitseq_0.7.5+dfsg-4_amd64.buildinfo.asc' removed './b2/bitseq_0.7.5+dfsg-4_amd64.buildinfo.asc'