Sat May 9 23:59:40 UTC 2020 I: starting to build bitseq/buster/i386 on jenkins on '2020-05-09 23:59' Sat May 9 23:59:40 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_11/5099/console.log Sat May 9 23:59:40 UTC 2020 I: Downloading source for buster/bitseq=0.7.5+dfsg-4 --2020-05-09 23:59:40-- 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% 166M=0s 2020-05-09 23:59:40 (166 MB/s) - ‘bitseq_0.7.5+dfsg-4.dsc’ saved [2039/2039] Sat May 9 23:59:40 UTC 2020 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----- Sat May 9 23:59:40 UTC 2020 I: Checking whether the package is not for us Sat May 9 23:59:40 UTC 2020 I: Starting 1st build on remote node profitbricks-build2-i386.debian.net. Sat May 9 23:59:40 UTC 2020 I: Preparing to do remote build '1' on profitbricks-build2-i386.debian.net. Sun May 10 00:09:21 UTC 2020 I: Deleting $TMPDIR on profitbricks-build2-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat May 9 11:59:42 -12 2020 I: pbuilder-time-stamp: 1589068782 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 [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 -> 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~), 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 ... 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 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 39.3 MB of archives. After unpacking 246 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 libpython2.7-minimal i386 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main i386 python2.7-minimal i386 2.7.16-2+deb10u1 [1381 kB] Get: 9 http://deb.debian.org/debian buster/main i386 python2-minimal i386 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main i386 python-minimal i386 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main i386 libssl1.1 i386 1.1.1d-0+deb10u3 [1537 kB] Get: 12 http://deb.debian.org/debian buster/main i386 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main i386 libexpat1 i386 2.2.6-2+deb10u1 [104 kB] Get: 14 http://deb.debian.org/debian buster/main i386 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main i386 libreadline7 i386 7.0-5 [156 kB] Get: 16 http://deb.debian.org/debian buster/main i386 libpython2.7-stdlib i386 2.7.16-2+deb10u1 [1934 kB] Get: 17 http://deb.debian.org/debian buster/main i386 python2.7 i386 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main i386 libpython2-stdlib i386 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main i386 libpython-stdlib i386 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main i386 python2 i386 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main i386 python i386 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main i386 liblocale-gettext-perl i386 1.07-3+b4 [19.3 kB] Get: 23 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 24 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 25 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 26 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 27 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 28 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 29 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 30 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 31 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 32 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 33 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 34 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 35 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 36 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 37 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 38 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 39 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 40 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 41 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 42 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6+deb10u1 [8451 kB] Get: 43 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 44 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 45 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 46 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 47 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 48 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 49 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Get: 50 http://deb.debian.org/debian buster/main i386 help2man i386 1.47.8 [177 kB] Get: 51 http://deb.debian.org/debian buster/main i386 libbam-dev i386 0.1.19-4 [136 kB] Get: 52 http://deb.debian.org/debian buster/main i386 libgfortran5 i386 8.3.0-6 [549 kB] Get: 53 http://deb.debian.org/debian buster/main i386 libblas3 i386 3.8.0-2 [142 kB] Get: 54 http://deb.debian.org/debian buster/main i386 libboost1.67-dev i386 1.67.0-13+deb10u1 [8388 kB] Get: 55 http://deb.debian.org/debian buster/main i386 libboost-dev i386 1.67.0.1 [3864 B] Get: 56 http://deb.debian.org/debian buster/main i386 liblapack3 i386 3.8.0-2 [1974 kB] Get: 57 http://deb.debian.org/debian buster/main i386 python-pkg-resources all 40.8.0-1 [182 kB] Get: 58 http://deb.debian.org/debian buster/main i386 python-numpy i386 1:1.16.2-1 [2096 kB] Get: 59 http://deb.debian.org/debian buster/main i386 zlib1g-dev i386 1:1.2.11.dfsg-1 [216 kB] Fetched 39.3 MB in 17s (2323 kB/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 libpython2.7-minimal:i386. Preparing to unpack .../06-libpython2.7-minimal_2.7.16-2+deb10u1_i386.deb ... Unpacking libpython2.7-minimal:i386 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../07-python2.7-minimal_2.7.16-2+deb10u1_i386.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u1) ... Selecting previously unselected package python2-minimal. Preparing to unpack .../08-python2-minimal_2.7.16-1_i386.deb ... Unpacking python2-minimal (2.7.16-1) ... Selecting previously unselected package python-minimal. Preparing to unpack .../09-python-minimal_2.7.16-1_i386.deb ... Unpacking python-minimal (2.7.16-1) ... Selecting previously unselected package libssl1.1:i386. Preparing to unpack .../10-libssl1.1_1.1.1d-0+deb10u3_i386.deb ... Unpacking libssl1.1:i386 (1.1.1d-0+deb10u3) ... Selecting previously unselected package mime-support. Preparing to unpack .../11-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../12-libexpat1_2.2.6-2+deb10u1_i386.deb ... Unpacking libexpat1:i386 (2.2.6-2+deb10u1) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:i386. Preparing to unpack .../14-libreadline7_7.0-5_i386.deb ... Unpacking libreadline7:i386 (7.0-5) ... Selecting previously unselected package libpython2.7-stdlib:i386. Preparing to unpack .../15-libpython2.7-stdlib_2.7.16-2+deb10u1_i386.deb ... Unpacking libpython2.7-stdlib:i386 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7. Preparing to unpack .../16-python2.7_2.7.16-2+deb10u1_i386.deb ... Unpacking python2.7 (2.7.16-2+deb10u1) ... Selecting previously unselected package libpython2-stdlib:i386. Preparing to unpack .../17-libpython2-stdlib_2.7.16-1_i386.deb ... Unpacking libpython2-stdlib:i386 (2.7.16-1) ... Selecting previously unselected package libpython-stdlib:i386. Preparing to unpack .../18-libpython-stdlib_2.7.16-1_i386.deb ... Unpacking libpython-stdlib:i386 (2.7.16-1) ... Setting up libpython2.7-minimal:i386 (2.7.16-2+deb10u1) ... 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 ... 20699 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_i386.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (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 ... 20732 files and directories currently installed.) Preparing to unpack .../00-python_2.7.16-1_i386.deb ... Unpacking python (2.7.16-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../01-liblocale-gettext-perl_1.07-3+b4_i386.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../04-libmagic1_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic1:i386 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.35-4+deb10u1_i386.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.19.8.1-9_i386.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../07-libsigsegv2_2.12-2_i386.deb ... Unpacking libsigsegv2:i386 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../08-m4_1.4.18-2_i386.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../09-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../10-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../11-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../12-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../13-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../14-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../15-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../16-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../17-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../18-libelf1_0.176-1.1_i386.deb ... Unpacking libelf1:i386 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../19-dwz_0.12-3_i386.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:i386. Preparing to unpack .../20-libglib2.0-0_2.58.3-2+deb10u2_i386.deb ... Unpacking libglib2.0-0:i386 (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:i386. Preparing to unpack .../21-libicu63_63.1-6+deb10u1_i386.deb ... Unpacking libicu63:i386 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../22-libxml2_2.9.4+dfsg1-7+b3_i386.deb ... Unpacking libxml2:i386 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:i386. Preparing to unpack .../23-libcroco3_0.6.12-3_i386.deb ... Unpacking libcroco3:i386 (0.6.12-3) ... Selecting previously unselected package libncurses6:i386. Preparing to unpack .../24-libncurses6_6.1+20181013-2+deb10u2_i386.deb ... Unpacking libncurses6:i386 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.19.8.1-9_i386.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package help2man. Preparing to unpack .../29-help2man_1.47.8_i386.deb ... Unpacking help2man (1.47.8) ... Selecting previously unselected package libbam-dev. Preparing to unpack .../30-libbam-dev_0.1.19-4_i386.deb ... Unpacking libbam-dev (0.1.19-4) ... Selecting previously unselected package libgfortran5:i386. Preparing to unpack .../31-libgfortran5_8.3.0-6_i386.deb ... Unpacking libgfortran5:i386 (8.3.0-6) ... Selecting previously unselected package libblas3:i386. Preparing to unpack .../32-libblas3_3.8.0-2_i386.deb ... Unpacking libblas3:i386 (3.8.0-2) ... Selecting previously unselected package libboost1.67-dev:i386. Preparing to unpack .../33-libboost1.67-dev_1.67.0-13+deb10u1_i386.deb ... Unpacking libboost1.67-dev:i386 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-dev:i386. Preparing to unpack .../34-libboost-dev_1.67.0.1_i386.deb ... Unpacking libboost-dev:i386 (1.67.0.1) ... Selecting previously unselected package liblapack3:i386. Preparing to unpack .../35-liblapack3_3.8.0-2_i386.deb ... Unpacking liblapack3:i386 (3.8.0-2) ... Selecting previously unselected package python-pkg-resources. Preparing to unpack .../36-python-pkg-resources_40.8.0-1_all.deb ... Unpacking python-pkg-resources (40.8.0-1) ... Selecting previously unselected package python-numpy. Preparing to unpack .../37-python-numpy_1%3a1.16.2-1_i386.deb ... Unpacking python-numpy (1:1.16.2-1) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../38-zlib1g-dev_1%3a1.2.11.dfsg-1_i386.deb ... Unpacking zlib1g-dev:i386 (1:1.2.11.dfsg-1) ... Setting up libboost1.67-dev:i386 (1.67.0-13+deb10u1) ... Setting up libexpat1:i386 (2.2.6-2+deb10u1) ... Setting up libpipeline1:i386 (1.5.1-2) ... Setting up mime-support (3.62) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:i386 (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libssl1.1:i386 (1.1.1d-0+deb10u3) ... Setting up libmagic1:i386 (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libicu63:i386 (63.1-6+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:i386 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:i386 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libbam-dev (0.1.19-4) ... Setting up libgfortran5:i386 (8.3.0-6) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:i386 (0.0.6-3) ... Setting up libboost-dev:i386 (1.67.0.1) ... Setting up libbsd0:i386 (0.9.1-2) ... Setting up libelf1:i386 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:i386 (2.9.4+dfsg1-7+b3) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up libreadline7:i386 (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:i386 (2.7.16-2+deb10u1) ... Setting up help2man (1.47.8) ... Setting up libblas3:i386 (3.8.0-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-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:i386 (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 liblapack3:i386 (3.8.0-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-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:i386 (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:i386 (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 i386 fakeroot debian/rules clean dh clean dh_auto_clean make -j10 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 -j10 "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 In file included from TranscriptInfo.cpp:6: TranscriptInfo.cpp: In member function 'bool TranscriptInfo::updateGeneNames(const std::vector >&)': TranscriptInfo.cpp:228:15: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] warning("TranscriptInfo: Number of items in gene list (%ld) does not match number of transcripts (%ld).",geneList.size(),M); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ common.h:32:67: note: in definition of macro 'warning' #define warning(...) {fprintf(stderr,"WARNING: ");fprintf(stderr, __VA_ARGS__);} ^~~~~~~~~~~ TranscriptInfo.cpp: In member function 'bool TranscriptInfo::updateGeneNames(const std::map, std::__cxx11::basic_string >&)': TranscriptInfo.cpp:241:15: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::map, std::__cxx11::basic_string >::size_type' {aka 'unsigned int'} [-Wformat=] warning("TranscriptInfo: Number of items in TR->GE map (%ld) is less than the number of transcripts (%ld).",trGeneList.size(),M); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~ common.h:32:67: note: in definition of macro 'warning' #define warning(...) {fprintf(stderr,"WARNING: ");fprintf(stderr, __VA_ARGS__);} ^~~~~~~~~~~ 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 -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 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 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_i386.deb'. dpkg-deb: building package 'bitseq' in '../bitseq_0.7.5+dfsg-4_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bitseq_0.7.5+dfsg-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/20443 and its subdirectories I: Current time: Sat May 9 12:09:21 -12 2020 I: pbuilder-time-stamp: 1589069361 Sun May 10 00:09:21 UTC 2020 I: 1st build successful. Starting 2nd build on remote node profitbricks-build16-i386.debian.net. Sun May 10 00:09:22 UTC 2020 I: Preparing to do remote build '2' on profitbricks-build16-i386.debian.net. Sun May 10 00:10:06 UTC 2020 I: Deleting $TMPDIR on profitbricks-build16-i386.debian.net. Sun May 10 00:10:07 UTC 2020 I: bitseq_0.7.5+dfsg-4_i386.changes: Format: 1.8 Date: Fri, 21 Dec 2018 14:56:23 +0100 Source: bitseq Binary: bitseq bitseq-dbgsym Architecture: i386 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: 04c5d0efdb36ffdc38bc52fb064b8ba383ec31fc 12933912 bitseq-dbgsym_0.7.5+dfsg-4_i386.deb 709cce489d76bc1a28e0602ab44ec0d7eeb2215c 5447 bitseq_0.7.5+dfsg-4_i386.buildinfo c1f5a32b2f68e7fd3f4f2355aba2f16792bd3d9a 366932 bitseq_0.7.5+dfsg-4_i386.deb Checksums-Sha256: 0d2e6ea07892cadce29bbf97da19007dcc6f1115bf777b5993f8905eae0f1f05 12933912 bitseq-dbgsym_0.7.5+dfsg-4_i386.deb b83c40922f95c608a87c10b487ecf98c10eccfb762063265a516d07501eea094 5447 bitseq_0.7.5+dfsg-4_i386.buildinfo 7d4302bccb5ca87146d56116b919df384b1e34549f2250702b9603e63ee0f4be 366932 bitseq_0.7.5+dfsg-4_i386.deb Files: 90028075e764466ca1974e2b4c2d1f4f 12933912 debug optional bitseq-dbgsym_0.7.5+dfsg-4_i386.deb 30075a05957b55cb2a74263f70706631 5447 science optional bitseq_0.7.5+dfsg-4_i386.buildinfo 3bff38b61af5699e8537662fba4e521c 366932 science optional bitseq_0.7.5+dfsg-4_i386.deb Sun May 10 00:10:08 UTC 2020 I: diffoscope 143 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.twU3Ae5O8v/bitseq_0.7.5+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.twU3Ae5O8v/bitseq_0.7.5+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.twU3Ae5O8v/bitseq_0.7.5+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.twU3Ae5O8v/b1/bitseq_0.7.5+dfsg-4_i386.changes /srv/reproducible-results/rbuild-debian/tmp.twU3Ae5O8v/b2/bitseq_0.7.5+dfsg-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: 0.407s) 0.407s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.166s) 0.166s 10 calls diffoscope.comparators.binary.FilesystemFile Sun May 10 00:10:12 UTC 2020 I: diffoscope 143 found no differences in the changes files, and a .buildinfo file also exists. Sun May 10 00:10:12 UTC 2020 I: bitseq from buster built successfully and reproducibly on i386. Sun May 10 00:10:13 UTC 2020 I: Submitting .buildinfo files to external archives: Sun May 10 00:10:13 UTC 2020 I: Submitting 8.0K b1/bitseq_0.7.5+dfsg-4_i386.buildinfo.asc Sun May 10 00:10:14 UTC 2020 I: Submitting 8.0K b2/bitseq_0.7.5+dfsg-4_i386.buildinfo.asc Sun May 10 00:10:15 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun May 10 00:10:15 UTC 2020 I: Done submitting .buildinfo files. Sun May 10 00:10:15 UTC 2020 I: Removing signed bitseq_0.7.5+dfsg-4_i386.buildinfo.asc files: removed './b1/bitseq_0.7.5+dfsg-4_i386.buildinfo.asc' removed './b2/bitseq_0.7.5+dfsg-4_i386.buildinfo.asc'