Wed Jul 10 17:36:38 UTC 2019 I: starting to build dindel/buster/i386 on jenkins on '2019-07-10 17:36' Wed Jul 10 17:36:38 UTC 2019 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_15/252/console.log Wed Jul 10 17:36:38 UTC 2019 I: Downloading source for buster/dindel=1.01-wu1-3+dfsg-1 --2019-07-10 17:36:38-- http://deb.debian.org/debian/pool/main/d/dindel/dindel_1.01-wu1-3+dfsg-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 302 Found Location: http://cdn-fastly.deb.debian.org/debian/pool/main/d/dindel/dindel_1.01-wu1-3+dfsg-1.dsc [following] --2019-07-10 17:36:38-- http://cdn-fastly.deb.debian.org/debian/pool/main/d/dindel/dindel_1.01-wu1-3+dfsg-1.dsc Reusing existing connection to 78.137.99.97:3128. Proxy request sent, awaiting response... 200 OK Length: 2154 (2.1K) Saving to: ‘dindel_1.01-wu1-3+dfsg-1.dsc’ 0K .. 100% 87.8M=0s 2019-07-10 17:36:38 (87.8 MB/s) - ‘dindel_1.01-wu1-3+dfsg-1.dsc’ saved [2154/2154] Wed Jul 10 17:36:38 UTC 2019 I: dindel_1.01-wu1-3+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: dindel Binary: dindel Architecture: any Version: 1.01-wu1-3+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Animesh Sharma , Steffen Moeller , Andreas Tille Homepage: https://github.com/genome/dindel-tgi Standards-Version: 4.2.0 Vcs-Browser: https://salsa.debian.org/med-team/dindel Vcs-Git: https://salsa.debian.org/med-team/dindel.git Build-Depends: debhelper (>= 11~), seqan-dev (>= 1.4.1), libbam-dev, libboost-program-options-dev, libboost-math-dev, zlib1g-dev Package-List: dindel deb science optional arch=any Checksums-Sha1: 6086e661ffb1d15249cd8f287ab99cac545b6ed2 96376 dindel_1.01-wu1-3+dfsg.orig.tar.xz e0b587ca5dc8ab8d0794f0ad1ae0bb98fb610adf 6516 dindel_1.01-wu1-3+dfsg-1.debian.tar.xz Checksums-Sha256: 928808be1d71fc899bd5a790a17f1f8e09b94759e9790b20ba9ec16e63e00f1a 96376 dindel_1.01-wu1-3+dfsg.orig.tar.xz 447b55126d24aca7b27c743da2af2145a16efed167b9c338ccb5e63f43e9841e 6516 dindel_1.01-wu1-3+dfsg-1.debian.tar.xz Files: f0ab8e63c9eebb546a1c96185104654d 96376 dindel_1.01-wu1-3+dfsg.orig.tar.xz 3d8ea4762e2bf9236d29ae2fd62a813c 6516 dindel_1.01-wu1-3+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAltxdEcRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGQJhAAlT2+rrcI72Ai9q6ADx+Uy+OHYndPqCvs XgiZc12aEcsAGuxVqUsIUR9dAn9A0gsfuImOJnT0CoaRPNZYfiHWGqoeAi4ILuMu T2iAu/SfoQ9rjh0QDGROATy4TMBuZ9pvjy5FFI8Mlu+xzKbOTCj0ZiHzHLkQiEeh eCduABuqJP4B/T6EhhST5kPu2WJ2BYilBrQTXLb0i7iT6oYdqpp2MxWERwgNztlE o8QlgVmlhyKlX/HNsxm/whjxvdLVnqT9O6HqW2vjxaQ1uiy30SQ6ft8fGGdmHZP5 FZzx+SZXQPsjN/4DchYJHCZRG4n/UemJHnu54KRTVmW4dFQ2/VeCCtMLQzPTJvyw Lk7BLcKdeVxPTuM5YTuacyzwGUJzZdHok/ZNmy9JXD3k5o8UnFyCBrOcl4z7Xvtu dhxP5kTvJ3lECk6FzswfZZEpiNMX6ba8JYJ3VABCx3SnRsvIz6U1Xphdu3p+YeaT EFUi/0lSTbx8cRVQHa3mFQ1yMx0RS8DRxT9DvrLpGW2a/Ewenu4hVBG23rLv3lr1 zuut0YRmfJMpQWzkAW+k4t2Z0J4wZrykWmtG3fEewf+e1KvRk5Oxymr+a2C1bC6/ kqMXpMKo09PljrbaaIetLAPgBiRekO0wBybjRFiXqL4oCT6g3GmZYzyJnCU/Stpi f6vQNahDoGI= =zooF -----END PGP SIGNATURE----- Wed Jul 10 17:36:38 UTC 2019 I: Checking whether the package is not for us Wed Jul 10 17:36:38 UTC 2019 I: Starting 1st build on remote node profitbricks-build12-i386.debian.net. Wed Jul 10 17:36:38 UTC 2019 I: Preparing to do remote build '1' on profitbricks-build12-i386.debian.net. Wed Jul 10 17:51:58 UTC 2019 I: Deleting $TMPDIR on profitbricks-build12-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Jul 10 05:36:40 -12 2019 I: pbuilder-time-stamp: 1562780200 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 [dindel_1.01-wu1-3+dfsg-1.dsc] I: copying [./dindel_1.01-wu1-3+dfsg.orig.tar.xz] I: copying [./dindel_1.01-wu1-3+dfsg-1.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 Mon Aug 13 00:06:31 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 ./dindel_1.01-wu1-3+dfsg-1.dsc dpkg-source: info: extracting dindel in dindel-1.01-wu1-3+dfsg dpkg-source: info: unpacking dindel_1.01-wu1-3+dfsg.orig.tar.xz dpkg-source: info: unpacking dindel_1.01-wu1-3+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying modernize-Makefile.patch dpkg-source: info: applying compiler_errors.patch dpkg-source: info: applying fix-ftbfs-with-gcc6.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~), seqan-dev (>= 1.4.1), libbam-dev, libboost-program-options-dev, libboost-math-dev, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19231 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 seqan-dev (>= 1.4.1); however: Package seqan-dev is not installed. pbuilder-satisfydepends-dummy depends on libbam-dev; however: Package libbam-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-math-dev; however: Package libboost-math-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev 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} intltool-debian{a} libarchive-zip-perl{a} libbam-dev{a} libboost-math-dev{a} libboost-math1.67-dev{a} libboost-math1.67.0{a} libboost-program-options-dev{a} libboost-program-options1.67-dev{a} libboost-program-options1.67.0{a} libboost1.67-dev{a} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libsigsegv2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} seqan-dev{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, 43 newly installed, 0 to remove and 0 not upgraded. Need to get 31.1 MB of archives. After unpacking 233 MB will be used. Writing extended state information... Get: 1 http://cdn-fastly.deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://cdn-fastly.deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://cdn-fastly.deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://cdn-fastly.deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://cdn-fastly.deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://cdn-fastly.deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://cdn-fastly.deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://cdn-fastly.deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4 [242 kB] Get: 9 http://cdn-fastly.deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4 [124 kB] Get: 10 http://cdn-fastly.deb.debian.org/debian buster/main i386 file i386 1:5.35-4 [66.3 kB] Get: 11 http://cdn-fastly.deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 12 http://cdn-fastly.deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 13 http://cdn-fastly.deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 14 http://cdn-fastly.deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 15 http://cdn-fastly.deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://cdn-fastly.deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 17 http://cdn-fastly.deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://cdn-fastly.deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 19 http://cdn-fastly.deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 20 http://cdn-fastly.deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://cdn-fastly.deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://cdn-fastly.deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://cdn-fastly.deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 24 http://cdn-fastly.deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 25 http://cdn-fastly.deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2 [1333 kB] Get: 26 http://cdn-fastly.deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6 [8443 kB] Get: 27 http://cdn-fastly.deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 28 http://cdn-fastly.deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 29 http://cdn-fastly.deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2 [109 kB] Get: 30 http://cdn-fastly.deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 31 http://cdn-fastly.deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://cdn-fastly.deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 33 http://cdn-fastly.deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Get: 34 http://cdn-fastly.deb.debian.org/debian buster/main i386 libbam-dev i386 0.1.19-4 [136 kB] Get: 35 http://cdn-fastly.deb.debian.org/debian buster/main i386 libboost1.67-dev i386 1.67.0-13 [8386 kB] Get: 36 http://cdn-fastly.deb.debian.org/debian buster/main i386 libboost-math1.67.0 i386 1.67.0-13 [435 kB] Get: 37 http://cdn-fastly.deb.debian.org/debian buster/main i386 libboost-math1.67-dev i386 1.67.0-13 [711 kB] Get: 38 http://cdn-fastly.deb.debian.org/debian buster/main i386 libboost-math-dev i386 1.67.0.1 [3848 B] Get: 39 http://cdn-fastly.deb.debian.org/debian buster/main i386 libboost-program-options1.67.0 i386 1.67.0-13 [363 kB] Get: 40 http://cdn-fastly.deb.debian.org/debian buster/main i386 libboost-program-options1.67-dev i386 1.67.0-13 [393 kB] Get: 41 http://cdn-fastly.deb.debian.org/debian buster/main i386 libboost-program-options-dev i386 1.67.0.1 [3660 B] Get: 42 http://cdn-fastly.deb.debian.org/debian buster/main i386 seqan-dev all 1.4.2+dfsg-3 [1096 kB] Get: 43 http://cdn-fastly.deb.debian.org/debian buster/main i386 zlib1g-dev i386 1:1.2.11.dfsg-1 [216 kB] Fetched 31.1 MB in 30s (1047 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 ... 19231 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 sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4_i386.deb ... Unpacking libmagic-mgc (1:5.35-4) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../08-libmagic1_1%3a5.35-4_i386.deb ... Unpacking libmagic1:i386 (1:5.35-4) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4_i386.deb ... Unpacking file (1:5.35-4) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-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 .../11-libsigsegv2_2.12-2_i386.deb ... Unpacking libsigsegv2:i386 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_i386.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-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 .../20-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 .../21-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 .../22-libelf1_0.176-1.1_i386.deb ... Unpacking libelf1:i386 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.12-3_i386.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:i386. Preparing to unpack .../24-libglib2.0-0_2.58.3-2_i386.deb ... Unpacking libglib2.0-0:i386 (2.58.3-2) ... Selecting previously unselected package libicu63:i386. Preparing to unpack .../25-libicu63_63.1-6_i386.deb ... Unpacking libicu63:i386 (63.1-6) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../26-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 .../27-libcroco3_0.6.12-3_i386.deb ... Unpacking libcroco3:i386 (0.6.12-3) ... Selecting previously unselected package libncurses6:i386. Preparing to unpack .../28-libncurses6_6.1+20181013-2_i386.deb ... Unpacking libncurses6:i386 (6.1+20181013-2) ... Selecting previously unselected package gettext. Preparing to unpack .../29-gettext_0.19.8.1-9_i386.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../30-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 .../31-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../32-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package libbam-dev. Preparing to unpack .../33-libbam-dev_0.1.19-4_i386.deb ... Unpacking libbam-dev (0.1.19-4) ... Selecting previously unselected package libboost1.67-dev:i386. Preparing to unpack .../34-libboost1.67-dev_1.67.0-13_i386.deb ... Unpacking libboost1.67-dev:i386 (1.67.0-13) ... Selecting previously unselected package libboost-math1.67.0:i386. Preparing to unpack .../35-libboost-math1.67.0_1.67.0-13_i386.deb ... Unpacking libboost-math1.67.0:i386 (1.67.0-13) ... Selecting previously unselected package libboost-math1.67-dev:i386. Preparing to unpack .../36-libboost-math1.67-dev_1.67.0-13_i386.deb ... Unpacking libboost-math1.67-dev:i386 (1.67.0-13) ... Selecting previously unselected package libboost-math-dev:i386. Preparing to unpack .../37-libboost-math-dev_1.67.0.1_i386.deb ... Unpacking libboost-math-dev:i386 (1.67.0.1) ... Selecting previously unselected package libboost-program-options1.67.0:i386. Preparing to unpack .../38-libboost-program-options1.67.0_1.67.0-13_i386.deb ... Unpacking libboost-program-options1.67.0:i386 (1.67.0-13) ... Selecting previously unselected package libboost-program-options1.67-dev:i386. Preparing to unpack .../39-libboost-program-options1.67-dev_1.67.0-13_i386.deb ... Unpacking libboost-program-options1.67-dev:i386 (1.67.0-13) ... Selecting previously unselected package libboost-program-options-dev:i386. Preparing to unpack .../40-libboost-program-options-dev_1.67.0.1_i386.deb ... Unpacking libboost-program-options-dev:i386 (1.67.0.1) ... Selecting previously unselected package seqan-dev. Preparing to unpack .../41-seqan-dev_1.4.2+dfsg-3_all.deb ... Unpacking seqan-dev (1.4.2+dfsg-3) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../42-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) ... Setting up libboost-program-options1.67.0:i386 (1.67.0-13) ... Setting up libpipeline1:i386 (1.5.1-2) ... Setting up libmagic-mgc (1:5.35-4) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libboost-program-options1.67-dev:i386 (1.67.0-13) ... Setting up libglib2.0-0:i386 (2.58.3-2) ... No schema files found: doing nothing. Setting up libmagic1:i386 (1:5.35-4) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4) ... Setting up libboost-math1.67.0:i386 (1.67.0-13) ... Setting up libicu63:i386 (63.1-6) ... Setting up autotools-dev (20180224.1) ... Setting up libboost-program-options-dev:i386 (1.67.0.1) ... Setting up libncurses6:i386 (6.1+20181013-2) ... 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 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 libbsd0:i386 (0.9.1-2) ... Setting up libelf1:i386 (0.176-1.1) ... Setting up libxml2:i386 (2.9.4+dfsg1-7+b3) ... Setting up seqan-dev (1.4.2+dfsg-3) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libboost-math1.67-dev:i386 (1.67.0-13) ... Setting up libtool (2.4.6-9) ... Setting up libboost-math-dev:i386 (1.67.0.1) ... Setting up m4 (1.4.18-2) ... 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 gettext (0.19.8.1-9) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... 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/dindel-1.01-wu1-3+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 dindel dpkg-buildpackage: info: source version 1.01-wu1-3+dfsg-1 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 distclean make[1]: Entering directory '/build/dindel-1.01-wu1-3+dfsg' rm -f DInDel.o HapBlock.o HaplotypeDistribution.o ObservationModelFB.o GetCandidates.o Faster.o *.o rm -f dindel make[1]: Leaving directory '/build/dindel-1.01-wu1-3+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/dindel-1.01-wu1-3+dfsg' g++ -g -O2 -ffile-prefix-map=/build/dindel-1.01-wu1-3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/samtools -I/usr/include/seqan -I./ -Wno-deprecated -O3 -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL -c -o DInDel.o DInDel.cpp g++ -g -O2 -ffile-prefix-map=/build/dindel-1.01-wu1-3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/samtools -I/usr/include/seqan -I./ -Wno-deprecated -O3 -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL -c -o HapBlock.o HapBlock.cpp g++ -g -O2 -ffile-prefix-map=/build/dindel-1.01-wu1-3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/samtools -I/usr/include/seqan -I./ -Wno-deprecated -O3 -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL -c -o HaplotypeDistribution.o HaplotypeDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/dindel-1.01-wu1-3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/samtools -I/usr/include/seqan -I./ -Wno-deprecated -O3 -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL -c -o ObservationModelFB.o ObservationModelFB.cpp g++ -g -O2 -ffile-prefix-map=/build/dindel-1.01-wu1-3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/samtools -I/usr/include/seqan -I./ -Wno-deprecated -O3 -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL -c -o GetCandidates.o GetCandidates.cpp g++ -g -O2 -ffile-prefix-map=/build/dindel-1.01-wu1-3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/samtools -I/usr/include/seqan -I./ -Wno-deprecated -O3 -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL -c -o Faster.o Faster.cpp DInDel.cpp: In member function 'void DetInDel::empiricalDistributionMethod(int, const std::vector&, uint32_t, uint32_t, uint32_t, const AlignedCandidates&, OutputData&, OutputData&)': DInDel.cpp:525:12: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(cmd.str().c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~ DInDel.cpp:629:12: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(cmd.str().c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~ g++ -o dindel -g -O2 -ffile-prefix-map=/build/dindel-1.01-wu1-3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/samtools -I/usr/include/seqan -I./ -Wno-deprecated -O3 -std=gnu++98 DInDel.o HapBlock.o HaplotypeDistribution.o ObservationModelFB.o GetCandidates.o Faster.o -Wl,-z,relro -Wl,-z,now -lbam -lz -lboost_program_options -lpthread make[1]: Leaving directory '/build/dindel-1.01-wu1-3+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install make -j10 install DESTDIR=/build/dindel-1.01-wu1-3\+dfsg/debian/dindel AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/dindel-1.01-wu1-3+dfsg' install -d /build/dindel-1.01-wu1-3+dfsg/debian/dindel/usr/bin /build/dindel-1.01-wu1-3+dfsg/debian/dindel/usr/share/dindel install dindel /build/dindel-1.01-wu1-3+dfsg/debian/dindel/usr/bin cp -dr --no-preserve=ownership python/* /build/dindel-1.01-wu1-3+dfsg/debian/dindel/usr/share/dindel/ make[1]: Leaving directory '/build/dindel-1.01-wu1-3+dfsg' dh_install dh_installdocs dh_installchangelogs dh_installman 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 'dindel-dbgsym' in '../dindel-dbgsym_1.01-wu1-3+dfsg-1_i386.deb'. dpkg-deb: building package 'dindel' in '../dindel_1.01-wu1-3+dfsg-1_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../dindel_1.01-wu1-3+dfsg-1_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/11009 and its subdirectories I: Current time: Wed Jul 10 05:51:57 -12 2019 I: pbuilder-time-stamp: 1562781117 Wed Jul 10 17:51:58 UTC 2019 I: 1st build successful. Starting 2nd build on remote node profitbricks-build16-i386.debian.net. Wed Jul 10 17:51:58 UTC 2019 I: Preparing to do remote build '2' on profitbricks-build16-i386.debian.net. Wed Jul 10 17:52:59 UTC 2019 I: Deleting $TMPDIR on profitbricks-build16-i386.debian.net. Wed Jul 10 17:53:00 UTC 2019 I: dindel_1.01-wu1-3+dfsg-1_i386.changes: Format: 1.8 Date: Mon, 13 Aug 2018 14:03:51 +0200 Source: dindel Binary: dindel dindel-dbgsym Architecture: i386 Version: 1.01-wu1-3+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: dindel - determines indel calls from short-read data Changes: dindel (1.01-wu1-3+dfsg-1) unstable; urgency=medium . [ Steffen Moeller ] * [debian/upstream/metadata] Added registry ref to OMICtools, bio.tools, RRID . [ Andreas Tille ] * New upstream version * Package dindel-tgi since this seems to be actively maintained and contains some sensible enhancement. * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.0 * Update copyright Checksums-Sha1: da30948ad3bfcb0c50cfb447dfbbecbdf70f8028 4682120 dindel-dbgsym_1.01-wu1-3+dfsg-1_i386.deb 5755fd93c2c0bb47d80f6a8c010935d5249c1749 4889 dindel_1.01-wu1-3+dfsg-1_i386.buildinfo fff70ec01653194096779ca7e2749c2f39d41b78 382008 dindel_1.01-wu1-3+dfsg-1_i386.deb Checksums-Sha256: b79c086373c357374a93f64f9f4c1a475d9c7b83efef4a5750c6c6251325dfec 4682120 dindel-dbgsym_1.01-wu1-3+dfsg-1_i386.deb 28dd8eb81b75c03262b518796b53ab4e23085425ba67cd3f05fc640c6bb7459a 4889 dindel_1.01-wu1-3+dfsg-1_i386.buildinfo b466a248890aca302c90f4a47ed786389c1f08085958064b7382aa8953a850eb 382008 dindel_1.01-wu1-3+dfsg-1_i386.deb Files: d12442a0aa68a03772181fb04465bd26 4682120 debug optional dindel-dbgsym_1.01-wu1-3+dfsg-1_i386.deb 237abc9f59a0503e8e7a9c6c29b63eee 4889 science optional dindel_1.01-wu1-3+dfsg-1_i386.buildinfo e2d7bc7687c1642bfa01502b8de5ce5a 382008 science optional dindel_1.01-wu1-3+dfsg-1_i386.deb Wed Jul 10 17:53:01 UTC 2019 I: diffoscope 117 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.8l1wZ0kXxc/dindel_1.01-wu1-3+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.8l1wZ0kXxc/dindel_1.01-wu1-3+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.8l1wZ0kXxc/dindel_1.01-wu1-3+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.8l1wZ0kXxc/b1/dindel_1.01-wu1-3+dfsg-1_i386.changes /srv/reproducible-results/rbuild-debian/tmp.8l1wZ0kXxc/b2/dindel_1.01-wu1-3+dfsg-1_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: 0.699s) 0.699s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.378s) 0.378s 10 calls diffoscope.comparators.binary.FilesystemFile Wed Jul 10 17:53:03 UTC 2019 I: diffoscope 117 found no differences in the changes files, and a .buildinfo file also exists. Wed Jul 10 17:53:03 UTC 2019 I: dindel from buster built successfully and reproducibly on i386. Wed Jul 10 17:53:06 UTC 2019 I: Submitting .buildinfo files to external archives: Wed Jul 10 17:53:06 UTC 2019 I: Submitting 8.0K b1/dindel_1.01-wu1-3+dfsg-1_i386.buildinfo.asc Wed Jul 10 17:53:12 UTC 2019 I: Submitting 8.0K b2/dindel_1.01-wu1-3+dfsg-1_i386.buildinfo.asc Wed Jul 10 17:53:14 UTC 2019 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Jul 10 17:53:14 UTC 2019 I: Done submitting .buildinfo files. Wed Jul 10 17:53:14 UTC 2019 I: Removing signed dindel_1.01-wu1-3+dfsg-1_i386.buildinfo.asc files: removed './b1/dindel_1.01-wu1-3+dfsg-1_i386.buildinfo.asc' removed './b2/dindel_1.01-wu1-3+dfsg-1_i386.buildinfo.asc'