Sat May 2 13:47:19 UTC 2020 I: starting to build tvc/buster/i386 on jenkins on '2020-05-02 13:47' Sat May 2 13:47:19 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_3/4420/console.log Sat May 2 13:47:19 UTC 2020 I: Downloading source for buster/tvc=5.0.3+git20151221.80e144e+dfsg-2 --2020-05-02 13:47:19-- http://deb.debian.org/debian/pool/main/t/tvc/tvc_5.0.3+git20151221.80e144e+dfsg-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2195 (2.1K) Saving to: ‘tvc_5.0.3+git20151221.80e144e+dfsg-2.dsc’ 0K .. 100% 30.7M=0s 2020-05-02 13:47:19 (30.7 MB/s) - ‘tvc_5.0.3+git20151221.80e144e+dfsg-2.dsc’ saved [2195/2195] Sat May 2 13:47:19 UTC 2020 I: tvc_5.0.3+git20151221.80e144e+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: tvc Binary: tvc Architecture: any Version: 5.0.3+git20151221.80e144e+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Dominique Belhachemi , Andreas Tille Homepage: http://ioncommunity.thermofisher.com Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/tvc Vcs-Git: https://salsa.debian.org/med-team/tvc.git Build-Depends: debhelper (>= 11~), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev Package-List: tvc deb science optional arch=any Checksums-Sha1: cd0223b1b1c96a2cc5a25fbc64e4e36a00347788 744668 tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz 5bf32cab110f81123fa6228760873522f91a28c7 8384 tvc_5.0.3+git20151221.80e144e+dfsg-2.debian.tar.xz Checksums-Sha256: 3339f118d2fe983bc028630d5bf5238b6e91b70a85e8046a742588a6c342740c 744668 tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz d8b8a2ab92084d238a162f395e978ef910708576c2de79d9f574b4da689cf7c5 8384 tvc_5.0.3+git20151221.80e144e+dfsg-2.debian.tar.xz Files: 68b468ca5054fb3260ad9de40131b632 744668 tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz 6c8fe33e5042e4a4f334cd3a8a5d35a8 8384 tvc_5.0.3+git20151221.80e144e+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlwSCDMRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtF/KxAAl9SuHEsZM9wG9EfSwIcGN7qvhhB4tgh6 c+5p91ldgAUFsQBM3/c0UNW2bNn0VuE1JZ6L0NbHi7PfN/LFGbuBAbJlwYKnmsMq b3PssxEoJ6ljjcuiAuFxcM8DOIBujJ1Ao5nNDAFAG+C1wXtIC8GxdCohyB6U9JLy pOoSHLOR5qJ1DKOIU8sWSJP2/fv/YoWG1wVj/mMQJryd7oyiNwKR6d6ePJj6CCJb v1Cayv/XgtNZv6SdD/wKWCsB8QLzPSsJeq2l/sf3Ra53WmHmwf6iJvffRD36MzvT 6PZKiqUr9XqbXKwK6VG4hnmHENmBc0W4XQgkeqlevHHK2ehvaY1ZvIRlOtU+MarG HuKOL+xYzfgLGYzrgK5EoPsdzWrxcH9GRcSwtK7JxeczOsPXTLAOLqVI3ACIQTGI abM6kI93cgLsglIRv8PRdB+4J3+ps6S6nH+ujrRHkkDs48SHBsDw4gaKZPfT/SbZ 9pXQ1Y+Oxf1hpcvqrRVTCVdbyivzoX2wwekkzu2Q3lpRI+6XZnV5foqNFYHwRCWx kTSLlbRmUEdjEZK4hoJ0Hv7RzcrnkYV0GeIXCW37YEFQeLC9pJlucX++PC2gLpwY tgVgQw+EYuUogGzie59ZQqY5laKG3SmZqpbxmmVs6MfGLY1uHnjZPrCylql4LAWK dLScGM8UIts= =7/XT -----END PGP SIGNATURE----- Sat May 2 13:47:19 UTC 2020 I: Checking whether the package is not for us Sat May 2 13:47:19 UTC 2020 I: Starting 1st build on remote node profitbricks-build2-i386.debian.net. Sat May 2 13:47:19 UTC 2020 I: Preparing to do remote build '1' on profitbricks-build2-i386.debian.net. Sat May 2 13:58:31 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 2 01:47:22 -12 2020 I: pbuilder-time-stamp: 1588427242 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 [tvc_5.0.3+git20151221.80e144e+dfsg-2.dsc] I: copying [./tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz] I: copying [./tvc_5.0.3+git20151221.80e144e+dfsg-2.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 Wed Dec 12 19:20:19 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 ./tvc_5.0.3+git20151221.80e144e+dfsg-2.dsc dpkg-source: info: extracting tvc in tvc-5.0.3+git20151221.80e144e+dfsg dpkg-source: info: unpacking tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz dpkg-source: info: unpacking tvc_5.0.3+git20151221.80e144e+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying cmake.patch dpkg-source: info: applying bamtools.patch dpkg-source: info: applying help.patch dpkg-source: info: applying hurd.patch dpkg-source: info: applying sse.patch dpkg-source: info: applying use_debian_packaged_smithwaterman.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~), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-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 cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on libjsoncpp-dev; however: Package libjsoncpp-dev is not installed. pbuilder-satisfydepends-dummy depends on libarmadillo-dev; however: Package libarmadillo-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 libsmithwaterman-dev; however: Package libsmithwaterman-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} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13{a} libarmadillo-dev{a} libarmadillo9{a} libarpack2{a} libarpack2-dev{a} libbamtools-dev{a} libbamtools2.5.1{a} libblas-dev{a} libblas3{a} libboost-math-dev{a} libboost-math1.67-dev{a} libboost-math1.67.0{a} libboost1.67-dev{a} libbsd0{a} libcroco3{a} libcurl4{a} libdisorder-dev{a} libdisorder0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libgssapi-krb5-2{a} libhdf5-103{a} libhdf5-cpp-103{a} libhdf5-dev{a} libicu63{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjsoncpp-dev{a} libjsoncpp1{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-2.4-2{a} libldap-common{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libprocps7{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsmithwaterman-dev{a} libsmithwaterman0{a} libssh2-1{a} libssl1.1{a} libsuperlu-dev{a} libsuperlu5{a} libsz2{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} lsb-base{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 91 newly installed, 0 to remove and 0 not upgraded. Need to get 49.8 MB of archives. After unpacking 301 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 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 8 http://deb.debian.org/debian buster/main i386 libprocps7 i386 2:3.3.15-2 [62.7 kB] Get: 9 http://deb.debian.org/debian buster/main i386 lsb-base all 10.2019051400 [28.4 kB] Get: 10 http://deb.debian.org/debian buster/main i386 procps i386 2:3.3.15-2 [259 kB] Get: 11 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 12 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 13 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 14 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 15 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 16 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 17 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 18 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 19 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 20 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 21 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 22 http://deb.debian.org/debian buster/main i386 cmake-data all 3.13.4-1 [1476 kB] Get: 23 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6 [8443 kB] Get: 24 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 25 http://deb.debian.org/debian buster/main i386 libarchive13 i386 3.3.3-4+deb10u1 [351 kB] Get: 26 http://deb.debian.org/debian buster/main i386 libkeyutils1 i386 1.6-6 [15.4 kB] Get: 27 http://deb.debian.org/debian buster/main i386 libkrb5support0 i386 1.17-3 [68.6 kB] Get: 28 http://deb.debian.org/debian buster/main i386 libk5crypto3 i386 1.17-3 [126 kB] Get: 29 http://deb.debian.org/debian buster/main i386 libssl1.1 i386 1.1.1d-0+deb10u2 [1538 kB] Get: 30 http://deb.debian.org/debian buster/main i386 libkrb5-3 i386 1.17-3 [396 kB] Get: 31 http://deb.debian.org/debian buster/main i386 libgssapi-krb5-2 i386 1.17-3 [168 kB] Get: 32 http://deb.debian.org/debian buster/main i386 libsasl2-modules-db i386 2.1.27+dfsg-1+deb10u1 [70.1 kB] Get: 33 http://deb.debian.org/debian buster/main i386 libsasl2-2 i386 2.1.27+dfsg-1+deb10u1 [110 kB] Get: 34 http://deb.debian.org/debian buster/main i386 libldap-common all 2.4.47+dfsg-3+deb10u1 [89.6 kB] Get: 35 http://deb.debian.org/debian buster/main i386 libldap-2.4-2 i386 2.4.47+dfsg-3+deb10u1 [236 kB] Get: 36 http://deb.debian.org/debian buster/main i386 libnghttp2-14 i386 1.36.0-2+deb10u1 [90.3 kB] Get: 37 http://deb.debian.org/debian buster/main i386 libpsl5 i386 0.20.2-2 [54.4 kB] Get: 38 http://deb.debian.org/debian buster/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2 [64.2 kB] Get: 39 http://deb.debian.org/debian buster/main i386 libssh2-1 i386 1.8.0-2.1 [147 kB] Get: 40 http://deb.debian.org/debian buster/main i386 libcurl4 i386 7.64.0-4 [358 kB] Get: 41 http://deb.debian.org/debian buster/main i386 libexpat1 i386 2.2.6-2+deb10u1 [104 kB] Get: 42 http://deb.debian.org/debian buster/main i386 libjsoncpp1 i386 1.7.4-3 [85.0 kB] Get: 43 http://deb.debian.org/debian buster/main i386 librhash0 i386 1.3.8-1 [135 kB] Get: 44 http://deb.debian.org/debian buster/main i386 libuv1 i386 1.24.1-1 [116 kB] Get: 45 http://deb.debian.org/debian buster/main i386 cmake i386 3.13.4-1 [3747 kB] Get: 46 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 47 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 48 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 49 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 50 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 51 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 52 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 53 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 54 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 55 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 56 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 57 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 58 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Get: 59 http://deb.debian.org/debian buster/main i386 hdf5-helpers i386 1.10.4+repack-10 [35.2 kB] Get: 60 http://deb.debian.org/debian buster/main i386 libaec0 i386 1.0.2-1 [22.6 kB] Get: 61 http://deb.debian.org/debian buster/main i386 libsz2 i386 1.0.2-1 [6720 B] Get: 62 http://deb.debian.org/debian buster/main i386 libaec-dev i386 1.0.2-1 [21.4 kB] Get: 63 http://deb.debian.org/debian buster/main i386 libgfortran5 i386 8.3.0-6 [549 kB] Get: 64 http://deb.debian.org/debian buster/main i386 libblas3 i386 3.8.0-2 [142 kB] Get: 65 http://deb.debian.org/debian buster/main i386 liblapack3 i386 3.8.0-2 [1974 kB] Get: 66 http://deb.debian.org/debian buster/main i386 libarpack2 i386 3.7.0-2 [103 kB] Get: 67 http://deb.debian.org/debian buster/main i386 libsuperlu5 i386 5.2.1+dfsg1-4 [160 kB] Get: 68 http://deb.debian.org/debian buster/main i386 libarmadillo9 i386 1:9.200.7+dfsg-1 [90.5 kB] Get: 69 http://deb.debian.org/debian buster/main i386 libblas-dev i386 3.8.0-2 [150 kB] Get: 70 http://deb.debian.org/debian buster/main i386 liblapack-dev i386 3.8.0-2 [2035 kB] Get: 71 http://deb.debian.org/debian buster/main i386 libarpack2-dev i386 3.7.0-2 [117 kB] Get: 72 http://deb.debian.org/debian buster/main i386 libhdf5-103 i386 1.10.4+repack-10 [1310 kB] Get: 73 http://deb.debian.org/debian buster/main i386 zlib1g-dev i386 1:1.2.11.dfsg-1 [216 kB] Get: 74 http://deb.debian.org/debian buster/main i386 libjpeg62-turbo i386 1:1.5.2-2+b1 [142 kB] Get: 75 http://deb.debian.org/debian buster/main i386 libjpeg62-turbo-dev i386 1:1.5.2-2+b1 [226 kB] Get: 76 http://deb.debian.org/debian buster/main i386 libjpeg-dev all 1:1.5.2-2 [57.5 kB] Get: 77 http://deb.debian.org/debian buster/main i386 libhdf5-cpp-103 i386 1.10.4+repack-10 [155 kB] Get: 78 http://deb.debian.org/debian buster/main i386 libhdf5-dev i386 1.10.4+repack-10 [2738 kB] Get: 79 http://deb.debian.org/debian buster/main i386 libsuperlu-dev i386 5.2.1+dfsg1-4 [18.4 kB] Get: 80 http://deb.debian.org/debian buster/main i386 libarmadillo-dev i386 1:9.200.7+dfsg-1 [360 kB] Get: 81 http://deb.debian.org/debian buster/main i386 libbamtools2.5.1 i386 2.5.1+dfsg-3 [173 kB] Get: 82 http://deb.debian.org/debian buster/main i386 libbamtools-dev i386 2.5.1+dfsg-3 [21.8 kB] Get: 83 http://deb.debian.org/debian buster/main i386 libboost1.67-dev i386 1.67.0-13+deb10u1 [8388 kB] Get: 84 http://deb.debian.org/debian buster/main i386 libboost-math1.67.0 i386 1.67.0-13+deb10u1 [437 kB] Get: 85 http://deb.debian.org/debian buster/main i386 libboost-math1.67-dev i386 1.67.0-13+deb10u1 [725 kB] Get: 86 http://deb.debian.org/debian buster/main i386 libboost-math-dev i386 1.67.0.1 [3848 B] Get: 87 http://deb.debian.org/debian buster/main i386 libdisorder0 i386 0.0.2+git20130809.8062ee1-1 [4296 B] Get: 88 http://deb.debian.org/debian buster/main i386 libdisorder-dev i386 0.0.2+git20130809.8062ee1-1 [4280 B] Get: 89 http://deb.debian.org/debian buster/main i386 libjsoncpp-dev i386 1.7.4-3 [87.7 kB] Get: 90 http://deb.debian.org/debian buster/main i386 libsmithwaterman0 i386 0.0+git20160702.2610e25-7 [38.8 kB] Get: 91 http://deb.debian.org/debian buster/main i386 libsmithwaterman-dev i386 0.0+git20160702.2610e25-7 [42.1 kB] Fetched 49.8 MB in 35s (1424 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 libncurses6:i386. Preparing to unpack .../06-libncurses6_6.1+20181013-2+deb10u2_i386.deb ... Unpacking libncurses6:i386 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package libprocps7:i386. Preparing to unpack .../07-libprocps7_2%3a3.3.15-2_i386.deb ... Unpacking libprocps7:i386 (2:3.3.15-2) ... Selecting previously unselected package lsb-base. Preparing to unpack .../08-lsb-base_10.2019051400_all.deb ... Unpacking lsb-base (10.2019051400) ... 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Unpacking libsmithwaterman-dev (0.0+git20160702.2610e25-7) ... 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 libdisorder0:i386 (0.0.2+git20130809.8062ee1-1) ... Setting up lsb-base (10.2019051400) ... Setting up libkeyutils1:i386 (1.6-6) ... Setting up libpsl5:i386 (0.20.2-2) ... Setting up hdf5-helpers (1.10.4+repack-10) ... 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+deb10u2) ... Setting up libprocps7:i386 (2:3.3.15-2) ... Setting up libsmithwaterman0 (0.0+git20160702.2610e25-7) ... Setting up libnghttp2-14:i386 (1.36.0-2+deb10u1) ... 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 libboost-math1.67.0:i386 (1.67.0-13+deb10u1) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u1) ... Setting up libaec0:i386 (1.0.2-1) ... Setting up libicu63:i386 (63.1-6) ... Setting up libkrb5support0:i386 (1.17-3) ... Setting up libsasl2-modules-db:i386 (2.1.27+dfsg-1+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libuv1:i386 (1.24.1-1) ... Setting up libjpeg62-turbo:i386 (1:1.5.2-2+b1) ... Setting up libjpeg62-turbo-dev:i386 (1:1.5.2-2+b1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2) ... Setting up libncurses6:i386 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:i386 (2.12-2) ... Setting up libbamtools2.5.1:i386 (2.5.1+dfsg-3) ... Setting up autopoint (0.19.8.1-9) ... Setting up libk5crypto3:i386 (1.17-3) ... Setting up libdisorder-dev:i386 (0.0.2+git20130809.8062ee1-1) ... Setting up libsasl2-2:i386 (2.1.27+dfsg-1+deb10u1) ... 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 librhash0:i386 (1.3.8-1) ... Setting up libuchardet0:i386 (0.0.6-3) ... Setting up procps (2:3.3.15-2) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libssh2-1:i386 (1.8.0-2.1) ... Setting up cmake-data (3.13.4-1) ... Setting up libkrb5-3:i386 (1.17-3) ... 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 libsz2:i386 (1.0.2-1) ... Setting up libjsoncpp1:i386 (1.7.4-3) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libjsoncpp-dev:i386 (1.7.4-3) ... Setting up libboost-math1.67-dev:i386 (1.67.0-13+deb10u1) ... Setting up libtool (2.4.6-9) ... Setting up libarchive13:i386 (3.3.3-4+deb10u1) ... Setting up libboost-math-dev:i386 (1.67.0.1) ... Setting up libaec-dev:i386 (1.0.2-1) ... Setting up libjpeg-dev (1:1.5.2-2) ... Setting up libldap-2.4-2:i386 (2.4.47+dfsg-3+deb10u1) ... Setting up m4 (1.4.18-2) ... 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 libbamtools-dev:i386 (2.5.1+dfsg-3) ... Setting up libhdf5-103:i386 (1.10.4+repack-10) ... 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 libgssapi-krb5-2:i386 (1.17-3) ... Setting up libcroco3:i386 (0.6.12-3) ... Setting up libsmithwaterman-dev (0.0+git20160702.2610e25-7) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libcurl4:i386 (7.64.0-4) ... Setting up libblas-dev:i386 (3.8.0-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so to provide /usr/lib/i386-linux-gnu/libblas.so (libblas.so-i386-linux-gnu) in auto mode 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 libhdf5-cpp-103:i386 (1.10.4+repack-10) ... Setting up libarpack2:i386 (3.7.0-2) ... Setting up libsuperlu5:i386 (5.2.1+dfsg1-4) ... 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 libhdf5-dev (1.10.4+repack-10) ... update-alternatives: using /usr/lib/i386-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/i386-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up liblapack-dev:i386 (3.8.0-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so to provide /usr/lib/i386-linux-gnu/liblapack.so (liblapack.so-i386-linux-gnu) in auto mode Setting up cmake (3.13.4-1) ... Setting up libarmadillo9 (1:9.200.7+dfsg-1) ... Setting up libsuperlu-dev:i386 (5.2.1+dfsg1-4) ... Setting up libarpack2-dev:i386 (3.7.0-2) ... Setting up po-debconf (1.0.21) ... Setting up libarmadillo-dev (1:9.200.7+dfsg-1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up debhelper (12.1.1) ... 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/tvc-5.0.3+git20151221.80e144e+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 tvc dpkg-buildpackage: info: source version 5.0.3+git20151221.80e144e+dfsg-2 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_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-i686-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/i386-linux-gnu .. -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- CMAKE_CXX_FLAGS: '-g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu dh_auto_build cd obj-i686-linux-gnu && make -j10 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake --color= make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake --color= Scanning dependencies of target tvcassembly make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' [ 1%] Building CXX object CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o [ 4%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp [ 4%] Building CXX object CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o [ 6%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o [ 7%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o [ 9%] Building CXX object CMakeFiles/tvcassembly.dir/IonVersion.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat 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-I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/TargetsManager.cpp /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/SampleManager.cpp /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat 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-I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/IonVersion.cpp Scanning dependencies of target tvcutils make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' [ 10%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o [ 12%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE 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-I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/Variant.cpp /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/TargetsManager.cpp /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HandleVariant.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -o tvcassembly -lbamtools -lz -lpthread -ljsoncpp [ 35%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/MetricsManager.cpp make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' [ 35%] Built target tvcassembly [ 37%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/tabix.cpp /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp: In function 'void TheSilenceOfTheArmadillos(std::ofstream&)': /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:9: warning: 'void arma::set_stream_err1(std::ostream&)' is deprecated [-Wdeprecated-declarations] arma::set_stream_err1(null_ostream); ^~~~~~~~~~~~~~~ In file included from /usr/include/armadillo:353, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:90:1: note: declared here set_stream_err1(std::ostream& user_stream) ^~~~~~~~~~~~~~~ /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:37: warning: 'void arma::set_stream_err1(std::ostream&)' is deprecated [-Wdeprecated-declarations] arma::set_stream_err1(null_ostream); ^ In file included from /usr/include/armadillo:353, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:90:1: note: declared here set_stream_err1(std::ostream& user_stream) ^~~~~~~~~~~~~~~ /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:37: warning: 'void arma::set_stream_err1(std::ostream&)' is deprecated [-Wdeprecated-declarations] arma::set_stream_err1(null_ostream); ^ In file included from /usr/include/armadillo:353, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:90:1: note: declared here set_stream_err1(std::ostream& user_stream) ^~~~~~~~~~~~~~~ /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:9: warning: 'void arma::set_stream_err2(std::ostream&)' is deprecated [-Wdeprecated-declarations] arma::set_stream_err2(null_ostream); ^~~~~~~~~~~~~~~ In file included from /usr/include/armadillo:353, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:101:1: note: declared here set_stream_err2(std::ostream& user_stream) ^~~~~~~~~~~~~~~ /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:37: warning: 'void arma::set_stream_err2(std::ostream&)' is deprecated [-Wdeprecated-declarations] arma::set_stream_err2(null_ostream); ^ In file included from /usr/include/armadillo:353, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:101:1: note: declared here set_stream_err2(std::ostream& user_stream) ^~~~~~~~~~~~~~~ /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:37: warning: 'void arma::set_stream_err2(std::ostream&)' is deprecated [-Wdeprecated-declarations] arma::set_stream_err2(null_ostream); ^ In file included from /usr/include/armadillo:353, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:101:1: note: declared here set_stream_err2(std::ostream& user_stream) ^~~~~~~~~~~~~~~ [ 42%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o [ 40%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o [ 40%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE 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-I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c: In function '_bgzf_check_EOF': /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c:678:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(buf, 1, 28, fp->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 46%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o [ 48%] Building CXX object CMakeFiles/tvcutils.dir/IonVersion.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment 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-ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/BiasGenerator.cpp /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/SigmaGenerator.cpp /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp: In function 'double VariantAssist::MannWhitneyU(std::vector&, std::vector&, bool)': /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:191:22: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 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Start 7: tvcutils_unify_vcf_call Start 8: tvcassembly_call 1/8 Test #8: tvcassembly_call ................................. Passed 0.06 sec 2/8 Test #4: tvcutils_call .................................... Passed 0.10 sec 3/8 Test #5: tvcutils_prepare_hotspots_call ................... Passed 0.09 sec 4/8 Test #6: tvcutils_validate_bed_call ....................... Passed 0.08 sec 5/8 Test #7: tvcutils_unify_vcf_call .......................... Passed 0.08 sec 6/8 Test #1: tvc_call ......................................... Passed 0.27 sec 7/8 Test #3: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 1.67 sec 8/8 Test #2: tvc_test_1_thread_sse_off ........................ Passed 1.72 sec 100% tests passed, 0 tests failed out of 8 Total Test time (real) = 1.80 sec make[1]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install cd obj-i686-linux-gnu && make -j10 install DESTDIR=/build/tvc-5.0.3\+git20151221.80e144e\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvcassembly.dir/build'. make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' [ 10%] Built target tvcassembly make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvcutils.dir/build'. make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' [ 31%] Built target tvcutils make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvc.dir/build'. make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' [100%] Built target tvc make[2]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvc -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcassembly -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcutils -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/variant_caller_pipeline.py -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/motifset.txt -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1 -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_original.bed -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/TSVC_variants.vcf -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/small_variants.vcf -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.dict -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bed -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta make[1]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' dh_installdocs dh_installchangelogs dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvc was not linked against liblapack.so.3 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvc was not linked against libblas.so.3 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvc debian/tvc/usr/bin/tvcutils were not linked against libdisorder.so.0 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-2_i386.deb'. dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-2_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../tvc_5.0.3+git20151221.80e144e+dfsg-2_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/28665 and its subdirectories I: Current time: Sat May 2 01:58:30 -12 2020 I: pbuilder-time-stamp: 1588427910 Sat May 2 13:58:31 UTC 2020 I: 1st build successful. Starting 2nd build on remote node profitbricks-build16-i386.debian.net. Sat May 2 13:58:31 UTC 2020 I: Preparing to do remote build '2' on profitbricks-build16-i386.debian.net. Sat May 2 13:59:25 UTC 2020 I: Deleting $TMPDIR on profitbricks-build16-i386.debian.net. Sat May 2 13:59:25 UTC 2020 I: tvc_5.0.3+git20151221.80e144e+dfsg-2_i386.changes: Format: 1.8 Date: Thu, 13 Dec 2018 08:07:07 +0100 Source: tvc Binary: tvc tvc-dbgsym Architecture: i386 Version: 5.0.3+git20151221.80e144e+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: tvc - genetic variant caller for Ion Torrent sequencing platforms Closes: 916322 Changes: tvc (5.0.3+git20151221.80e144e+dfsg-2) unstable; urgency=medium . [ Logan Rosen ] * Enable build with ld --as-needed Closes: #916322 . [ Andreas Tille ] * Remove trailing whitespace in debian/changelog Checksums-Sha1: 3cb42a4687d8bdc5dcda730aa67ca376aaa20c24 12713840 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-2_i386.deb 86dfa4fd510d1ddfdfa1a40a4f5218fdb71de797 6871 tvc_5.0.3+git20151221.80e144e+dfsg-2_i386.buildinfo 1983b860d0d273f34e508c559af9cc63242c8a6f 1093484 tvc_5.0.3+git20151221.80e144e+dfsg-2_i386.deb Checksums-Sha256: 009db5b70a4f230da89701a471b27abfcfd1679c3bf605fe13664550b1c99a20 12713840 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-2_i386.deb 73f090b7a4accaa5f58f0204f30593f7291dc41ead1ae94aef8fa33d339779af 6871 tvc_5.0.3+git20151221.80e144e+dfsg-2_i386.buildinfo 7e5408657f550c3ff67f141e7cfee77e300653fac1992802352d3982045f540d 1093484 tvc_5.0.3+git20151221.80e144e+dfsg-2_i386.deb Files: 2b2c8b5eb6248bf2aea3a001c4bccdfd 12713840 debug optional tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-2_i386.deb dd9c60b420fb1c8b8b6d21b2086436a5 6871 science optional tvc_5.0.3+git20151221.80e144e+dfsg-2_i386.buildinfo 42f9cae8beaf657dfe8475b62625c81f 1093484 science optional tvc_5.0.3+git20151221.80e144e+dfsg-2_i386.deb Sat May 2 13:59:27 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.sGDGyZaCqq/tvc_5.0.3+git20151221.80e144e+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.sGDGyZaCqq/tvc_5.0.3+git20151221.80e144e+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.sGDGyZaCqq/tvc_5.0.3+git20151221.80e144e+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.sGDGyZaCqq/b1/tvc_5.0.3+git20151221.80e144e+dfsg-2_i386.changes /srv/reproducible-results/rbuild-debian/tmp.sGDGyZaCqq/b2/tvc_5.0.3+git20151221.80e144e+dfsg-2_i386.changes ## close_archive (total time: 0.001s) 0.000s 22 calls diffoscope.comparators.xz.XzContainer 0.000s 10 calls diffoscope.comparators.deb.DebTarContainer 0.000s 12 calls diffoscope.comparators.tar.TarContainer 0.000s 8 calls diffoscope.comparators.deb.DebContainer ## command (total time: 282.094s) 122.284s 240 calls diff 107.478s 1856 calls readelf 35.830s 308 calls objdump 8.527s 6 calls objcopy 7.725s 22 calls xz 0.248s 11 calls cmp 0.001s 13 calls cmp (internal) ## compare_files (cumulative) (total time: 1100.295s) 204.744s 1 call abc.DotChangesFile 204.506s 2 calls abc.DebFile 204.130s 4 calls abc.XzFile 201.257s 2 calls abc.DebDataTarFile 199.368s 4 calls abc.ElfFile 72.796s 20 calls diffoscope.comparators.elf.ElfCodeSection 11.411s 65 calls diffoscope.comparators.elf.ElfSection 1.247s 2 calls diffoscope.comparators.elf.ElfStringSection 0.406s 2 calls abc.TarFile 0.286s 3 calls diffoscope.comparators.elf.MonkeyPatchedElfSection 0.082s 2 calls abc.TextFile 0.063s 2 calls abc.Md5sumsFile ## container_extract (total time: 8.573s) 7.729s 22 calls diffoscope.comparators.xz.XzContainer 0.590s 68 calls diffoscope.comparators.deb.DebTarContainer 0.243s 26 calls diffoscope.comparators.deb.DebContainer 0.011s 16 calls diffoscope.comparators.tar.TarContainer ## has_same_content_as (total time: 0.255s) 0.172s 14 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.048s 4 calls diffoscope.comparators.utils.archive.ArchiveMember 0.033s 2 calls diffoscope.comparators.debian.DebControlMember 0.001s 65 calls diffoscope.comparators.elf.ElfSection 0.000s 2 calls abc.Md5sumsFile 0.000s 20 calls diffoscope.comparators.elf.ElfCodeSection 0.000s 1 call abc.DotChangesFile 0.000s 1 call diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 3 calls diffoscope.comparators.elf.MonkeyPatchedElfSection 0.000s 2 calls diffoscope.comparators.elf.ElfStringSection ## main (total time: 234.681s) 234.525s 2 calls outputs 0.156s 1 call cleanup ## open_archive (total time: 0.001s) 0.000s 22 calls diffoscope.comparators.xz.XzContainer 0.000s 12 calls diffoscope.comparators.tar.TarContainer 0.000s 10 calls diffoscope.comparators.deb.DebTarContainer 0.000s 8 calls diffoscope.comparators.deb.DebContainer ## output (total time: 29.435s) 16.620s 1 call html 9.330s 1 call text 3.485s 1 call json ## recognizes (total time: 8.800s) 5.689s 702 calls diffoscope.comparators.utils.archive.ArchiveMember 1.348s 1170 calls diffoscope.comparators.elf.ElfSection 0.988s 1666 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.566s 360 calls diffoscope.comparators.elf.ElfCodeSection 0.083s 10 calls diffoscope.comparators.binary.FilesystemFile 0.070s 160 calls diffoscope.comparators.debian.DebControlMember 0.040s 36 calls diffoscope.comparators.elf.ElfStringSection 0.015s 54 calls diffoscope.comparators.elf.MonkeyPatchedElfSection 0.000s 8 calls abc.DotChangesFile Sat May 2 14:03:24 UTC 2020 E: tvc failed to build reproducibly in buster on i386. Sat May 2 14:05:00 UTC 2020 I: Submitting .buildinfo files to external archives: Sat May 2 14:05:00 UTC 2020 I: Submitting 8.0K b1/tvc_5.0.3+git20151221.80e144e+dfsg-2_i386.buildinfo.asc Sat May 2 14:05:01 UTC 2020 I: Submitting 8.0K b2/tvc_5.0.3+git20151221.80e144e+dfsg-2_i386.buildinfo.asc Sat May 2 14:05:02 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat May 2 14:05:02 UTC 2020 I: Done submitting .buildinfo files. Sat May 2 14:05:02 UTC 2020 I: Removing signed tvc_5.0.3+git20151221.80e144e+dfsg-2_i386.buildinfo.asc files: removed './b1/tvc_5.0.3+git20151221.80e144e+dfsg-2_i386.buildinfo.asc' removed './b2/tvc_5.0.3+git20151221.80e144e+dfsg-2_i386.buildinfo.asc'