Tue Jan 11 16:50:18 UTC 2022 I: starting to build tvc/bullseye/amd64 on jenkins on '2022-01-11 16:50' Tue Jan 11 16:50:18 UTC 2022 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_23/55860/console.log Tue Jan 11 16:50:18 UTC 2022 I: Downloading source for bullseye/tvc=5.0.3+git20151221.80e144e+dfsg-3 --2022-01-11 16:50:19-- http://cdn-fastly.deb.debian.org/debian/pool/main/t/tvc/tvc_5.0.3%2bgit20151221.80e144e%2bdfsg-3.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2200 (2.1K) Saving to: ‘tvc_5.0.3+git20151221.80e144e+dfsg-3.dsc’ 0K .. 100% 252M=0s 2022-01-11 16:50:19 (252 MB/s) - ‘tvc_5.0.3+git20151221.80e144e+dfsg-3.dsc’ saved [2200/2200] Tue Jan 11 16:50:19 UTC 2022 I: tvc_5.0.3+git20151221.80e144e+dfsg-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: tvc Binary: tvc Architecture: any Version: 5.0.3+git20151221.80e144e+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Dominique Belhachemi , Andreas Tille Homepage: http://ioncommunity.thermofisher.com Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/tvc Vcs-Git: https://salsa.debian.org/med-team/tvc.git Build-Depends: debhelper-compat (= 12), 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 784aa00453ced25b09efc46ed91b140cf1dc7868 8968 tvc_5.0.3+git20151221.80e144e+dfsg-3.debian.tar.xz Checksums-Sha256: 3339f118d2fe983bc028630d5bf5238b6e91b70a85e8046a742588a6c342740c 744668 tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz 8fa0c2fdd8670beb4b0ab726141010e619e4763d70ef292ab137c9bd12b9b506 8968 tvc_5.0.3+git20151221.80e144e+dfsg-3.debian.tar.xz Files: 68b468ca5054fb3260ad9de40131b632 744668 tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz be57abece3e5487df0f6939a38242aa7 8968 tvc_5.0.3+git20151221.80e144e+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCAAwFiEEkOLSwa0Uaht+u4kdu8F+uxOW8vcFAl5bTWkSHHN0dWFydEBk ZWJpYW4ub3JnAAoJELvBfrsTlvL3Wj0P/RPA3/JDLENaPvS8Z+hQOy/cIri64NFA ezi2Zl49RMqHyajLaT1CW3o/iDdXd4aweLbbvmfLrCjucRMdplm6RBQTPn9Ev1dj 1ja4LQJyxENqJqHWGdOL6dt9RCHIahMZYTV7LSaTaDk9f3QW0RREPbXrm/pD3uJu +PosQld9epddEd/T9zBcZIVPmUeW2oDue5k8TPspJcEeHVe1jRwM4eAuEeIvKYgg GItm/idx9b1jL+FcoIzCHeLo78nnIsKiHgbfw8+iexTFQ0ejh9A+cEp+LWpzISEj KirVJ1SAjzCoI9S1PNOX1kD1HCbDa+4+Yfq2CQ5QW1kLEnWmBKo+/M8OKz+Nm6kn D/zN9t9iAdi6yAJ/8whC42c4T1z7lci8G1RS/KFn9bFJF0LX6aC1/iZRlgARH0f3 qGb2PzvqLxTXKKzJLnaMMwD+ai83FQ8/A7FqOkFUoLMF4mQhC/E8uSsd4bWJC1j4 Wyxwkmkk+Ji+FXsuFdsqUycgFPeb+EFphUo20qPue6NKeLNBe43qjW5wMsfibaLK 4eaLe5woiXAoGVzyDKzRFjctyXaj0KtKw24uCNxGg/MI5P4Jw6E0I0Wh1eSb0DhV 4N06U0NTwEXlYSIB61p/J/bEDmM7qFQLYsKUol9JMzqQm8+VAzPXE7uUxUwJP8ae 45j1cyRXXKCe =OVd/ -----END PGP SIGNATURE----- Tue Jan 11 16:50:19 UTC 2022 I: Checking whether the package is not for us Tue Jan 11 16:50:19 UTC 2022 I: Starting 1st build on remote node ionos11-amd64.debian.net. Tue Jan 11 16:50:19 UTC 2022 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Tue Jan 11 16:52:31 UTC 2022 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Jan 11 04:50:21 -12 2022 I: pbuilder-time-stamp: 1641919821 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [tvc_5.0.3+git20151221.80e144e+dfsg-3.dsc] I: copying [./tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz] I: copying [./tvc_5.0.3+git20151221.80e144e+dfsg-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.jf9RCPrS/trustedkeys.kbx': General error gpgv: Signature made Sat Feb 29 17:51:37 2020 -12 gpgv: using RSA key 90E2D2C1AD146A1B7EBB891DBBC17EBB1396F2F7 gpgv: issuer "stuart@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-3.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-3.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 dpkg-source: info: applying python3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3319720/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='864f5a3b72a240a1a7d19784c367a5b9' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3319720' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.eHhHGsAgeH/pbuilderrc_2d83 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.eHhHGsAgeH/b1 --logfile b1/build.log tvc_5.0.3+git20151221.80e144e+dfsg-3.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 5.10.0-10-amd64 #1 SMP Debian 5.10.84-1 (2021-12-08) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 4 08:25 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Jul 28 07:09 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 28 07:09 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jul 28 07:09 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 28 07:09 more -rwsr-xr-x 1 root root 55528 Jul 28 07:09 mount -rwxr-xr-x 1 root root 18664 Jul 28 07:09 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jan 6 21:24 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jul 28 07:09 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 28 07:09 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 28 07:09 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/3319720/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 12), 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 ... 19655 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-compat (= 12); however: Package debhelper-compat 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} bsdextrautils{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} libarmadillo10{a} libarpack2{a} libarpack2-dev{a} libbamtools-dev{a} libbamtools2.5.1{a} libblas-dev{a} libblas3{a} libboost-math-dev{a} libboost-math1.74-dev{a} libboost-math1.74.0{a} libboost1.74-dev{a} libbrotli1{a} libcurl4{a} libdebhelper-perl{a} libdisorder-dev{a} libdisorder0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libhdf5-103-1{a} libhdf5-cpp-103-1{a} libhdf5-dev{a} libhdf5-fortran-102{a} libhdf5-hl-100{a} libhdf5-hl-cpp-100{a} libhdf5-hl-fortran-100{a} libicu67{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjsoncpp-dev{a} libjsoncpp24{a} liblapack-dev{a} liblapack3{a} libldap-2.4-2{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libprocps8{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsmithwaterman-dev{a} libsmithwaterman0{a} libssh2-1{a} libsub-override-perl{a} libsuperlu-dev{a} libsuperlu5{a} libsz2{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{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 libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 87 newly installed, 0 to remove and 0 not upgraded. Need to get 52.8 MB of archives. After unpacking 326 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2 [102 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 cmake-data all 3.18.4-2+deb11u1 [1725 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libarchive13 amd64 3.4.3-2+b1 [343 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1 [69.1 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1 [106 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3 [232 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u1 [341 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2 [96.9 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libjsoncpp24 amd64 1.9.4-4 [78.9 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 librhash0 amd64 1.4.1-2 [129 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libuv1 amd64 1.40.0-2 [132 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 cmake amd64 3.18.4-2+deb11u1 [5593 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 hdf5-helpers amd64 1.10.6+repack-4+deb11u1 [40.4 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 libaec0 amd64 1.0.4-1 [20.3 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 libsz2 amd64 1.0.4-1 [6760 B] Get: 54 http://deb.debian.org/debian bullseye/main amd64 libaec-dev amd64 1.0.4-1 [18.7 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3 [153 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3 [2166 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 libarpack2 amd64 3.8.0-1 [103 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libsuperlu5 amd64 5.2.2+dfsg1-2 [163 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 libarmadillo10 amd64 1:10.1.2+dfsg-6+b1 [98.8 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 libblas-dev amd64 3.9.0-3 [161 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 liblapack-dev amd64 3.9.0-3 [4247 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 libarpack2-dev amd64 3.8.0-1 [117 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 libhdf5-103-1 amd64 1.10.6+repack-4+deb11u1 [1189 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 libhdf5-fortran-102 amd64 1.10.6+repack-4+deb11u1 [105 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 libhdf5-hl-100 amd64 1.10.6+repack-4+deb11u1 [81.8 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 libhdf5-hl-fortran-100 amd64 1.10.6+repack-4+deb11u1 [56.8 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 libhdf5-cpp-103-1 amd64 1.10.6+repack-4+deb11u1 [141 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libhdf5-hl-cpp-100 amd64 1.10.6+repack-4+deb11u1 [37.7 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo-dev amd64 1:2.0.6-4 [278 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libjpeg-dev amd64 1:2.0.6-4 [67.8 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libhdf5-dev amd64 1.10.6+repack-4+deb11u1 [2438 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libsuperlu-dev amd64 5.2.2+dfsg1-2 [21.4 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libarmadillo-dev amd64 1:10.1.2+dfsg-6+b1 [387 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 libbamtools2.5.1 amd64 2.5.1+dfsg-9 [158 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 libbamtools-dev amd64 2.5.1+dfsg-9 [208 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libboost1.74-dev amd64 1.74.0-9 [9534 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 libboost-math1.74.0 amd64 1.74.0-9 [521 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 libboost-math1.74-dev amd64 1.74.0-9 [599 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 libboost-math-dev amd64 1.74.0.3 [4532 B] Get: 83 http://deb.debian.org/debian bullseye/main amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-2 [4344 B] Get: 84 http://deb.debian.org/debian bullseye/main amd64 libdisorder-dev amd64 0.0.2+git20130809.8062ee1-2 [4348 B] Get: 85 http://deb.debian.org/debian bullseye/main amd64 libjsoncpp-dev amd64 1.9.4-4 [25.4 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-11 [36.2 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 libsmithwaterman-dev amd64 0.0+git20160702.2610e25-11 [39.1 kB] Fetched 52.8 MB in 1s (35.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19655 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_amd64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../05-libncurses6_6.2+20201114-2_amd64.deb ... Unpacking libncurses6:amd64 (6.2+20201114-2) ... Selecting previously unselected package libprocps8:amd64. Preparing to unpack .../06-libprocps8_2%3a3.3.17-5_amd64.deb ... Unpacking libprocps8:amd64 (2:3.3.17-5) ... Selecting previously unselected package procps. Preparing to unpack .../07-procps_2%3a3.3.17-5_amd64.deb ... Unpacking procps (2:3.3.17-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../08-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../09-libmagic-mgc_1%3a5.39-3_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../10-libmagic1_1%3a5.39-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../11-file_1%3a5.39-3_amd64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../12-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../13-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../14-m4_1.4.18-5_amd64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../15-autoconf_2.69-14_all.deb ... 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Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../22-libarchive13_3.4.3-2+b1_amd64.deb ... Unpacking libarchive13:amd64 (3.4.3-2+b1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../23-libbrotli1_1.0.9-2+b2_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../24-libsasl2-modules-db_2.1.27+dfsg-2.1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../25-libsasl2-2_2.1.27+dfsg-2.1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27+dfsg-2.1) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../26-libldap-2.4-2_2.4.57+dfsg-3_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.57+dfsg-3) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../27-libnghttp2-14_1.43.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.43.0-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../28-libpsl5_0.21.0-1.2_amd64.deb ... Unpacking libpsl5:amd64 (0.21.0-1.2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../29-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../30-libssh2-1_1.9.0-2_amd64.deb ... Unpacking libssh2-1:amd64 (1.9.0-2) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../31-libcurl4_7.74.0-1.3+deb11u1_amd64.deb ... Unpacking libcurl4:amd64 (7.74.0-1.3+deb11u1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../32-libexpat1_2.2.10-2_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-2) ... 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Preparing to unpack .../39-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../40-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../41-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../42-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../43-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../44-libelf1_0.183-1_amd64.deb ... Unpacking libelf1:amd64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../45-dwz_0.13+20210201-1_amd64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package gettext. Preparing to unpack .../46-gettext_0.21-4_amd64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../47-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 .../48-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../49-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package hdf5-helpers. Preparing to unpack .../50-hdf5-helpers_1.10.6+repack-4+deb11u1_amd64.deb ... Unpacking hdf5-helpers (1.10.6+repack-4+deb11u1) ... Selecting previously unselected package libaec0:amd64. Preparing to unpack .../51-libaec0_1.0.4-1_amd64.deb ... Unpacking libaec0:amd64 (1.0.4-1) ... Selecting previously unselected package libsz2:amd64. Preparing to unpack .../52-libsz2_1.0.4-1_amd64.deb ... Unpacking libsz2:amd64 (1.0.4-1) ... Selecting previously unselected package libaec-dev:amd64. Preparing to unpack .../53-libaec-dev_1.0.4-1_amd64.deb ... Unpacking libaec-dev:amd64 (1.0.4-1) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../54-libblas3_3.9.0-3_amd64.deb ... Unpacking libblas3:amd64 (3.9.0-3) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../55-libgfortran5_10.2.1-6_amd64.deb ... Unpacking libgfortran5:amd64 (10.2.1-6) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../56-liblapack3_3.9.0-3_amd64.deb ... Unpacking liblapack3:amd64 (3.9.0-3) ... Selecting previously unselected package libarpack2:amd64. Preparing to unpack .../57-libarpack2_3.8.0-1_amd64.deb ... Unpacking libarpack2:amd64 (3.8.0-1) ... Selecting previously unselected package libsuperlu5:amd64. Preparing to unpack .../58-libsuperlu5_5.2.2+dfsg1-2_amd64.deb ... Unpacking libsuperlu5:amd64 (5.2.2+dfsg1-2) ... Selecting previously unselected package libarmadillo10. Preparing to unpack .../59-libarmadillo10_1%3a10.1.2+dfsg-6+b1_amd64.deb ... Unpacking libarmadillo10 (1:10.1.2+dfsg-6+b1) ... Selecting previously unselected package libblas-dev:amd64. Preparing to unpack .../60-libblas-dev_3.9.0-3_amd64.deb ... Unpacking libblas-dev:amd64 (3.9.0-3) ... Selecting previously unselected package liblapack-dev:amd64. Preparing to unpack .../61-liblapack-dev_3.9.0-3_amd64.deb ... Unpacking liblapack-dev:amd64 (3.9.0-3) ... Selecting previously unselected package libarpack2-dev:amd64. Preparing to unpack .../62-libarpack2-dev_3.8.0-1_amd64.deb ... Unpacking libarpack2-dev:amd64 (3.8.0-1) ... Selecting previously unselected package libhdf5-103-1:amd64. Preparing to unpack .../63-libhdf5-103-1_1.10.6+repack-4+deb11u1_amd64.deb ... Unpacking libhdf5-103-1:amd64 (1.10.6+repack-4+deb11u1) ... Selecting previously unselected package libhdf5-fortran-102:amd64. Preparing to unpack .../64-libhdf5-fortran-102_1.10.6+repack-4+deb11u1_amd64.deb ... Unpacking libhdf5-fortran-102:amd64 (1.10.6+repack-4+deb11u1) ... Selecting previously unselected package libhdf5-hl-100:amd64. Preparing to unpack .../65-libhdf5-hl-100_1.10.6+repack-4+deb11u1_amd64.deb ... Unpacking libhdf5-hl-100:amd64 (1.10.6+repack-4+deb11u1) ... Selecting previously unselected package libhdf5-hl-fortran-100:amd64. Preparing to unpack .../66-libhdf5-hl-fortran-100_1.10.6+repack-4+deb11u1_amd64.deb ... Unpacking libhdf5-hl-fortran-100:amd64 (1.10.6+repack-4+deb11u1) ... Selecting previously unselected package libhdf5-cpp-103-1:amd64. Preparing to unpack .../67-libhdf5-cpp-103-1_1.10.6+repack-4+deb11u1_amd64.deb ... Unpacking libhdf5-cpp-103-1:amd64 (1.10.6+repack-4+deb11u1) ... Selecting previously unselected package libhdf5-hl-cpp-100:amd64. Preparing to unpack .../68-libhdf5-hl-cpp-100_1.10.6+repack-4+deb11u1_amd64.deb ... Unpacking libhdf5-hl-cpp-100:amd64 (1.10.6+repack-4+deb11u1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../69-zlib1g-dev_1%3a1.2.11.dfsg-2_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../70-libjpeg62-turbo_1%3a2.0.6-4_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.0.6-4) ... Selecting previously unselected package libjpeg62-turbo-dev:amd64. Preparing to unpack .../71-libjpeg62-turbo-dev_1%3a2.0.6-4_amd64.deb ... Unpacking libjpeg62-turbo-dev:amd64 (1:2.0.6-4) ... Selecting previously unselected package libjpeg-dev:amd64. Preparing to unpack .../72-libjpeg-dev_1%3a2.0.6-4_amd64.deb ... Unpacking libjpeg-dev:amd64 (1:2.0.6-4) ... Selecting previously unselected package libhdf5-dev. 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Setting up bsdextrautils (2.36.1-8) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up hdf5-helpers (1.10.6+repack-4+deb11u1) ... Setting up libicu67:amd64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up libsmithwaterman0 (0.0+git20160702.2610e25-11) ... Setting up libnghttp2-14:amd64 (1.43.0-1) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libaec0:amd64 (1.0.4-1) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1) ... Setting up autotools-dev (20180224.1+nmu1) ... 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Building tag database... -> Finished parsing the build-deps 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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../tvc_5.0.3+git20151221.80e144e+dfsg-3_source.changes dpkg-buildpackage: info: source package tvc dpkg-buildpackage: info: source version 5.0.3+git20151221.80e144e+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Stuart Prescott dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-x86_64-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/x86_64-linux-gnu .. -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- CMAKE_CXX_FLAGS: '-g -O2 -fdebug-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3' -- 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-x86_64-linux-gnu dh_auto_build cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-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-x86_64-linux-gnu/CMakeFiles /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend 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-x86_64-linux-gnu' cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake --color= Dependee "/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake" is newer than depender "/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvcassembly.dir/depend.internal". 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Scanning dependencies of target tvcassembly make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-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-x86_64-linux-gnu' Scanning dependencies of target tvcutils [ 1%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.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 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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 -fdebug-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp Scanning dependencies of target tvc [ 20%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' /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 -fdebug-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/Variant.cpp make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' [ 21%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/split.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 -fdebug-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/split.cpp [ 23%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/VariantCaller.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 -fdebug-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp [ 24%] 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 -fdebug-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/tabix.cpp In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/Util/Utils.cpp:12: In function 'char* strncpy(char*, const char*, size_t)', inlined from 'char* GetProcessParam(const char*, const char*)' at /build/tvc-5.0.3+git20151221.80e144e+dfsg/Util/Utils.cpp:503:15: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/tvc-5.0.3+git20151221.80e144e+dfsg/Util/Utils.cpp: In function 'char* GetProcessParam(const char*, const char*)': /build/tvc-5.0.3+git20151221.80e144e+dfsg/Util/Utils.cpp:503:37: note: length computed here 503 | strncpy (keyword, buf, strlen (buf)-1); | ~~~~~~~^~~~~ [ 26%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o /usr/bin/cc -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 -fdebug-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/index.c.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c: In function 'ti_index_core': /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c:336:35: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int32_t' {aka 'int'} changes value from 'last_bin = 4294967295' to '-1' [-Woverflow] 336 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ [ 27%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o /usr/bin/cc -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 -fdebug-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 [ 29%] 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 -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 -fdebug-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvcutils.dir/IonVersion.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/IonVersion.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] 678 | fread(buf, 1, 28, fp->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 30%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.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 -fdebug-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/BAMWalkerEngine.cpp [ 32%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib 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/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/VcfFormat.cpp [ 47%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.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 -fdebug-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads/ExtendedReadInfo.cpp [ 49%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.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 -fdebug-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/ErrorMotifs.cpp [ 50%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.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 -fdebug-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/LocalContext.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] 36 | arma::set_stream_err1(null_ostream); | ^~~~~~~~~~~~~~~ In file included from /usr/include/armadillo:349, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:90:1: note: declared here 90 | 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] 36 | arma::set_stream_err1(null_ostream); | ^ In file included from /usr/include/armadillo:349, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:90:1: note: declared here 90 | 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] 37 | arma::set_stream_err2(null_ostream); | ^~~~~~~~~~~~~~~ In file included from /usr/include/armadillo:349, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:101:1: note: declared here 101 | 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] 37 | arma::set_stream_err2(null_ostream); | ^ In file included from /usr/include/armadillo:349, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:101:1: note: declared here 101 | set_stream_err2(std::ostream& user_stream) | ^~~~~~~~~~~~~~~ /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp: In member function 'void RecalibrationHandler::ReadRecalibrationFromComments(const BamTools::SamHeader&, const std::map, int>&)': /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:240:18: warning: 'Reader' is deprecated: Use CharReader and CharReaderBuilder instead. [-Wdeprecated-declarations] 240 | Json::Reader recal_reader; | ^~~~~~~~~~~~ In file included from /usr/include/jsoncpp/json/json.h:11, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/CalibrationHelper.h:23, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/LinearCalibrationModel.h:16, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.h:19, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:7: /usr/include/jsoncpp/json/reader.h:37:63: note: declared here 37 | "Use CharReader and CharReaderBuilder instead.") JSON_API Reader { | ^~~~~~ /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:240:18: warning: 'Json::Reader::Reader()' is deprecated: Use CharReader and CharReaderBuilder instead [-Wdeprecated-declarations] 240 | Json::Reader recal_reader; | ^~~~~~~~~~~~ In file included from /usr/include/jsoncpp/json/json.h:11, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/CalibrationHelper.h:23, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/LinearCalibrationModel.h:16, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.h:19, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:7: /usr/include/jsoncpp/json/reader.h:56:3: note: declared here 56 | Reader(); | ^~~~~~ [ 52%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib 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-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 -fdebug-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/external/vcflib/tabixpp/index.c.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c: In function 'ti_index_core': /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c:336:35: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int32_t' {aka 'int'} changes value from 'last_bin = 4294967295' to '-1' [-Woverflow] 336 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ [ 80%] Building C object CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o /usr/bin/cc -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 -fdebug-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/external/vcflib/tabixpp/bgzf.c.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c [ 81%] Linking CXX executable tvcutils /usr/bin/cmake -E cmake_link_script CMakeFiles/tvcutils.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -Wl,-z,relro -rdynamic CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o CMakeFiles/tvcutils.dir/IonVersion.cpp.o -o tvcutils -lbamtools -lz -ljsoncpp -lsmithwaterman -ldisorder /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] 678 | fread(buf, 1, 28, fp->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 83%] Building CXX object CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.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 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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 -fdebug-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/Util/OptArgs.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp [ 92%] Building CXX object CMakeFiles/tvc.dir/realignment/Realigner.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 -fdebug-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/realignment/Realigner.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment/Realigner.cpp /build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/LinearCalibrationModel.cpp: In member function 'void LinearCalibrationModel::SaveModelFileToBamComments(std::vector >&, const string&) const': /build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/LinearCalibrationModel.cpp:708:20: warning: 'FastWriter' is deprecated: Use StreamWriterBuilder instead [-Wdeprecated-declarations] 708 | Json::FastWriter writer; | ^~~~~~ In file included from /usr/include/jsoncpp/json/json.h:13, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/CalibrationHelper.h:23, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/LinearCalibrationModel.h:16, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/LinearCalibrationModel.cpp:13: /usr/include/jsoncpp/json/writer.h:168:70: note: declared here 168 | class JSONCPP_DEPRECATED("Use StreamWriterBuilder instead") JSON_API FastWriter | ^~~~~~~~~~ [ 93%] Building C object CMakeFiles/tvc.dir/file-io/ion_util.c.o /usr/bin/cc -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 -fdebug-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/file-io/ion_util.c.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io/ion_util.c [ 95%] Building C object CMakeFiles/tvc.dir/file-io/ion_error.c.o /usr/bin/cc -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 -fdebug-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/file-io/ion_error.c.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io/ion_error.c [ 96%] Building CXX object CMakeFiles/tvc.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 -fdebug-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/IonVersion.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/IonVersion.cpp [ 98%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.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 -fdebug-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller/TreephaserSSE.cpp [100%] Linking CXX executable tvc /usr/bin/cmake -E cmake_link_script CMakeFiles/tvc.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -Wl,-z,relro -rdynamic CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o CMakeFiles/tvc.dir/external/vcflib/split.cpp.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o CMakeFiles/tvc.dir/Util/OptArgs.cpp.o CMakeFiles/tvc.dir/realignment/Realigner.cpp.o CMakeFiles/tvc.dir/file-io/ion_util.c.o CMakeFiles/tvc.dir/file-io/ion_error.c.o CMakeFiles/tvc.dir/IonVersion.cpp.o CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o -o tvc -lbamtools -lz -lpthread -lblas -llapack -larmadillo -ljsoncpp -lsmithwaterman -ldisorder make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' [100%] Built target tvc make[2]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' dh_auto_test cd obj-x86_64-linux-gnu && make -j15 test ARGS\+=-j15 make[1]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process -j15 Test project /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu Start 1: tvc_call Start 2: tvc_test_1_thread_sse_on Start 3: tvc_test_1_thread_sse_off Start 4: tvc_test_4_threads_sse_on_with_parameter_file Start 5: tvc_test_4_threads_sse_off_with_parameter_file Start 6: tvcutils_call Start 7: tvcutils_prepare_hotspots_call Start 8: tvcutils_validate_bed_call Start 9: tvcutils_unify_vcf_call Start 10: tvcassembly_call 1/10 Test #1: tvc_call ......................................... 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Passed 1.51 sec 100% tests passed, 0 tests failed out of 10 Total Test time (real) = 1.52 sec make[1]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-x86_64-linux-gnu && make -j15 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-x86_64-linux-gnu' /usr/bin/cmake -S/build/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-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-x86_64-linux-gnu/CMakeFiles /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend 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-x86_64-linux-gnu' cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-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-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving 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done for 'CMakeFiles/tvc.dir/build'. make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' [ 20%] Built target tvcutils [ 30%] Built target tvcassembly [100%] Built target tvc make[2]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-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/targetseq_germline_lowstringency_p1_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/ocp_somatic_lowstringency_pgm_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/ampliseqexome_germline_lowstringency_p1_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_unmerged_detail.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/test_merged_plain.bed -- 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/test.bam.bai -- 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/reference.fasta.fai -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta -- 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/expected -- 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/expected/TSVC_variants.vcf make[1]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' dh_installdocs dh_installchangelogs dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvcutils debian/tvc/usr/bin/tvc 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' in '../tvc_5.0.3+git20151221.80e144e+dfsg-3_amd64.deb'. dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../tvc_5.0.3+git20151221.80e144e+dfsg-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload 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/3319720 and its subdirectories I: Current time: Tue Jan 11 04:52:30 -12 2022 I: pbuilder-time-stamp: 1641919950 Tue Jan 11 16:52:31 UTC 2022 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Tue Jan 11 16:52:31 UTC 2022 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Tue Jan 11 16:53:54 UTC 2022 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Tue Jan 11 16:53:54 UTC 2022 I: tvc_5.0.3+git20151221.80e144e+dfsg-3_amd64.changes: Format: 1.8 Date: Sun, 01 Mar 2020 15:57:45 +1100 Source: tvc Binary: tvc tvc-dbgsym Architecture: amd64 Version: 5.0.3+git20151221.80e144e+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Stuart Prescott Description: tvc - genetic variant caller for Ion Torrent sequencing platforms Closes: 945720 Changes: tvc (5.0.3+git20151221.80e144e+dfsg-3) unstable; urgency=medium . * Team upload. * Use Python 3 in scripts (Closes: #945720). * Add Rules-Requires-Root: no. * Update Standards-Version to 4.5.0 (no changes required). * Switch to debhelper-compat (= 12). Checksums-Sha1: d8badca1beddd49d498f18658ae1e2edc53b3104 10855948 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3_amd64.deb 7012d958d7d011d159c8502a54a6c94da7e90149 7296 tvc_5.0.3+git20151221.80e144e+dfsg-3_amd64.buildinfo 071e9c2b0dd0e8ba353ae8bf525c807b0910587f 1069904 tvc_5.0.3+git20151221.80e144e+dfsg-3_amd64.deb Checksums-Sha256: 3b4928442aa55983f5d5c063608f14eab03c1b936617ef3102b61fa8bdfe949d 10855948 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3_amd64.deb 07d944967b33a429d484d663f04f3d009d959b637a21254ce1986194c38634d0 7296 tvc_5.0.3+git20151221.80e144e+dfsg-3_amd64.buildinfo 502ae540e0f6caa6eead10ca2840eefa35ef5f40d305e564307b859877a705a5 1069904 tvc_5.0.3+git20151221.80e144e+dfsg-3_amd64.deb Files: 936b7723fe50b0f05c6adc10150c6381 10855948 debug optional tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3_amd64.deb b48fa29aa4f7fc7dd18dcea58ac1b801 7296 science optional tvc_5.0.3+git20151221.80e144e+dfsg-3_amd64.buildinfo f6a95b529a0fa29a5a7e37f5cb5c15d8 1069904 science optional tvc_5.0.3+git20151221.80e144e+dfsg-3_amd64.deb Tue Jan 11 16:53:55 UTC 2022 I: will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.eHhHGsAgeH/tvc_5.0.3+git20151221.80e144e+dfsg-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.eHhHGsAgeH/tvc_5.0.3+git20151221.80e144e+dfsg-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.eHhHGsAgeH/tvc_5.0.3+git20151221.80e144e+dfsg-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.eHhHGsAgeH/b1/tvc_5.0.3+git20151221.80e144e+dfsg-3_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.eHhHGsAgeH/b2/tvc_5.0.3+git20151221.80e144e+dfsg-3_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.388s) 0.388s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.148s) 0.147s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Tue Jan 11 16:53:56 UTC 2022 I: found no differences in the changes files, and a .buildinfo file also exists. Tue Jan 11 16:53:56 UTC 2022 I: tvc from bullseye built successfully and reproducibly on amd64. Tue Jan 11 16:53:57 UTC 2022 I: Submitting .buildinfo files to external archives: Tue Jan 11 16:53:57 UTC 2022 I: Submitting 8.0K b1/tvc_5.0.3+git20151221.80e144e+dfsg-3_amd64.buildinfo.asc Tue Jan 11 16:53:59 UTC 2022 I: Submitting 8.0K b2/tvc_5.0.3+git20151221.80e144e+dfsg-3_amd64.buildinfo.asc Tue Jan 11 16:54:00 UTC 2022 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Jan 11 16:54:00 UTC 2022 I: Done submitting .buildinfo files. Tue Jan 11 16:54:00 UTC 2022 I: Removing signed tvc_5.0.3+git20151221.80e144e+dfsg-3_amd64.buildinfo.asc files: removed './b1/tvc_5.0.3+git20151221.80e144e+dfsg-3_amd64.buildinfo.asc' removed './b2/tvc_5.0.3+git20151221.80e144e+dfsg-3_amd64.buildinfo.asc'