Fri May 5 11:21:32 UTC 2023 I: starting to build tvc/bookworm/armhf on jenkins on '2023-05-05 11:21' Fri May 5 11:21:32 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_31/67/console.log Fri May 5 11:21:32 UTC 2023 I: Downloading source for bookworm/tvc=5.0.3+git20151221.80e144e+dfsg-5 --2023-05-05 11:21:32-- http://cdn-fastly.deb.debian.org/debian/pool/main/t/tvc/tvc_5.0.3%2bgit20151221.80e144e%2bdfsg-5.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2227 (2.2K) [text/prs.lines.tag] Saving to: ‘tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc’ 0K .. 100% 221M=0s 2023-05-05 11:21:32 (221 MB/s) - ‘tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc’ saved [2227/2227] Fri May 5 11:21:32 UTC 2023 I: tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: tvc Binary: tvc Architecture: any Version: 5.0.3+git20151221.80e144e+dfsg-5 Maintainer: Debian Med Packaging Team Uploaders: Dominique Belhachemi , Andreas Tille Homepage: http://ioncommunity.thermofisher.com Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/tvc Vcs-Git: https://salsa.debian.org/med-team/tvc.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), 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 7d0306db9bc6dc0e7cd4dede9e0a4fc26451cb66 9800 tvc_5.0.3+git20151221.80e144e+dfsg-5.debian.tar.xz Checksums-Sha256: 3339f118d2fe983bc028630d5bf5238b6e91b70a85e8046a742588a6c342740c 744668 tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz ea878d69c94a1606583404cf23717d6a1dcc537bc4e6bd2c559ad2650939a52f 9800 tvc_5.0.3+git20151221.80e144e+dfsg-5.debian.tar.xz Files: 68b468ca5054fb3260ad9de40131b632 744668 tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz 57be1c85cdcb34a4bc11e0493cbe5570 9800 tvc_5.0.3+git20151221.80e144e+dfsg-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEELWW8HrlmWm6X+XMKs/WUUoUhnh8FAmMXaFAUHG1kYmlsYWxA ZGlzcm9vdC5vcmcACgkQs/WUUoUhnh+ysRAAiyxZr7pHEECCI+zBkWyVyHtCbKXV 92OCJejyYySi8hxtO5sWWmzAOItLKK2myc5v9tT7KcWHMqXVI+bpcODJQrEuc4r2 flZVmncIMhbf3jQ74V7acpHAg3H5bfL9MaOIU/oSv/TWHhze3hUqbO4ve+YfQ/Se tS6PZ2OPU/9aMwB/LrHZ2iVIoVg4pqZGuJvnuaREY2h0hEeqvyia4NP/YMyF3GiJ AAG3Q6EEH02jXuWOMIJzeeXQy34gYo7+eXleJWWsyAD44kXZG5SviIAkiz+g3iju PxxpPc5Uc9I2IiYK7eszn8Lo50RHh96V2dnt/h2y0D9An2po+T4nmqrVnZgtUwWt Vu+F7drjYwvxle7LMzDO91e7Q/StoFpZ68wT5uM6vt/f7SVbynlBYkx5WmzzXXU0 clsk8ULkNjHRun8W7BD90q0aRIKzYXF/fgmNod+F6cUqFEnoWSeBV1ffJfmqWcsA fGlAl8Zbxp218ARhEI5ChBuJafF3X7qshr2kMmst6L4ANeMmuJSCMfGToSsr7IyF ucGnYuJSaM6TiGFDpEMeQ8K2SmXJIQpJmZLrrKSgogRVCVTbEn6aJMvx2CcPZ3K9 DEG7/a98g0c2pscQuOtOxHCpQhf7IhR3HN3JDiDgWWngNa/TwM5AlLD+gSF9ZvsP 28/UEK2eq2cT8P4= =PDPe -----END PGP SIGNATURE----- Fri May 5 11:21:32 UTC 2023 I: Checking whether the package is not for us Fri May 5 11:21:32 UTC 2023 I: Starting 1st build on remote node virt64c-armhf-rb.debian.net. Fri May 5 11:21:32 UTC 2023 I: Preparing to do remote build '1' on virt64c-armhf-rb.debian.net. Fri May 5 11:30:12 UTC 2023 I: Deleting $TMPDIR on virt64c-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu May 4 23:21:38 -12 2023 I: pbuilder-time-stamp: 1683285698 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. 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-5.dsc] I: copying [./tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz] I: copying [./tvc_5.0.3+git20151221.80e144e+dfsg-5.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Sep 6 03:33:36 2022 -12 gpgv: using RSA key 2D65BC1EB9665A6E97F9730AB3F5945285219E1F gpgv: issuer "mdbilal@disroot.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc: no acceptable signature found 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-5.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 dpkg-source: info: applying gcc11.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/30698/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='e3f9aaeb6c1043d882ecdd7b118a95bd' 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='30698' 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/r-b-build.BDljuEVv/pbuilderrc_qbjO --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.BDljuEVv/b1 --logfile b1/build.log tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt64c 5.10.0-22-arm64 #1 SMP Debian 5.10.178-3 (2023-04-22) aarch64 GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash -rwxr-xr-x 1 root root 133220 Sep 20 2022 date -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd -rwxr-xr-x 1 root root 68104 Sep 20 2022 df -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 67548 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch -rwxr-xr-x 1 root root 67548 Sep 20 2022 true -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/30698/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: armhf 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 (= 13), 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 ... 19329 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 (= 13); 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} libarmadillo11{a} libarpack2{a} libarpack2-dev{a} libbamtools-dev{a} libbamtools2.5.2{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} libcurl4-openssl-dev{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} libicu72{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjsoncpp-dev{a} libjsoncpp25{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libproc2-0{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsmithwaterman-dev{a} libsmithwaterman0{a} libssh2-1{a} libssl-dev{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 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 50.6 MB of archives. After unpacking 306 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf libproc2-0 armhf 2:4.0.2-3 [54.2 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf procps armhf 2:4.0.2-3 [695 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 11 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf libarchive13 armhf 3.6.2-1 [299 kB] Get: 21 http://deb.debian.org/debian bookworm/main armhf libbrotli1 armhf 1.0.9-2+b6 [271 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-10 [19.0 kB] Get: 23 http://deb.debian.org/debian bookworm/main armhf libsasl2-2 armhf 2.1.28+dfsg-10 [52.3 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5 [158 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf libnghttp2-14 armhf 1.52.0-1 [60.8 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf libpsl5 armhf 0.21.2-1 [57.5 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf libssh2-1 armhf 1.10.0-3+b1 [163 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf libcurl4 armhf 7.88.1-9 [347 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf libexpat1 armhf 2.5.0-1 [79.9 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf libjsoncpp25 armhf 1.9.5-4 [68.6 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf librhash0 armhf 1.4.3-3 [146 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf libuv1 armhf 1.44.2-1 [126 kB] Get: 34 http://deb.debian.org/debian bookworm/main armhf cmake-data all 3.25.1-1 [2026 kB] Get: 35 http://deb.debian.org/debian bookworm/main armhf cmake armhf 3.25.1-1 [4263 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 41 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 42 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 43 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 44 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 45 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 46 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 49 http://deb.debian.org/debian bookworm/main armhf hdf5-helpers armhf 1.10.8+repack1-1 [27.9 kB] Get: 50 http://deb.debian.org/debian bookworm/main armhf libaec0 armhf 1.0.6-1+b1 [19.8 kB] Get: 51 http://deb.debian.org/debian bookworm/main armhf libsz2 armhf 1.0.6-1+b1 [7864 B] Get: 52 http://deb.debian.org/debian bookworm/main armhf libaec-dev armhf 1.0.6-1+b1 [18.1 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf libblas3 armhf 3.11.0-2 [105 kB] Get: 54 http://deb.debian.org/debian bookworm/main armhf libgfortran5 armhf 12.2.0-14 [246 kB] Get: 55 http://deb.debian.org/debian bookworm/main armhf liblapack3 armhf 3.11.0-2 [1724 kB] Get: 56 http://deb.debian.org/debian bookworm/main armhf libarpack2 armhf 3.8.0-3 [82.5 kB] Get: 57 http://deb.debian.org/debian bookworm/main armhf libsuperlu5 armhf 5.3.0+dfsg1-2+b1 [139 kB] Get: 58 http://deb.debian.org/debian bookworm/main armhf libarmadillo11 armhf 1:11.4.2+dfsg-1 [96.6 kB] Get: 59 http://deb.debian.org/debian bookworm/main armhf libblas-dev armhf 3.11.0-2 [115 kB] Get: 60 http://deb.debian.org/debian bookworm/main armhf liblapack-dev armhf 3.11.0-2 [1798 kB] Get: 61 http://deb.debian.org/debian bookworm/main armhf libarpack2-dev armhf 3.8.0-3 [99.7 kB] Get: 62 http://deb.debian.org/debian bookworm/main armhf libhdf5-103-1 armhf 1.10.8+repack1-1 [1183 kB] Get: 63 http://deb.debian.org/debian bookworm/main armhf libhdf5-fortran-102 armhf 1.10.8+repack1-1 [82.1 kB] Get: 64 http://deb.debian.org/debian bookworm/main armhf libhdf5-hl-100 armhf 1.10.8+repack1-1 [65.3 kB] Get: 65 http://deb.debian.org/debian bookworm/main armhf libhdf5-hl-fortran-100 armhf 1.10.8+repack1-1 [38.8 kB] Get: 66 http://deb.debian.org/debian bookworm/main armhf libhdf5-cpp-103-1 armhf 1.10.8+repack1-1 [119 kB] Get: 67 http://deb.debian.org/debian bookworm/main armhf libhdf5-hl-cpp-100 armhf 1.10.8+repack1-1 [25.2 kB] Get: 68 http://deb.debian.org/debian bookworm/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB] Get: 69 http://deb.debian.org/debian bookworm/main armhf libjpeg62-turbo armhf 1:2.1.5-2 [143 kB] Get: 70 http://deb.debian.org/debian bookworm/main armhf libjpeg62-turbo-dev armhf 1:2.1.5-2 [260 kB] Get: 71 http://deb.debian.org/debian bookworm/main armhf libjpeg-dev armhf 1:2.1.5-2 [71.8 kB] Get: 72 http://deb.debian.org/debian bookworm/main armhf libcurl4-openssl-dev armhf 7.88.1-9 [453 kB] Get: 73 http://deb.debian.org/debian bookworm/main armhf libssl-dev armhf 3.0.8-1 [2132 kB] Get: 74 http://deb.debian.org/debian bookworm/main armhf libhdf5-dev armhf 1.10.8+repack1-1 [2573 kB] Get: 75 http://deb.debian.org/debian bookworm/main armhf libsuperlu-dev armhf 5.3.0+dfsg1-2+b1 [22.4 kB] Get: 76 http://deb.debian.org/debian bookworm/main armhf libarmadillo-dev armhf 1:11.4.2+dfsg-1 [403 kB] Get: 77 http://deb.debian.org/debian bookworm/main armhf libbamtools2.5.2 armhf 2.5.2+dfsg-4 [130 kB] Get: 78 http://deb.debian.org/debian bookworm/main armhf libbamtools-dev armhf 2.5.2+dfsg-4 [198 kB] Get: 79 http://deb.debian.org/debian bookworm/main armhf libboost1.74-dev armhf 1.74.0+ds1-20 [9510 kB] Get: 80 http://deb.debian.org/debian bookworm/main armhf libboost-math1.74.0 armhf 1.74.0+ds1-20 [324 kB] Get: 81 http://deb.debian.org/debian bookworm/main armhf libboost-math1.74-dev armhf 1.74.0+ds1-20 [383 kB] Get: 82 http://deb.debian.org/debian bookworm/main armhf libboost-math-dev armhf 1.74.0.3 [4532 B] Get: 83 http://deb.debian.org/debian bookworm/main armhf libdisorder0 armhf 0.0.2+git20130809.8062ee1-4+b1 [5220 B] Get: 84 http://deb.debian.org/debian bookworm/main armhf libdisorder-dev armhf 0.0.2+git20130809.8062ee1-4+b1 [4732 B] Get: 85 http://deb.debian.org/debian bookworm/main armhf libjsoncpp-dev armhf 1.9.5-4 [26.4 kB] Get: 86 http://deb.debian.org/debian bookworm/main armhf libsmithwaterman0 armhf 0.0+git20160702.2610e25-12+b1 [33.0 kB] Get: 87 http://deb.debian.org/debian bookworm/main armhf libsmithwaterman-dev armhf 0.0+git20160702.2610e25-12+b1 [38.2 kB] Fetched 50.6 MB in 7s (6817 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:armhf. (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 ... 19329 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.2-3_armhf.deb ... Unpacking libproc2-0:armhf (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../01-procps_2%3a4.0.2-3_armhf.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.44-3_armhf.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../04-libmagic1_1%3a5.44-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.44-3_armhf.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-12_armhf.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../07-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.22.4-10_armhf.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.38.1-5+b1_armhf.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../10-libpipeline1_1.5.7-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.11.2-2_armhf.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.19-3_armhf.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../17-libicu72_72.1-3_armhf.deb ... Unpacking libicu72:armhf (72.1-3) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../18-libxml2_2.9.14+dfsg-1.2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.2) ... Selecting previously unselected package libarchive13:armhf. Preparing to unpack .../19-libarchive13_3.6.2-1_armhf.deb ... Unpacking libarchive13:armhf (3.6.2-1) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../20-libbrotli1_1.0.9-2+b6_armhf.deb ... Unpacking libbrotli1:armhf (1.0.9-2+b6) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../21-libsasl2-modules-db_2.1.28+dfsg-10_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../22-libsasl2-2_2.1.28+dfsg-10_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:armhf. Preparing to unpack .../23-libldap-2.5-0_2.5.13+dfsg-5_armhf.deb ... Unpacking libldap-2.5-0:armhf (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../24-libnghttp2-14_1.52.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.52.0-1) ... Selecting previously unselected package libpsl5:armhf. Preparing to unpack .../25-libpsl5_0.21.2-1_armhf.deb ... Unpacking libpsl5:armhf (0.21.2-1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../26-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:armhf. Preparing to unpack .../27-libssh2-1_1.10.0-3+b1_armhf.deb ... Unpacking libssh2-1:armhf (1.10.0-3+b1) ... Selecting previously unselected package libcurl4:armhf. Preparing to unpack .../28-libcurl4_7.88.1-9_armhf.deb ... Unpacking libcurl4:armhf (7.88.1-9) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../29-libexpat1_2.5.0-1_armhf.deb ... Unpacking libexpat1:armhf (2.5.0-1) ... Selecting previously unselected package libjsoncpp25:armhf. Preparing to unpack .../30-libjsoncpp25_1.9.5-4_armhf.deb ... Unpacking libjsoncpp25:armhf (1.9.5-4) ... Selecting previously unselected package librhash0:armhf. Preparing to unpack .../31-librhash0_1.4.3-3_armhf.deb ... Unpacking librhash0:armhf (1.4.3-3) ... Selecting previously unselected package libuv1:armhf. Preparing to unpack .../32-libuv1_1.44.2-1_armhf.deb ... Unpacking libuv1:armhf (1.44.2-1) ... Selecting previously unselected package cmake-data. Preparing to unpack .../33-cmake-data_3.25.1-1_all.deb ... Unpacking cmake-data (3.25.1-1) ... Selecting previously unselected package cmake. Preparing to unpack .../34-cmake_3.25.1-1_armhf.deb ... Unpacking cmake (3.25.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../35-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../36-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../37-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../38-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 .../39-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../40-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../41-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../42-libelf1_0.188-2.1_armhf.deb ... Unpacking libelf1:armhf (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../43-dwz_0.15-1_armhf.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package gettext. Preparing to unpack .../44-gettext_0.21-12_armhf.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../45-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../46-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../47-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package hdf5-helpers. Preparing to unpack .../48-hdf5-helpers_1.10.8+repack1-1_armhf.deb ... Unpacking hdf5-helpers (1.10.8+repack1-1) ... Selecting previously unselected package libaec0:armhf. Preparing to unpack .../49-libaec0_1.0.6-1+b1_armhf.deb ... Unpacking libaec0:armhf (1.0.6-1+b1) ... Selecting previously unselected package libsz2:armhf. Preparing to unpack .../50-libsz2_1.0.6-1+b1_armhf.deb ... Unpacking libsz2:armhf (1.0.6-1+b1) ... Selecting previously unselected package libaec-dev:armhf. Preparing to unpack .../51-libaec-dev_1.0.6-1+b1_armhf.deb ... Unpacking libaec-dev:armhf (1.0.6-1+b1) ... Selecting previously unselected package libblas3:armhf. Preparing to unpack .../52-libblas3_3.11.0-2_armhf.deb ... Unpacking libblas3:armhf (3.11.0-2) ... Selecting previously unselected package libgfortran5:armhf. Preparing to unpack .../53-libgfortran5_12.2.0-14_armhf.deb ... Unpacking libgfortran5:armhf (12.2.0-14) ... Selecting previously unselected package liblapack3:armhf. Preparing to unpack .../54-liblapack3_3.11.0-2_armhf.deb ... Unpacking liblapack3:armhf (3.11.0-2) ... Selecting previously unselected package libarpack2:armhf. Preparing to unpack .../55-libarpack2_3.8.0-3_armhf.deb ... Unpacking libarpack2:armhf (3.8.0-3) ... Selecting previously unselected package libsuperlu5:armhf. Preparing to unpack .../56-libsuperlu5_5.3.0+dfsg1-2+b1_armhf.deb ... Unpacking libsuperlu5:armhf (5.3.0+dfsg1-2+b1) ... Selecting previously unselected package libarmadillo11. Preparing to unpack .../57-libarmadillo11_1%3a11.4.2+dfsg-1_armhf.deb ... Unpacking libarmadillo11 (1:11.4.2+dfsg-1) ... Selecting previously unselected package libblas-dev:armhf. Preparing to unpack .../58-libblas-dev_3.11.0-2_armhf.deb ... Unpacking libblas-dev:armhf (3.11.0-2) ... Selecting previously unselected package liblapack-dev:armhf. Preparing to unpack .../59-liblapack-dev_3.11.0-2_armhf.deb ... Unpacking liblapack-dev:armhf (3.11.0-2) ... Selecting previously unselected package libarpack2-dev:armhf. Preparing to unpack .../60-libarpack2-dev_3.8.0-3_armhf.deb ... Unpacking libarpack2-dev:armhf (3.8.0-3) ... Selecting previously unselected package libhdf5-103-1:armhf. Preparing to unpack .../61-libhdf5-103-1_1.10.8+repack1-1_armhf.deb ... Unpacking libhdf5-103-1:armhf (1.10.8+repack1-1) ... Selecting previously unselected package libhdf5-fortran-102:armhf. Preparing to unpack .../62-libhdf5-fortran-102_1.10.8+repack1-1_armhf.deb ... Unpacking libhdf5-fortran-102:armhf (1.10.8+repack1-1) ... Selecting previously unselected package libhdf5-hl-100:armhf. Preparing to unpack .../63-libhdf5-hl-100_1.10.8+repack1-1_armhf.deb ... Unpacking libhdf5-hl-100:armhf (1.10.8+repack1-1) ... Selecting previously unselected package libhdf5-hl-fortran-100:armhf. Preparing to unpack .../64-libhdf5-hl-fortran-100_1.10.8+repack1-1_armhf.deb ... Unpacking libhdf5-hl-fortran-100:armhf (1.10.8+repack1-1) ... Selecting previously unselected package libhdf5-cpp-103-1:armhf. Preparing to unpack .../65-libhdf5-cpp-103-1_1.10.8+repack1-1_armhf.deb ... Unpacking libhdf5-cpp-103-1:armhf (1.10.8+repack1-1) ... Selecting previously unselected package libhdf5-hl-cpp-100:armhf. Preparing to unpack .../66-libhdf5-hl-cpp-100_1.10.8+repack1-1_armhf.deb ... Unpacking libhdf5-hl-cpp-100:armhf (1.10.8+repack1-1) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../67-zlib1g-dev_1%3a1.2.13.dfsg-1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.13.dfsg-1) ... Selecting previously unselected package libjpeg62-turbo:armhf. Preparing to unpack .../68-libjpeg62-turbo_1%3a2.1.5-2_armhf.deb ... Unpacking libjpeg62-turbo:armhf (1:2.1.5-2) ... Selecting previously unselected package libjpeg62-turbo-dev:armhf. Preparing to unpack .../69-libjpeg62-turbo-dev_1%3a2.1.5-2_armhf.deb ... Unpacking libjpeg62-turbo-dev:armhf (1:2.1.5-2) ... Selecting previously unselected package libjpeg-dev:armhf. Preparing to unpack .../70-libjpeg-dev_1%3a2.1.5-2_armhf.deb ... Unpacking libjpeg-dev:armhf (1:2.1.5-2) ... Selecting previously unselected package libcurl4-openssl-dev:armhf. Preparing to unpack .../71-libcurl4-openssl-dev_7.88.1-9_armhf.deb ... Unpacking libcurl4-openssl-dev:armhf (7.88.1-9) ... Selecting previously unselected package libssl-dev:armhf. Preparing to unpack .../72-libssl-dev_3.0.8-1_armhf.deb ... Unpacking libssl-dev:armhf (3.0.8-1) ... Selecting previously unselected package libhdf5-dev. Preparing to unpack .../73-libhdf5-dev_1.10.8+repack1-1_armhf.deb ... Unpacking libhdf5-dev (1.10.8+repack1-1) ... Selecting previously unselected package libsuperlu-dev:armhf. Preparing to unpack .../74-libsuperlu-dev_5.3.0+dfsg1-2+b1_armhf.deb ... Unpacking libsuperlu-dev:armhf (5.3.0+dfsg1-2+b1) ... Selecting previously unselected package libarmadillo-dev. Preparing to unpack .../75-libarmadillo-dev_1%3a11.4.2+dfsg-1_armhf.deb ... Unpacking libarmadillo-dev (1:11.4.2+dfsg-1) ... Selecting previously unselected package libbamtools2.5.2:armhf. Preparing to unpack .../76-libbamtools2.5.2_2.5.2+dfsg-4_armhf.deb ... Unpacking libbamtools2.5.2:armhf (2.5.2+dfsg-4) ... Selecting previously unselected package libbamtools-dev:armhf. Preparing to unpack .../77-libbamtools-dev_2.5.2+dfsg-4_armhf.deb ... Unpacking libbamtools-dev:armhf (2.5.2+dfsg-4) ... Selecting previously unselected package libboost1.74-dev:armhf. Preparing to unpack .../78-libboost1.74-dev_1.74.0+ds1-20_armhf.deb ... 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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-5_source.changes dpkg-buildpackage: info: source package tvc dpkg-buildpackage: info: source version 5.0.3+git20151221.80e144e+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Mohammed Bilal dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-arm-linux-gnueabihf && 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_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf .. CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- 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 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY 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make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' [ 1%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o [ 3%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o [ 4%] Building CXX object 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-DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o -MF CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o.d -o CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/IndelAssembly/IndelAssembly.cpp [ 6%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o -MF CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o.d -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/prepare_hotspots.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:36:24: 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:385, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:92:1: note: declared here 92 | set_stream_err1(std::ostream& user_stream) | ^~~~~~~~~~~~~~~ /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:24: warning: 'void arma::set_stream_err2(std::ostream&)' is deprecated [-Wdeprecated-declarations] 37 | arma::set_stream_err2(null_ostream); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/armadillo_bits/debug.hpp:103:1: note: declared here 103 | set_stream_err2(std::ostream& user_stream) | ^~~~~~~~~~~~~~~ [ 7%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io 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-I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o -MF 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-I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/BAMWalkerEngine.cpp [ 12%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o -MF CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o.d -o CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/SampleManager.cpp [ 14%] Building CXX object CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o -MF CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o.d -o CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp In file included from /usr/include/c++/12/vector:70, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.h:11, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp:4: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void OptArgs::StringToDoubleVector(std::vector&, const std::string&, const std::string&, char)' at /build/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp:474:21: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 15%] 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 -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o 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-I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o -MF CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o.d -o CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/Util/Utils.cpp [ 18%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/SampleManager.cpp [ 20%] Building CXX object CMakeFiles/tvcassembly.dir/IonVersion.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -MF CMakeFiles/tvcassembly.dir/IonVersion.cpp.o.d -o CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/IonVersion.cpp [ 21%] Linking CXX executable tvcassembly /usr/bin/cmake -E cmake_link_script CMakeFiles/tvcassembly.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -o tvcassembly -lbamtools -lz -lpthread -ljsoncpp make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' [ 21%] Built target tvcassembly [ 23%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/TargetsManager.cpp [ 25%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o -MF CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o.d -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp [ 26%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HandleVariant.cpp [ 28%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HotspotReader.cpp In file included from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.h:64, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:19: /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp: In instantiation of 'void markov_chain::optimal_path() [with T = unsigned int]': /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:64:3: required from 'void markov_chain::initialize(_ForwardIterator, _ForwardIterator, T, T) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; T = unsigned int]' /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:38:13: required from 'markov_chain::markov_chain(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; T = unsigned int]' /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:550:69: required from here /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:114:13: warning: ignoring return value of 'constexpr bool std::operator!=(const reverse_iterator<_Iterator>&, const reverse_iterator<_Iterator>&) [with _Iterator = __gnu_cxx::__normal_iterator*, vector > >]', declared with attribute 'nodiscard' [-Wunused-result] 114 | for (; it != rend(), vit != values.rend(); it++, vit++) { | ~~~^~~~~~~~~ In file included from /usr/include/c++/12/string:47, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:7: /usr/include/c++/12/bits/stl_iterator.h:458:5: note: declared here 458 | operator!=(const reverse_iterator<_Iterator>& __x, | ^~~~~~~~ [ 29%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o -MF CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o.d -o CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/TargetsManager.cpp In file included from /usr/include/c++/12/vector:70, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:13: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {markov_state}; _Tp = markov_state; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {markov_state}; _Tp = markov_state; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {markov_state}; _Tp = markov_state; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = markov_state; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void markov_chain::generate_states(T, T) [with T = unsigned int]' at /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:78:21: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 31%] Building CXX object CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o -MF CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o.d -o CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp [ 32%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/MetricsManager.cpp [ 34%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o -MF CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/Variant.cpp [ 35%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/MiscUtil.cpp In file included from /usr/include/c++/12/vector:70, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.h:11, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp:4: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void OptArgs::StringToDoubleVector(std::vector&, const std::string&, const std::string&, char)' at /build/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp:474:21: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 37%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/ExtendParameters.cpp [ 39%] 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 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o -MF CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/split.cpp [ 40%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o -MF CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/tabix.cpp [ 42%] 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 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o -MF CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o.d -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:336:42: 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; | ^~~~~~~~ [ 43%] 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 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o -MF CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c /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:678:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 678 | fread(buf, 1, 28, fp->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 45%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp [ 46%] 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 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/IonVersion.cpp.o -MF CMakeFiles/tvcutils.dir/IonVersion.cpp.o.d -o CMakeFiles/tvcutils.dir/IonVersion.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/IonVersion.cpp [ 48%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/VcfFormat.cpp In file included from /usr/include/c++/12/map:60, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.h:14, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:7: /usr/include/c++/12/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair, std::allocator >, LinearCalibrationModel>}; _Key = std::__cxx11::basic_string; _Val = std::pair, LinearCalibrationModel>; _KeyOfValue = std::_Select1st, LinearCalibrationModel> >; _Compare = std::less >; _Alloc = std::allocator, LinearCalibrationModel> >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, LinearCalibrationModel>, std::_Select1st, LinearCalibrationModel> >, std::less >, std::allocator, LinearCalibrationModel> > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.h:12: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const DPTreephaser&}; _Tp = DPTreephaser; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = DPTreephaser; _Alloc = std::allocator]', inlined from 'PersistingThreadObjects::PersistingThreadObjects(const InputStructures&)' at /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:323:38: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair, std::allocator >, LinearCalibrationModel>}; _Key = std::__cxx11::basic_string; _Tp = LinearCalibrationModel; _Compare = std::less >; _Alloc = std::allocator, LinearCalibrationModel> >]', inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair, LinearCalibrationModel>; _Key = std::__cxx11::basic_string; _Tp = LinearCalibrationModel; _Compare = std::less >; _Alloc = std::allocator, LinearCalibrationModel> >]' at /usr/include/c++/12/bits/stl_map.h:858:27, inlined from 'void RecalibrationHandler::ReadRecalibrationFromComments(const BamTools::SamHeader&, const std::map, int>&)' at /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:272:36: /usr/include/c++/12/bits/stl_map.h:638:45: note: parameter passing for argument of type 'std::map, LinearCalibrationModel>::const_iterator' {aka 'std::_Rb_tree, std::pair, LinearCalibrationModel>, std::_Select1st, LinearCalibrationModel> >, std::less >, std::allocator, LinearCalibrationModel> > >::const_iterator'} changed in GCC 7.1 638 | return _M_t._M_emplace_hint_unique(__pos, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 639 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 50%] Linking CXX executable tvcutils /usr/bin/cmake -E cmake_link_script CMakeFiles/tvcutils.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/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 make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' [ 50%] Built target tvcutils [ 51%] 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 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads/ExtendedReadInfo.cpp [ 53%] 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 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/ErrorMotifs.cpp [ 54%] 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 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/LocalContext.cpp [ 56%] 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 -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/ClassifyVariant.cpp [ 57%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.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 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/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/DecisionTreeData.cpp [ 60%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp [ 62%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HypothesisEvaluator.cpp /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp: In function 'double VariantAssist::MannWhitneyU(std::vector&, std::vector&, bool)': /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:191:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 191 | fprintf(stdout, "ref.size()=%lu; ", ref.size()); | ~~^ ~~~~~~~~~~ | | | | | std::vector::size_type {aka unsigned int} | long unsigned int | %u /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:192:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 192 | fprintf(stdout, "var.size()=%lu; ", var.size()); | ~~^ ~~~~~~~~~~ | | | | | std::vector::size_type {aka unsigned int} | long unsigned int | %u /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:193:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 193 | fprintf(stdout, "both.size()=%lu; ", both.size()); | ~~^ ~~~~~~~~~~~ | | | | | std::vector::size_type {aka unsigned int} | long unsigned int | %u [ 64%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o.d -o 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-I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/BiasGenerator.cpp [ 67%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/SigmaGenerator.cpp [ 68%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.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 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-I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o -MF CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o.d -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:336:42: 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; | ^~~~~~~~ [ 82%] 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 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 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-I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/Util/OptArgs.cpp.o -MF CMakeFiles/tvc.dir/Util/OptArgs.cpp.o.d -o CMakeFiles/tvc.dir/Util/OptArgs.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp [ 93%] 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 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/realignment/Realigner.cpp.o -MF CMakeFiles/tvc.dir/realignment/Realigner.cpp.o.d -o CMakeFiles/tvc.dir/realignment/Realigner.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment/Realigner.cpp In file included from /usr/include/c++/12/vector:70, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.h:11, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp:4: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void OptArgs::StringToDoubleVector(std::vector&, const std::string&, const std::string&, char)' at /build/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp:474:21: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 95%] 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 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/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: tvc_call 1: Test command: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvc 1: Working Directory: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf 1: Test timeout computed to be: 10000000 test 2 Start 2: tvc_test_1_thread_sse_off 2: Test command: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvc "--input-bam" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--use-sse-basecaller" "off" "--trim-ampliseq-primers" "on" "--num-threads" "1" "--output-dir" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/test1" "--output-vcf" "small_variants.vcf" 2: Working Directory: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf 2: Test timeout computed to be: 10000000 test 3 Start 3: tvc_test_4_threads_sse_off_with_parameter_file 3: Test command: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvc "--input-bam" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--parameters-file" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json" "--use-sse-basecaller" "off" "--trim-ampliseq-primers" "on" "--num-threads" "4" "--output-dir" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/test2" "--output-vcf" "small_variants.vcf" 3: Working Directory: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf 3: Test timeout computed to be: 10000000 1: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 1: 1: Usage: tvc [options] 1: 1: General options: 1: -h,--help print this help message and exit 1: -v,--version print version and exit 1: -n,--num-threads INT number of worker threads [2] 1: -N,--num-variants-per-thread INT worker thread batch size [500] 1: --parameters-file FILE json file with algorithm control parameters [optional] 1: 1: Inputs: 1: -r,--reference FILE reference fasta file [required] 1: -b,--input-bam FILE bam file with mapped reads [required] 1: -g,--sample-name STRING sample for which variants are called (In case of input BAM files with multiple samples) [optional if there is only one sample] 1: --force-sample-name STRING force all read groups to have this sample name [off] 1: -t,--target-file FILE only process targets in this bed file [optional] 1: --trim-ampliseq-primers on/off match reads to targets and trim the ends that reach outside them [off] 1: -D,--downsample-to-coverage INT ?? [2000] 1: --model-file FILE HP recalibration model input file. 1: --recal-model-hp-thres INT Lower threshold for HP recalibration. 1: 1: Outputs: 1: -O,--output-dir DIRECTORY base directory for all output files [current dir] 1: -o,--output-vcf FILE vcf file with variant calling results [required] 1: --suppress-reference-genotypes on/off write reference calls into the filtered variants vcf [on] 1: --suppress-no-calls on/off write filtered variants into the filtered variants vcf [on] 1: --suppress-nocall-genotypes on/off do not report a genotype for filtered variants [on] 1: 1: Variant candidate generation (FreeBayes): 1: --allow-snps on/off allow generation of snp candidates [on] 1: --allow-indels on/off allow generation of indel candidates [on] 1: --allow-mnps on/off allow generation of mnp candidates [on] 1: --allow-complex on/off allow generation of block substitution candidates [off] 1: --max-complex-gap INT maximum number of reference alleles between two alternate alleles to allow merging of the alternate alleles [1] 1: -m,--use-best-n-alleles INT maximum number of snp alleles [2] 1: -M,--min-mapping-qv INT do not use reads with mapping quality below this [4] 1: -U,--read-snp-limit INT do not use reads with number of snps above this [10] 1: -z,--read-max-mismatch-fraction FLOAT do not use reads with fraction of mismatches above this [1.0] 1: --gen-min-alt-allele-freq FLOAT minimum required alt allele frequency to generate a candidate [0.2] 1: --gen-min-indel-alt-allele-freq FLOAT minimum required alt allele frequency to generate a homopolymer indel candidate [0.2] 1: --gen-min-coverage INT minimum required coverage to generate a candidate [6] 1: 1: External variant candidates: 1: -c,--input-vcf FILE vcf.gz file (+.tbi) with additional candidate variant locations and alleles [optional] 1: --process-input-positions-only on/off only generate candidates at locations from input-vcf [off] 1: --use-input-allele-only on/off only consider provided alleles for locations in input-vcf [off] 1: 1: Variant candidate scoring options: 1: --min-delta-for-flow FLOAT minimum prediction delta for scoring flows [0.1] 1: --max-flows-to-test INT maximum number of scoring flows [10] 1: --outlier-probability FLOAT probability for outlier reads [0.01] 1: --heavy-tailed INT degrees of freedom in t-dist modeling signal residual heavy tail [3] 1: --suppress-recalibration on/off Suppress homopolymer recalibration [on]. 1: --do-snp-realignment on/off Realign reads in the vicinity of candidate snp variants [on]. 1: --do-mnp-realignment on/off Realign reads in the vicinity of candidate mnp variants [do-snp-realignment]. 1: --realignment-threshold FLOAT Max. allowed fraction of reads where realignment causes an alignment change [1.0]. 1: 1: Advanced variant candidate scoring options: 1: --use-sse-basecaller on/off Switch to use the vectorized version of the basecaller [off]. 1: --resolve-clipped-bases on/off If 'true', the basecaller is used to solve soft clipped bases [off]. 1: --prediction-precision FLOAT prior weight in bias estimator [30.0] 1: --shift-likelihood-penalty FLOAT penalize log-likelihood for solutions involving large systematic bias [0.3] 1: --minimum-sigma-prior FLOAT prior variance per data point, constant [0.085] 1: --slope-sigma-prior FLOAT prior rate of increase of variance over minimum by signal [0.0084] 1: --sigma-prior-weight FLOAT weight of prior estimate of variance compared to observations [1.0] 1: --k-zero FLOAT variance increase for adding systematic bias [3.0] 1: --sse-relative-safety-level FLOAT dampen strand bias detection for SSE events for low coverage [0.025] 1: --tune-sbias FLOAT dampen strand bias detection for low coverage [0.01] 1: --max-detail-level INT number of evaluated frequencies for a given hypothesis, reduce for very high coverage, set to zero to disable this option [0] 1: 1: Variant filtering: 1: -k,--snp-min-coverage INT filter out snps with total coverage below this [6] 1: -C,--snp-min-cov-each-strand INT filter out snps with coverage on either strand below this [0] 1: -B,--snp-min-variant-score FLOAT filter out snps with QUAL score below this [10.0] 1: -s,--snp-strand-bias FLOAT filter out snps with strand bias above this [0.95] given pval < snp-strand-bias-pval 1: --snp-strand-bias-pval FLOAT filter out snps with pval below this [1.0] given strand bias > snp-strand-bias 1: -A,--snp-min-allele-freq FLOAT minimum required alt allele frequency for non-reference snp calls [0.2] 1: --mnp-min-coverage INT filter out mnps with total coverage below this [snp-min-coverage] 1: --mnp-min-cov-each-strand INT filter out mnps with coverage on either strand below this, [snp-min-cov-each-strand] 1: --mnp-min-variant-score FLOAT filter out mnps with QUAL score below this [snp-min-variant-score] 1: --mnp-strand-bias FLOAT filter out mnps with strand bias above this [snp-strand-bias] given pval < mnp-strand-bias-pval 1: --mnp-strand-bias-pval FLOAT filter out mnps with pval below this [snp-strand-bias-pval] given strand bias > mnp-strand-bias 1: --mnp-min-allele-freq FLOAT minimum required alt allele frequency for non-reference mnp calls [snp-min-allele-freq] 1: --indel-min-coverage INT filter out indels with total coverage below this [30] 1: --indel-min-cov-each-strand INT filter out indels with coverage on either strand below this [1] 1: --indel-min-variant-score FLOAT filter out indels with QUAL score below this [10.0] 1: -S,--indel-strand-bias FLOAT filter out indels with strand bias above this [0.95] given pval < indel-strand-bias-pval 1: --indel-strand-bias-pval FLOAT filter out indels with pval below this [1.0] given strand bias > indel-strand-bias 1: --indel-min-allele-freq FLOAT minimum required alt allele frequency for non-reference indel call [0.2] 1: --hotspot-min-coverage INT filter out hotspot variants with total coverage below this [6] 1: --hotspot-min-cov-each-strand INT filter out hotspot variants with coverage on either strand below this [snp-min-cov-each-strand] 1: --hotspot-min-variant-score FLOAT filter out hotspot variants with QUAL score below this [snp-min-variant-score] 1: --hotspot-strand-bias FLOAT filter out hotspot variants with strand bias above this [0.95] given pval < hotspot-strand-bias-pval 1: --hotspot-strand-bias-pval FLOAT filter out hotspot variants with pval below this [1.0] given strand bias > hotspot-strand-bias 1: -H,--hotspot-min-allele-freq FLOAT minimum required alt allele frequency for non-reference hotspot variant call [0.2] 1: -L,--hp-max-length INT filter out indels in homopolymers above this [8] 1: -e,--error-motifs FILE table of systematic error motifs and their error rates [optional] 1: --sse-prob-threshold FLOAT filter out variants in motifs with error rates above this [0.2] 1: --min-ratio-reads-non-sse-strand FLOAT minimum required alt allele frequency for variants with error motifs on opposite strand [0.2] 1: --indel-as-hpindel on/off apply indel filters to non HP indels [off] 1: 1: Position bias variant filtering: 1: --use-position-bias on/off enable the position bias filter [off] 1: --position-bias FLOAT filter out variants with position bias relative to soft clip ends in reads > position-bias [0.75] 1: --position-bias-pval FLOAT filter out if position bias above position-bias given pval < position-bias-pval [0.05] 1: --position-bias-ref-fraction FLOAT skip position bias filter if (reference read count)/(reference + alt allele read count) <= to this [0.05] 1: 1: Filters that depend on scoring across alleles: 1: --data-quality-stringency FLOAT minimum mean log-likelihood delta per read [4.0] 1: --read-rejection-threshold FLOAT filter variants where large numbers of reads are rejected as outliers [0.5] 1: --filter-unusual-predictions FLOAT posterior log likelihood threshold for accepting bias estimate [0.3] 1: --filter-deletion-predictions FLOAT check post-evaluation systematic bias in deletions; a high value like 100 effectively turns off this filter [100.0] 1: --filter-insertion-predictions FLOAT check post-evaluation systematic bias in insertions; a high value like 100 effectively turns off this filter [100.0] 1: 1: --heal-snps on/off suppress in/dels not participating in diploid variant genotypes if the genotype contains a SNP or MNP [on]. 1: 1: Debugging: 1: -d,--debug INT (0/1/2) display extra debug messages [0] 1: --do-json-diagnostic on/off (devel) dump internal state to json file (uses much more time/memory/disk) [off] 1: --postprocessed-bam FILE (devel) save tvc-processed reads to an (unsorted) BAM file [optional] 1: --do-minimal-diagnostic on/off (devel) provide minimal read information for called variants [off] 1: --override-limits on/off (devel) disable limit-check on input parameters [off]. 1: 2: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 2: 2: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf 2: hp-max-length = 8 (integer, builtin default) 2: sse-prob-threshold = 0.2 (double, builtin default) 2: min-ratio-reads-non-sse-strand = 0.2 (double, builtin default) 2: sse-relative-safety-level = 0.025 (double, builtin default) 2: do-snp-realignment = true (boolean, builtin default) 2: do-mnp-realignment = true (boolean, builtin default) 2: realignment-threshold = 1 (double, builtin default) 2: indel-as-hpindel = false (boolean, builtin default) 2: data-quality-stringency = 4 (double, builtin default) 2: read-rejection-threshold = 0.5 (double, builtin default) 2: use-position-bias = false (boolean, builtin default) 2: position-bias-ref-fraction = 0.05 (double, builtin default) 2: position-bias = 0.75 (double, builtin default) 2: position-bias-pval = 0.05 (double, builtin default) 2: downsample-to-coverage = 2000 (integer, builtin default) 2: tune-sbias = 0.01 (double, builtin default) 2: suppress-reference-genotypes = true (boolean, builtin default) 2: suppress-nocall-genotypes = true (boolean, builtin default) 2: suppress-no-calls = true (boolean, builtin default) 2: heal-snps = true (boolean, builtin default) 2: snp-min-cov-each-strand = 0 (integer, builtin default) 2: snp-min-variant-score = 10 (double, builtin default) 2: snp-min-allele-freq = 0.2 (double, builtin default) 2: snp-min-coverage = 6 (integer, builtin default) 2: snp-strand-bias = 0.95 (double, builtin default) 2: snp-strand-bias-pval = 1 (double, builtin default) 2: mnp-min-cov-each-strand = 0 (integer, builtin default) 2: mnp-min-variant-score = 10 (double, builtin default) 2: mnp-min-allele-freq = 0.2 (double, builtin default) 2: mnp-min-coverage = 6 (integer, builtin default) 2: mnp-strand-bias = 0.95 (double, builtin default) 2: mnp-strand-bias-pval = 1 (double, builtin default) 2: indel-min-cov-each-strand = 1 (integer, builtin default) 2: indel-min-variant-score = 10 (double, builtin default) 2: indel-min-allele-freq = 0.2 (double, builtin default) 2: indel-min-coverage = 15 (integer, builtin default) 2: indel-strand-bias = 0.85 (double, builtin default) 2: indel-strand-bias-pval = 1 (double, builtin default) 2: hotspot-min-cov-each-strand = 0 (integer, builtin default) 2: hotspot-min-variant-score = 10 (double, builtin default) 2: hotspot-min-allele-freq = 0.2 (double, builtin default) 2: hotspot-min-coverage = 6 (integer, builtin default) 2: hotspot-strand-bias = 0.95 (double, builtin default) 2: hotspot-strand-bias-pval = 1 (double, builtin default) 2: max-flows-to-test = 10 (integer, builtin default) 2: min-delta-for-flow = 0.1 (double, builtin default) 2: prediction-precision = 30 (double, builtin default) 2: outlier-probability = 0.01 (double, builtin default) 2: germline-prior-strength = 0 (double, builtin default) 2: heavy-tailed = 3 (integer, builtin default) 2: filter-unusual-predictions = 0.3 (double, builtin default) 2: soft-clip-bias-checker = 0.1 (double, builtin default) 2: filter-deletion-predictions = 100 (double, builtin default) 2: filter-insertion-predictions = 100 (double, builtin default) 2: max-detail-level = 0 (integer, builtin default) 2: shift-likelihood-penalty = 0.3 (double, builtin default) 2: minimum-sigma-prior = 0.085 (double, builtin default) 2: slope-sigma-prior = 0.0084 (double, builtin default) 2: sigma-prior-weight = 1 (double, builtin default) 2: k-zero = 3 (double, builtin default) 2: num-threads = 1 (integer, command line option) 2: num-variants-per-thread = 250 (integer, builtin default) 2: use-sse-basecaller = false (boolean, command line option) 2: do-json-diagnostic = false (boolean, builtin default) 2: do-minimal-diagnostic = false (boolean, builtin default) 2: process-input-positions-only = false (boolean, builtin default) 2: suppress-recalibration = true (boolean, builtin default) 2: resolve-clipped-bases = false (boolean, builtin default) 2: prefix-exclude = 6 2: allow-indels = true (boolean, builtin default) 2: allow-snps = true (boolean, builtin default) 2: allow-mnps = true (boolean, builtin default) 2: allow-complex = false (boolean, builtin default) 2: left-align-indels = false (boolean, builtin default) 2: use-best-n-alleles = 2 (integer, builtin default) 2: use-input-allele-only = false (boolean, builtin default) 2: min-mapping-qv = 4 (integer, builtin default) 2: read-snp-limit = 10 (integer, builtin default) 2: read-max-mismatch-fraction = 1 (double, builtin default) 2: max-complex-gap = 1 (integer, builtin default) 2: gen-min-alt-allele-freq = 0.2 (double, builtin default) 2: gen-min-coverage = 6 (integer, builtin default) 2: gen-min-indel-alt-allele-freq = 0.2 (double, builtin default) 2: override-limits = false (boolean, builtin default) 2: Limit check parameter hp-max-length: lim. 1 <= 8? OK! 2: Limit check parameter sse-prob-threshold: lim. 0 <= 0.2 <= lim. 1? OK! 2: Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK! 2: Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK! 2: Limit check parameter realignment-threshold: lim. 0 <= 1 <= lim. 1? OK! 2: Limit check parameter data-quality-stringency: lim. 0 <= 4? OK! 2: Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK! 2: Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK! 2: Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK! 2: Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK! 2: Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK! 2: Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK! 2: Limit check parameter snp-min-cov-each-strand: lim. 0 <= 0? OK! 2: Limit check parameter snp-min-variant-score: lim. 0 <= 10? OK! 2: Limit check parameter snp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 2: Limit check parameter snp-min-coverage: lim. 0 <= 6? OK! 2: Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 2: Limit check parameter snp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 2: Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 0? OK! 2: Limit check parameter mnp-min-variant-score: lim. 0 <= 10? OK! 2: Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 2: Limit check parameter mnp-min-coverage: lim. 0 <= 6? OK! 2: Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 2: Limit check parameter mnp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 2: Limit check parameter indel-min-cov-each-strand: lim. 0 <= 1? OK! 2: Limit check parameter indel-min-variant-score: lim. 0 <= 10? OK! 2: Limit check parameter indel-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 2: Limit check parameter indel-min-coverage: lim. 0 <= 15? OK! 2: Limit check parameter indel-strand-bias: lim. 0.5 <= 0.85 <= lim. 1? OK! 2: Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 2: Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 0? OK! 2: Limit check parameter hotspot-min-variant-score: lim. 0 <= 10? OK! 2: Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 2: Limit check parameter hotspot-min-coverage: lim. 0 <= 6? OK! 2: Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 2: Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 2: Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK! 2: Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK! 2: Limit check parameter prediction-precision: lim. 0.1 <= 30? OK! 2: Limit check parameter outlier-probability: lim. 0 <= 0.01 <= lim. 1? OK! 2: Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK! 2: Limit check parameter heavy-tailed: lim. 1 <= 3? OK! 2: Limit check parameter filter-unusual-predictions: lim. 0 <= 0.3? OK! 2: Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK! 2: Limit check parameter filter-deletion-predictions: lim. 0 <= 100? OK! 2: Limit check parameter filter-insertion-predictions: lim. 0 <= 100? OK! 2: Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK! 2: Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK! 2: Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK! 2: Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK! 2: Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK! 2: Limit check parameter k-zero: lim. 0 <= 3? OK! 2: Limit check parameter num-threads: lim. 1 <= 1 <= lim. 128? OK! 2: Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK! 2: Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK! 2: Limit check parameter min-mapping-qv: lim. 0 <= 4? OK! 2: Limit check parameter read-snp-limit: lim. 0 <= 10? OK! 2: Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK! 2: Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 2: Limit check parameter gen-min-coverage: lim. 0 <= 6? OK! 2: Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 2: TargetsManager: Loaded targets file /build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed 2: TargetsManager: 1 target(s) 2: TargetsManager: Trimming of AmpliSeq primers is enabled 1/8 Test #1: tvc_call ......................................... Passed 0.03 sec test 4 Start 4: tvcutils_call 4: Test command: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils 4: Working Directory: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf 4: Test timeout computed to be: 10000000 4: 4: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. 4: 4: Usage: tvcutils [options] 4: 4: Commands: 4: prepare_hotspots Convert BED or VCF file into a valid hotspot file 4: validate_bed Validate targets or hotspots file 4: unify_vcf Unify variants and annotations from all sources (tvc,IndelAssembly,hotpots) 4: 2/8 Test #4: tvcutils_call .................................... Passed 0.01 sec test 5 Start 5: tvcutils_prepare_hotspots_call 5: Test command: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils "prepare_hotspots" 5: Working Directory: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf 5: Test timeout computed to be: 10000000 3: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 3: 3: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf 3: hp-max-length = 8 (integer, parameters json file) 3: sse-prob-threshold = 1 (double, parameters json file) 3: min-ratio-reads-non-sse-strand = 0.2 (double, builtin default) 3: sse-relative-safety-level = 0.025 (double, builtin default) 3: do-snp-realignment = false (boolean, parameters json file) 3: do-mnp-realignment = false (boolean, parameters json file) 3: realignment-threshold = 0 (double, parameters json file) 3: indel-as-hpindel = false (boolean, parameters json file) 3: data-quality-stringency = 10 (double, parameters json file) 3: read-rejection-threshold = 0.5 (double, builtin default) 3: use-position-bias = false (boolean, parameters json file) 3: position-bias-ref-fraction = 0.05 (double, parameters json file) 3: position-bias = 0.75 (double, parameters json file) 3: position-bias-pval = 0.05 (double, parameters json file) 3: downsample-to-coverage = 2000 (integer, parameters json file) 3: tune-sbias = 0.01 (double, builtin default) 3: suppress-reference-genotypes = true (boolean, builtin default) 3: suppress-nocall-genotypes = true (boolean, builtin default) 3: suppress-no-calls = true (boolean, builtin default) 3: heal-snps = true (boolean, builtin default) 3: snp-min-cov-each-strand = 4 (integer, parameters json file) 3: snp-min-variant-score = 6 (double, parameters json file) 3: snp-min-allele-freq = 0.02 (double, parameters json file) 3: snp-min-coverage = 100 (integer, parameters json file) 3: snp-strand-bias = 0.95 (double, parameters json file) 3: snp-strand-bias-pval = 0.01 (double, parameters json file) 3: mnp-min-cov-each-strand = 4 (integer, parameters json file) 3: mnp-min-variant-score = 6 (double, parameters json file) 3: mnp-min-allele-freq = 0.02 (double, parameters json file) 3: mnp-min-coverage = 100 (integer, parameters json file) 3: mnp-strand-bias = 0.95 (double, parameters json file) 3: mnp-strand-bias-pval = 0.01 (double, parameters json file) 3: indel-min-cov-each-strand = 4 (integer, parameters json file) 3: indel-min-variant-score = 6 (double, parameters json file) 3: indel-min-allele-freq = 0.02 (double, parameters json file) 3: indel-min-coverage = 100 (integer, parameters json file) 3: indel-strand-bias = 0.9 (double, parameters json file) 3: indel-strand-bias-pval = 1 (double, parameters json file) 3: hotspot-min-cov-each-strand = 4 (integer, parameters json file) 3: hotspot-min-variant-score = 6 (double, parameters json file) 3: hotspot-min-allele-freq = 0.02 (double, parameters json file) 3: hotspot-min-coverage = 100 (integer, parameters json file) 3: hotspot-strand-bias = 0.95 (double, parameters json file) 3: hotspot-strand-bias-pval = 0.01 (double, parameters json file) 3: max-flows-to-test = 10 (integer, builtin default) 3: min-delta-for-flow = 0.1 (double, builtin default) 3: prediction-precision = 1 (double, parameters json file) 3: outlier-probability = 0.005 (double, parameters json file) 3: germline-prior-strength = 0 (double, builtin default) 3: heavy-tailed = 3 (integer, parameters json file) 3: filter-unusual-predictions = 0.12 (double, parameters json file) 3: soft-clip-bias-checker = 0.1 (double, builtin default) 3: filter-deletion-predictions = 0.2 (double, parameters json file) 3: filter-insertion-predictions = 0.2 (double, parameters json file) 3: max-detail-level = 0 (integer, builtin default) 3: shift-likelihood-penalty = 0.3 (double, builtin default) 3: minimum-sigma-prior = 0.085 (double, builtin default) 3: slope-sigma-prior = 0.0084 (double, builtin default) 3: sigma-prior-weight = 1 (double, builtin default) 3: k-zero = 3 (double, builtin default) 3: num-threads = 4 (integer, command line option) 3: num-variants-per-thread = 250 (integer, builtin default) 3: use-sse-basecaller = false (boolean, command line option) 3: do-json-diagnostic = false (boolean, builtin default) 3: do-minimal-diagnostic = false (boolean, builtin default) 3: process-input-positions-only = false (boolean, builtin default) 3: suppress-recalibration = false (boolean, parameters json file) 3: resolve-clipped-bases = false (boolean, builtin default) 3: prefix-exclude = 6 3: allow-indels = true (boolean, parameters json file) 3: allow-snps = true (boolean, parameters json file) 3: allow-mnps = true (boolean, parameters json file) 3: allow-complex = false (boolean, parameters json file) 3: left-align-indels = false (boolean, builtin default) 3: use-best-n-alleles = 2 (integer, builtin default) 3: use-input-allele-only = false (boolean, builtin default) 3: min-mapping-qv = 4 (integer, parameters json file) 3: read-snp-limit = 10 (integer, parameters json file) 3: read-max-mismatch-fraction = 1 (double, parameters json file) 3: max-complex-gap = 1 (integer, builtin default) 3: gen-min-alt-allele-freq = 0.01 (double, parameters json file) 3: gen-min-coverage = 6 (integer, parameters json file) 3: gen-min-indel-alt-allele-freq = 0.01 (double, parameters json file) 3: override-limits = false (boolean, builtin default) 3: Limit check parameter hp-max-length: lim. 1 <= 8? OK! 3: Limit check parameter sse-prob-threshold: lim. 0 <= 1 <= lim. 1? OK! 3: Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK! 3: Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK! 3: Limit check parameter realignment-threshold: lim. 0 <= 0 <= lim. 1? OK! 3: Limit check parameter data-quality-stringency: lim. 0 <= 10? OK! 3: Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK! 3: Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK! 3: Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK! 3: Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK! 3: Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK! 3: Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK! 3: Limit check parameter snp-min-cov-each-strand: lim. 0 <= 4? OK! 3: Limit check parameter snp-min-variant-score: lim. 0 <= 6? OK! 3: Limit check parameter snp-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 3: Limit check parameter snp-min-coverage: lim. 0 <= 100? OK! 3: Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 3: Limit check parameter snp-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK! 3: Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 4? OK! 3: Limit check parameter mnp-min-variant-score: lim. 0 <= 6? OK! 3: Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 3: Limit check parameter mnp-min-coverage: lim. 0 <= 100? OK! 3: Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 3: Limit check parameter mnp-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK! 3: Limit check parameter indel-min-cov-each-strand: lim. 0 <= 4? OK! 3: Limit check parameter indel-min-variant-score: lim. 0 <= 6? OK! 3: Limit check parameter indel-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 3: Limit check parameter indel-min-coverage: lim. 0 <= 100? OK! 3: Limit check parameter indel-strand-bias: lim. 0.5 <= 0.9 <= lim. 1? OK! 3: Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 3: Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 4? OK! 3: Limit check parameter hotspot-min-variant-score: lim. 0 <= 6? OK! 3: Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 3: Limit check parameter hotspot-min-coverage: lim. 0 <= 100? OK! 3: Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 3: Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK! 3: Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK! 3: Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK! 3: Limit check parameter prediction-precision: lim. 0.1 <= 1? OK! 3: Limit check parameter outlier-probability: lim. 0 <= 0.005 <= lim. 1? OK! 3: Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK! 3: Limit check parameter heavy-tailed: lim. 1 <= 3? OK! 3: Limit check parameter filter-unusual-predictions: lim. 0 <= 0.12? OK! 3: Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK! 3: Limit check parameter filter-deletion-predictions: lim. 0 <= 0.2? OK! 3: Limit check parameter filter-insertion-predictions: lim. 0 <= 0.2? OK! 3: Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK! 3: Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK! 3: Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK! 3: Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK! 3: Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK! 3: Limit check parameter k-zero: lim. 0 <= 3? OK! 3: Limit check parameter num-threads: lim. 1 <= 4 <= lim. 128? OK! 3: Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK! 3: Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK! 3: Limit check parameter min-mapping-qv: lim. 0 <= 4? OK! 3: Limit check parameter read-snp-limit: lim. 0 <= 10? OK! 3: Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK! 3: Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.01 <= lim. 1? OK! 3: Limit check parameter gen-min-coverage: lim. 0 <= 6? OK! 3: Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.01 <= lim. 1? OK! 3: TargetsManager: Loaded targets file /build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed 3: TargetsManager: 1 target(s) 3: TargetsManager: Trimming of AmpliSeq primers is enabled 2: SampleManager: Found 1 read group(s) and 1 sample(s). 2: SampleManager: Primary sample "85" (default) present in 1 read group(s) 2: TVC found a total of 1 different flow orders of max flow lengths: 500 3: SampleManager: Found 1 read group(s) and 1 sample(s). 3: SampleManager: Primary sample "85" (default) present in 1 read group(s) 3: TVC found a total of 1 different flow orders of max flow lengths: 500 5: 5: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. 5: 5: Usage: tvcutils prepare_hotspots [options] 5: 5: General options: 5: -b,--input-bed FILE input is a hotspots BED file (either -b or -v required) 5: -v,--input-vcf FILE input is a hotspots VCF file (either -b or -v required) 5: -d,--output-bed FILE output left-aligned hotspots in BED format [none] 5: -o,--output-vcf FILE output is a hotspots VCF file. To be used as input to --hotspot-vcf argument of variant_caller_pipeline.py (recommended) [none] 5: -r,--reference FILE FASTA file containing reference genome (required) 5: -a,--left-alignment on/off perform left-alignment of indels [off] 5: -s,--allow-block-substitutions on/off do not filter out block substitution hotspots [on] 5: -u,--unmerged-bed FILE input a target bed file to filter out hotspots that contain a junction of 2 amplicons (optional) 5: 3/8 Test #5: tvcutils_prepare_hotspots_call ................... Passed 0.01 sec test 6 Start 6: tvcutils_validate_bed_call 6: Test command: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils "validate_bed" 6: Working Directory: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf 6: Test timeout computed to be: 10000000 6: 6: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. 6: 6: Usage: tvcutils validate_bed [options] 6: 6: Input selection options (must provide one): 6: --target-regions-bed FILE input is a target regions BED file (required) 6: --hotspots-bed FILE input is a hotspots BED file (required) 6: 6: General options: 6: --reference FILE FASTA file containing reference genome (required) 6: --validation-log FILE log file for user-readable warning/error messages [stdout] 6: --meta-json FILE save validation and file statistics to json file [none] 6: --unmerged-detail-bed FILE output a valid unmerged BED. To be used as input to --primer-trim-bed argument of variant_caller_pipeline.py (recommended) [none] 6: --unmerged-plain-bed FILE output a valid merged BED. To be used as input to --region-bed argument of variant_caller_pipeline.py (recommended) [none] 6: --merged-detail-bed FILE output an (almost) valid bedDetail merged BED [none] 6: --merged-plain-bed FILE output a valid plain merged BED [none] 6: --effective-bed FILE output a valid effective BED [none] 6: 4/8 Test #6: tvcutils_validate_bed_call ....................... Passed 0.01 sec test 7 Start 7: tvcutils_unify_vcf_call 7: Test command: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils "unify_vcf" 7: Working Directory: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf 7: Test timeout computed to be: 10000000 7: Parameter novel-tvc-vcf is required and empty. 7: 7: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. 7: 7: Usage: tvcutils unify_vcf [options] 7: 7: General options: 7: -t,--novel-tvc-vcf FILE small variants VCF file produced by TVC (required) 7: -i,--novel-assembly-vcf FILE long indels VCF file produced by TVCASSEMBLY (optional) 7: -a,--hotspot-annotation-vcf FILE hotspot annotations VCF file (optional) 7: -a,--hotspot-annotation-vcf FILE hotspot annotations VCF file (optional) 7: -f,--reference-fasta FILE FASTA file containing reference genome (required) 7: -b,--target-file FILE target regions BED file (optional) 7: -o,--output-vcf FILE output merged and annotated VCF or VCF.GZ file (required) 7: -j,--tvc-metrics FILE JSON file with tvc metrics (optional) 7: -d,--input-depth FILE output of samtools depth. if provided, will cause generation of gvcf (optional, stdin ok) 7: -m,--min-depth INT minimum coverage depth in GVCF output (optional) 7: 5/8 Test #7: tvcutils_unify_vcf_call .......................... Passed 0.01 sec test 8 Start 8: tvcassembly_call 8: Test command: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcassembly 8: Working Directory: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf 8: Test timeout computed to be: 10000000 8: tvcassembly 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller - Long Indel Assembly 8: 8: Usage: tvcassembly [options] 8: 8: General options: 8: -h,--help print this help message and exit 8: -v,--version print version and exit 8: -n,--num-threads INT number of worker threads [2] 8: --parameters-file FILE json file with algorithm control parameters [optional] 8: -r,--reference FILE reference fasta file [required] 8: -b,--input-bam FILE bam file with mapped reads [required] 8: -t,--target-file FILE only process targets in this bed file [optional] 8: -o,--output-vcf FILE vcf file with variant calling results [required] 8: -g,--sample-name STRING sample for which variants are called (In case of input BAM files with multiple samples) [optional if there is only one sample] 8: --force-sample-name STRING force all read groups to have this sample name [off] 8: 8: --kmer_len INT (klen) Size of the smallest k-mer used in assembly [19]. 8: --min_var_count INT (mincount) Minimum support for a variant to be evaluated [5]. 8: --short_suffix_match INT (ssm) Minimum sequence match on both sides of the variant [5]. 8: --min_indel_size INT (mis) Minimum size indel reported by assembly [4]. 8: --max_hp_length INT (maxhp) Variants containing HP larger than this are not reported [8]. 8: --min_var_freq FLOAT (minfreq) Minimum frequency of the variant to be reported [0.15]. 8: --min_var_score FLOAT (minscore) Minimum score of the variant to be reported [10]. 8: --relative_strand_bias FLOAT (stbias) Variants with strand bias above this are not reported [0.80]. 8: --output_mnv INT (mnv) Output multi-nucleotide variants assembled in a region with multiple adjacent variants [0]. 8: 6/8 Test #8: tvcassembly_call ................................. Passed 0.01 sec 2: Recalibration was detected from comment lines in bam file(s): 2: 1 unique blocks of recalibration info detected. 2: Loading systematic error contexts. 3: Recalibration was detected from comment lines in bam file(s): 3: 1 unique blocks of recalibration info detected. 3: Loading systematic error contexts. 3: Loaded. 2: Loaded. 2: Recalibration model: suppressed 2: 2: 2: [tvc] Normal termination. Processing time: 1 seconds. 3: 3: 3: [tvc] Normal termination. Processing time: 1 seconds. 7/8 Test #2: tvc_test_1_thread_sse_off ........................ Passed 2.14 sec 8/8 Test #3: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 2.16 sec 100% tests passed, 0 tests failed out of 8 Total Test time (real) = 2.19 sec make[1]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/tvc/ cd obj-arm-linux-gnueabihf && make -j3 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-arm-linux-gnueabihf' /usr/bin/cmake -S/build/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvc -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcassembly -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcutils -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/variant_caller_pipeline.py -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_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/ampliseq_somatic_lowstringency_pgm_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_germline_lowstringency_pgm_parameters.json -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse -- 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/sse/motifset.txt -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1 -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai -- 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_unmerged_detail.bed -- 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/reference.fasta -- 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/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 -- 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/test_merged_plain.bed -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam make[1]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' dh_installdocs dh_installchangelogs dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/tvc/usr/bin/tvcutils contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/tvc/usr/bin/tvc contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/tvc/usr/bin/tvcassembly contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin 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-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_armhf.deb'. dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.deb'. dpkg-genbuildinfo --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.buildinfo dpkg-genchanges --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.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/30698 and its subdirectories I: Current time: Thu May 4 23:29:43 -12 2023 I: pbuilder-time-stamp: 1683286183 Fri May 5 11:30:14 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ff4a-armhf-rb.debian.net. Fri May 5 11:30:14 UTC 2023 I: Preparing to do remote build '2' on ff4a-armhf-rb.debian.net. Fri May 5 11:41:03 UTC 2023 I: Deleting $TMPDIR on ff4a-armhf-rb.debian.net. Fri May 5 11:41:05 UTC 2023 I: tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.changes: Format: 1.8 Date: Mon, 05 Sep 2022 17:20:03 +0000 Source: tvc Binary: tvc tvc-dbgsym Architecture: armhf Version: 5.0.3+git20151221.80e144e+dfsg-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Mohammed Bilal Description: tvc - genetic variant caller for Ion Torrent sequencing platforms Changes: tvc (5.0.3+git20151221.80e144e+dfsg-5) unstable; urgency=medium . * Team upload. * Add autopkgtest * Standards-Version: 4.6.1 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit. Checksums-Sha1: e802a824683643474924e6cb9bb10433a8d27d92 11151776 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_armhf.deb 580fffa4f11fd66b70fa872fabf1e0dcc8c6d7c0 7225 tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.buildinfo 057c883b88df55242752c190589c22967c761a4c 978116 tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.deb Checksums-Sha256: 6e013f279f3653112350051779995ecb48ea523c85c5bb68414b0dfea7653c0a 11151776 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_armhf.deb 7dfcecc039d3bb8f8dfcd35e64c49cd1b6fb0d0d0466feac35ecbeeb92332574 7225 tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.buildinfo c24cba41a5d53400581fdab55e70f94d316b3d0c37c5ad3136e0ebac941c7404 978116 tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.deb Files: 1421867826a94db3422c3c9c24dbdccd 11151776 debug optional tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_armhf.deb cd23eaa0f31133eb36c94b6ca7b82f6b 7225 science optional tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.buildinfo 4964f83487cd380ee84aa6da48ba8279 978116 science optional tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.deb Fri May 5 11:41:07 UTC 2023 I: diffoscope 241 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.BDljuEVv/tvc_5.0.3+git20151221.80e144e+dfsg-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.BDljuEVv/tvc_5.0.3+git20151221.80e144e+dfsg-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.BDljuEVv/tvc_5.0.3+git20151221.80e144e+dfsg-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.BDljuEVv/b1/tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.BDljuEVv/b2/tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.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: 0.498s) 0.498s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.144s) 0.144s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Fri May 5 11:41:08 UTC 2023 I: diffoscope 241 found no differences in the changes files, and a .buildinfo file also exists. Fri May 5 11:41:08 UTC 2023 I: tvc from bookworm built successfully and reproducibly on armhf. Fri May 5 11:41:10 UTC 2023 I: Submitting .buildinfo files to external archives: Fri May 5 11:41:10 UTC 2023 I: Submitting 8.0K b1/tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.buildinfo.asc Fri May 5 11:41:11 UTC 2023 I: Submitting 8.0K b2/tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.buildinfo.asc Fri May 5 11:41:12 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri May 5 11:41:12 UTC 2023 I: Done submitting .buildinfo files. Fri May 5 11:41:12 UTC 2023 I: Removing signed tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.buildinfo.asc files: removed './b1/tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.buildinfo.asc' removed './b2/tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.buildinfo.asc'