Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/t/tvc/tvc_5.0.3+git20151221.80e144e+dfsg-3+b2_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/tvc-5.0.3+git20151221.80e144e+dfsg-3+b2k3gfer2r/tvc_5.0.3+git20151221.80e144e+dfsg-3+b2_amd64.buildinfo Get source package info: tvc=5.0.3+git20151221.80e144e+dfsg-3 Source URL: http://snapshot.notset.fr/mr/package/tvc/5.0.3+git20151221.80e144e+dfsg-3/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.3-1 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.48 bash=5.1~rc3-1 binutils=2.35.1-4 binutils-common=2.35.1-4 binutils-x86-64-linux-gnu=2.35.1-4 bsdextrautils=2.36.1-2 bsdutils=1:2.36.1-2 build-essential=12.8 bzip2=1.0.8-4 cmake=3.18.4-1+b1 cmake-data=3.18.4-1 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.1-1 dash=0.5.11+git20200708+dd9ef66-2 debconf=1.5.74 debhelper=13.3 debianutils=4.11.2 dh-autoreconf=19 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13+20201015-2 file=1:5.39-3 findutils=4.7.0+git20201010-2 g++=4:10.2.0-1 g++-10=10.2.1-1 gcc=4:10.2.0-1 gcc-10=10.2.1-1 gcc-10-base=10.2.1-1 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 hdf5-helpers=1.10.6+repack-2 hostname=3.23 init-system-helpers=1.59 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libaec-dev=1.0.4-1 libaec0=1.0.4-1 libarchive-zip-perl=1.68-1 libarchive13=3.4.3-2 libarmadillo-dev=1:10.1.2+dfsg-1 libarmadillo10=1:10.1.2+dfsg-1 libarpack2=3.8.0-1 libarpack2-dev=3.8.0-1 libasan6=10.2.1-1 libatomic1=10.2.1-1 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3.1 libaudit1=1:2.8.5-3.1 libbamtools-dev=2.5.1+dfsg-7+b1 libbamtools2.5.1=2.5.1+dfsg-7+b1 libbinutils=2.35.1-4 libblas-dev=3.9.0-3 libblas3=3.9.0-3 libblkid1=2.36.1-2 libboost-math-dev=1.71.0.3 libboost-math1.71-dev=1.71.0-7+b2 libboost-math1.71.0=1.71.0-7+b2 libboost1.71-dev=1.71.0-7+b2 libbrotli1=1.0.9-2+b2 libbz2-1.0=1.0.8-4 libc-bin=2.31-5 libc-dev-bin=2.31-5 libc6=2.31-5 libc6-dev=2.31-5 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-1 libcom-err2=1.45.6-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-4 libctf0=2.35.1-4 libcurl4=7.72.0-1 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.255 libdebhelper-perl=13.3 libdisorder-dev=0.0.2+git20130809.8062ee1-2 libdisorder0=0.0.2+git20130809.8062ee1-2 libdpkg-perl=1.20.5 libelf1=0.182-1 libexpat1=2.2.10-1 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.9.0-1 libgcc-10-dev=10.2.1-1 libgcc-s1=10.2.1-1 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libgfortran5=10.2.1-1 libglib2.0-0=2.66.3-2 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.6.15-4 libgomp1=10.2.1-1 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libhdf5-103-1=1.10.6+repack-2 libhdf5-cpp-103-1=1.10.6+repack-2 libhdf5-dev=1.10.6+repack-2 libhdf5-fortran-102=1.10.6+repack-2 libhdf5-hl-100=1.10.6+repack-2 libhdf5-hl-cpp-100=1.10.6+repack-2 libhdf5-hl-fortran-100=1.10.6+repack-2 libhogweed6=3.6-2 libicu67=67.1-5 libidn2-0=2.3.0-4 libisl23=0.23-1 libitm1=10.2.1-1 libjpeg-dev=1:2.0.5-1.1 libjpeg62-turbo=1:2.0.5-1.1 libjpeg62-turbo-dev=1:2.0.5-1.1 libjsoncpp-dev=1.9.4-3 libjsoncpp24=1.9.4-3 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblapack-dev=3.9.0-3 liblapack3=3.9.0-3 libldap-2.4-2=2.4.56+dfsg-1 liblsan0=10.2.1-1 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-2 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libncurses6=6.2+20201114-1 libncursesw6=6.2+20201114-1 libnettle8=3.6-2 libnghttp2-14=1.42.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.23.21-2 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpcre2-8-0=10.35-2 libpcre3=2:8.39-13 libperl5.32=5.32.0-5 libpipeline1=1.5.3-1 libprocps8=2:3.3.16-5 libpsl5=0.21.0-1.1 libquadmath0=10.2.1-1 librhash0=1.4.0-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.5.0-3 libselinux1=3.1-2+b1 libsigsegv2=2.12-2 libsmartcols1=2.36.1-2 libsmithwaterman-dev=0.0+git20160702.2610e25-11 libsmithwaterman0=0.0+git20160702.2610e25-11 libssh2-1=1.9.0-1 libssl1.1=1.1.1h-1 libstdc++-10-dev=10.2.1-1 libstdc++6=10.2.1-1 libsub-override-perl=0.09-2 libsuperlu-dev=5.2.2+dfsg1-2 libsuperlu5=5.2.2+dfsg1-2 libsystemd0=247.1-3 libsz2=1.0.4-1 libtasn1-6=4.16.0-2 libtinfo6=6.2+20201114-1 libtirpc-common=1.2.6-3 libtirpc-dev=1.2.6-3 libtirpc3=1.2.6-3 libtool=2.4.6-14 libtsan0=10.2.1-1 libubsan1=10.2.1-1 libuchardet0=0.0.7-1 libudev1=247.1-3 libunistring2=0.9.10-4 libuuid1=2.36.1-2 libuv1=1.40.0-1 libxml2=2.9.10+dfsg-6.3+b1 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.9.11-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20201114-1 ncurses-bin=6.2+20201114-1 patch=2.7.6-6 perl=5.32.0-5 perl-base=5.32.0-5 perl-modules-5.32=5.32.0-5 po-debconf=1.0.21 procps=2:3.3.16-5 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-5 tar=1.32+dfsg-1 util-linux=2.36.1-2 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201215T204137Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201207T144442Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d tvc=5.0.3+git20151221.80e144e+dfsg-3 && mkdir -p /build/tvc-g439xf && dpkg-source --no-check -x /*.dsc /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg && cd /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg && { printf '%s' 'tvc (5.0.3+git20151221.80e144e+dfsg-3+b2) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against libjsoncpp24 -- amd64 / i386 Build Daemon (x86-ubc-01) Wed, 09 Dec 2020 17:29:52 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/tvc-g439xf" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1607534992" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/tvc-g439xf /tmp/tvc-5.0.3+git20151221.80e144e+dfsg-3+b2k3gfer2r bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201207T144442Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.2Di3yJQ_pq as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.2Di3yJQ_pq Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-2). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20201207T144442Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201207T144442Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (982 kB/s) Selecting previously unselected package libfakeroot:amd64. (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 ... 4614 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-5) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201215T204137Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201207T144442Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.2Di3yJQ_pq Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201215T204137Z unstable InRelease [153 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20201207T144442Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20201215T204137Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201215T204137Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201215T204137Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20201215T204137Z unstable/main amd64 Packages [11.6 MB] Fetched 34.3 MB in 29s (1179 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.2Di3yJQ_pq I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d tvc=5.0.3+git20151221.80e144e+dfsg-3 && mkdir -p /build/tvc-g439xf && dpkg-source --no-check -x /*.dsc /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg && cd /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg && { printf '%s' 'tvc (5.0.3+git20151221.80e144e+dfsg-3+b2) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against libjsoncpp24 -- amd64 / i386 Build Daemon (x86-ubc-01) Wed, 09 Dec 2020 17:29:52 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/tvc-g439xf"' exec /tmp/mmdebstrap.2Di3yJQ_pq Reading package lists... NOTICE: 'tvc' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/tvc.git Please use: git clone https://salsa.debian.org/med-team/tvc.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 756 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main tvc 5.0.3+git20151221.80e144e+dfsg-3 (dsc) [2200 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main tvc 5.0.3+git20151221.80e144e+dfsg-3 (tar) [745 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main tvc 5.0.3+git20151221.80e144e+dfsg-3 (diff) [8968 B] Fetched 756 kB in 1s (1001 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'tvc_5.0.3+git20151221.80e144e+dfsg-3.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting tvc in /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg dpkg-source: info: unpacking tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz dpkg-source: info: unpacking tvc_5.0.3+git20151221.80e144e+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying cmake.patch dpkg-source: info: applying bamtools.patch dpkg-source: info: applying help.patch dpkg-source: info: applying hurd.patch dpkg-source: info: applying sse.patch dpkg-source: info: applying use_debian_packaged_smithwaterman.patch dpkg-source: info: applying python3.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1607534992" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.2Di3yJQ_pq dpkg-buildpackage: info: source package tvc dpkg-buildpackage: info: source version 5.0.3+git20151221.80e144e+dfsg-3+b2 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by amd64 / i386 Build Daemon (x86-ubc-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu .. -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- CMAKE_CXX_FLAGS: '-g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3' -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu dh_auto_build -a cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend make[3]: Entering directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' cd /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' cd /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' cd /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake --color= Dependee "/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake" is newer than depender "/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvcutils.dir/depend.internal". Dependee "/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvcutils.dir/depend.internal". Dependee "/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake" is newer than depender "/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvc.dir/depend.internal". Dependee "/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvc.dir/depend.internal". Dependee "/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake" is newer than depender "/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvcassembly.dir/depend.internal". Dependee "/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvcassembly.dir/depend.internal". Scanning dependencies of target tvcassembly make[3]: Leaving directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build Scanning dependencies of target tvcutils make[3]: Leaving directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build make[3]: Entering directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' [ 1%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/IndelAssembly/IndelAssembly.cpp [ 3%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/tvcutils.cpp [ 4%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/prepare_hotspots.cpp Scanning dependencies of target tvc make[3]: Leaving directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build make[3]: Entering directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' [ 6%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp [ 7%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/validate_bed.cpp /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp: In function ‘void TheSilenceOfTheArmadillos(std::ofstream&)’: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:9: warning: ‘void arma::set_stream_err1(std::ostream&)’ is deprecated [-Wdeprecated-declarations] 36 | arma::set_stream_err1(null_ostream); | ^~~~~~~~~~~~~~~ In file included from /usr/include/armadillo:349, from /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:90:1: note: declared here 90 | set_stream_err1(std::ostream& user_stream) | ^~~~~~~~~~~~~~~ /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:37: warning: ‘void arma::set_stream_err1(std::ostream&)’ is deprecated [-Wdeprecated-declarations] 36 | arma::set_stream_err1(null_ostream); | ^ In file included from /usr/include/armadillo:349, from /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:90:1: note: declared here 90 | set_stream_err1(std::ostream& user_stream) | ^~~~~~~~~~~~~~~ /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:9: warning: ‘void arma::set_stream_err2(std::ostream&)’ is deprecated [-Wdeprecated-declarations] 37 | arma::set_stream_err2(null_ostream); | ^~~~~~~~~~~~~~~ In file included from /usr/include/armadillo:349, from /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:101:1: note: declared here 101 | set_stream_err2(std::ostream& user_stream) | ^~~~~~~~~~~~~~~ /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:37: warning: ‘void arma::set_stream_err2(std::ostream&)’ is deprecated [-Wdeprecated-declarations] 37 | arma::set_stream_err2(null_ostream); | ^ In file included from /usr/include/armadillo:349, from /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:101:1: note: declared here 101 | set_stream_err2(std::ostream& user_stream) | ^~~~~~~~~~~~~~~ [ 9%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping 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CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp [ 12%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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-I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/TargetsManager.cpp [ 15%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib 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-I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/SampleManager.cpp [ 16%] Building CXX object CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping 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-DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp [ 20%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/OrderedBAMWriter.cpp [ 21%] Building CXX object CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util/Utils.cpp [ 23%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/SampleManager.cpp [ 24%] Building CXX object CMakeFiles/tvcassembly.dir/IonVersion.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/IonVersion.cpp In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util/Utils.cpp:12: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘char* GetProcessParam(const char*, const char*)’ at /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util/Utils.cpp:503:15: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util/Utils.cpp: In function ‘char* GetProcessParam(const char*, const char*)’: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util/Utils.cpp:503:37: note: length computed here 503 | strncpy (keyword, buf, strlen (buf)-1); | ~~~~~~~^~~~~ [ 26%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/Variant.cpp [ 27%] Linking CXX executable tvcassembly /usr/bin/cmake -E cmake_link_script CMakeFiles/tvcassembly.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -Wl,-z,relro -rdynamic CMakeFiles/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 [ 29%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/TargetsManager.cpp make[3]: Leaving directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' [ 29%] Built target tvcassembly [ 30%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/split.cpp [ 32%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp 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-fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/tabix.cpp [ 33%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o /usr/bin/cc -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c: In function ‘ti_index_core’: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c:336:35: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow] 336 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ [ 35%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o /usr/bin/cc -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c: In function ‘_bgzf_check_EOF’: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c:678:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 678 | fread(buf, 1, 28, fp->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 36%] Building CXX object CMakeFiles/tvcutils.dir/IonVersion.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval 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[ 38%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HandleVariant.cpp [ 40%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller 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-I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/MiscUtil.cpp [ 44%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval 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/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/ExtendParameters.cpp [ 46%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp: In member function ‘void RecalibrationHandler::ReadRecalibrationFromComments(const BamTools::SamHeader&, const std::map, int>&)’: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:240:18: warning: ‘Reader’ is deprecated: Use CharReader and CharReaderBuilder instead. [-Wdeprecated-declarations] 240 | Json::Reader recal_reader; | ^~~~~~~~~~~~ In file included from /usr/include/jsoncpp/json/json.h:11, from /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/CalibrationHelper.h:23, from /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/LinearCalibrationModel.h:16, from /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.h:19, from /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:7: /usr/include/jsoncpp/json/reader.h:37:63: note: declared here 37 | "Use CharReader and CharReaderBuilder instead.") JSON_API Reader { | ^~~~~~ /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:240:18: warning: ‘Json::Reader::Reader()’ is deprecated: Use CharReader and CharReaderBuilder instead [-Wdeprecated-declarations] 240 | Json::Reader recal_reader; | ^~~~~~~~~~~~ In file included from /usr/include/jsoncpp/json/json.h:11, from /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/CalibrationHelper.h:23, from /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/LinearCalibrationModel.h:16, from /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.h:19, from /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp:7: /usr/include/jsoncpp/json/reader.h:56:3: note: declared here 56 | Reader(); | ^~~~~~ [ 47%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/VcfFormat.cpp [ 49%] Linking CXX executable tvcutils /usr/bin/cmake -E cmake_link_script CMakeFiles/tvcutils.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -Wl,-z,relro -rdynamic CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o CMakeFiles/tvcutils.dir/IonVersion.cpp.o -o tvcutils -lbamtools -lz -ljsoncpp -lsmithwaterman -ldisorder make[3]: Leaving directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' [ 49%] Built target tvcutils [ 50%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools 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-I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/ShortStack.cpp [ 72%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/StackEngine.cpp [ 73%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/CrossHypotheses.cpp [ 75%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/Variant.cpp [ 76%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/split.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/external/vcflib/split.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/split.cpp [ 78%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/tabix.cpp [ 80%] Building C object CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o /usr/bin/cc -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c: In function ‘ti_index_core’: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c:336:35: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow] 336 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ [ 81%] Building C object CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o /usr/bin/cc -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c: In function ‘_bgzf_check_EOF’: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c:678:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 678 | fread(buf, 1, 28, fp->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 83%] Building CXX object CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src/AlleleParser.cpp [ 84%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller/PIDloop.cpp [ 86%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller/DPTreephaser.cpp [ 87%] Building CXX object CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/LinearCalibrationModel.cpp /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/LinearCalibrationModel.cpp: In member function ‘void LinearCalibrationModel::SaveModelFileToBamComments(std::vector >&, const string&) const’: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/LinearCalibrationModel.cpp:708:20: warning: ‘FastWriter’ is deprecated: Use StreamWriterBuilder instead [-Wdeprecated-declarations] 708 | Json::FastWriter writer; | ^~~~~~ In file included from /usr/include/jsoncpp/json/json.h:13, from /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/CalibrationHelper.h:23, from /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/LinearCalibrationModel.h:16, from /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/LinearCalibrationModel.cpp:13: /usr/include/jsoncpp/json/writer.h:168:70: note: declared here 168 | class JSONCPP_DEPRECATED("Use StreamWriterBuilder instead") JSON_API FastWriter | ^~~~~~~~~~ [ 89%] Building CXX object CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/FlowAlignment.cpp [ 90%] Building CXX object CMakeFiles/tvc.dir/Util/OptArgs.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/Util/OptArgs.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp [ 92%] Building CXX object CMakeFiles/tvc.dir/realignment/Realigner.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/realignment/Realigner.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment/Realigner.cpp [ 93%] Building C object CMakeFiles/tvc.dir/file-io/ion_util.c.o /usr/bin/cc -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/file-io/ion_util.c.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io/ion_util.c [ 95%] Building C object CMakeFiles/tvc.dir/file-io/ion_error.c.o /usr/bin/cc -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/file-io/ion_error.c.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io/ion_error.c [ 96%] Building CXX object CMakeFiles/tvc.dir/IonVersion.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/IonVersion.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/IonVersion.cpp [ 98%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o -c /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller/TreephaserSSE.cpp [100%] Linking CXX executable tvc /usr/bin/cmake -E cmake_link_script CMakeFiles/tvc.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -Wl,-z,relro -rdynamic CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o CMakeFiles/tvc.dir/external/vcflib/split.cpp.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o CMakeFiles/tvc.dir/Util/OptArgs.cpp.o CMakeFiles/tvc.dir/realignment/Realigner.cpp.o CMakeFiles/tvc.dir/file-io/ion_util.c.o CMakeFiles/tvc.dir/file-io/ion_error.c.o CMakeFiles/tvc.dir/IonVersion.cpp.o CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o -o tvc -lbamtools -lz -lpthread -lblas -llapack -larmadillo -ljsoncpp -lsmithwaterman -ldisorder make[3]: Leaving directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' [100%] Built target tvc make[2]: Leaving directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start 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Passed 8.56 sec 100% tests passed, 0 tests failed out of 10 Total Test time (real) = 8.58 sec make[1]: Leaving directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install -a cd obj-x86_64-linux-gnu && make -j4 install DESTDIR=/build/tvc-g439xf/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-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 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/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color= make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend make[3]: Entering directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' cd /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build make[3]: Leaving directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build make[3]: Entering directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvcassembly.dir/build'. make[3]: Leaving directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvcutils.dir/build'. make[3]: Leaving directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build [ 20%] Built target tvcutils [ 30%] Built target tvcassembly make[3]: Entering directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvc.dir/build'. make[3]: Leaving directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' [100%] Built target tvc make[2]: Leaving directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' 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/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/motifset.txt -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1 -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_original.bed -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bed -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/TSVC_variants.vcf -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/small_variants.vcf -- Installing: /build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.dict make[1]: Leaving directory '/build/tvc-g439xf/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' dh_installdocs -a dh_installchangelogs -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvc debian/tvc/usr/bin/tvcutils were not linked against libdisorder.so.0 (they use none of the library's symbols) dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-3+b2_amd64.deb'. dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3+b2_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../tvc_5.0.3+git20151221.80e144e+dfsg-3+b2_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/tvc-g439xf /tmp/tvc-5.0.3+git20151221.80e144e+dfsg-3+b2k3gfer2r I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.2Di3yJQ_pq... I: success in 1245.5411 seconds md5: tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3+b2_amd64.deb: OK md5: tvc_5.0.3+git20151221.80e144e+dfsg-3+b2_amd64.deb: OK sha1: tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3+b2_amd64.deb: OK sha1: tvc_5.0.3+git20151221.80e144e+dfsg-3+b2_amd64.deb: OK sha256: tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3+b2_amd64.deb: OK sha256: tvc_5.0.3+git20151221.80e144e+dfsg-3+b2_amd64.deb: OK Checksums: OK