Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/s/sniffles/sniffles_1.0.12b+ds-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/sniffles-1.0.12b+ds-1_3txq2jv/sniffles_1.0.12b+ds-1_amd64.buildinfo Get source package info: sniffles=1.0.12b+ds-1 Source URL: http://snapshot.notset.fr/mr/package/sniffles/1.0.12b+ds-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.2-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.48 bash=5.1~rc3-1 binutils=2.35.1-3 binutils-common=2.35.1-3 binutils-x86-64-linux-gnu=2.35.1-3 bsdextrautils=2.36.1-2 bsdutils=1:2.36.1-1 build-essential=12.8 bzip2=1.0.8-4 cmake=3.18.4-1 cmake-data=3.18.4-1 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.0-19 dash=0.5.11+git20200708+dd9ef66-2 debconf=1.5.74 debhelper=13.2.1 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=0.13-5 file=1:5.39-3 findutils=4.7.0+git20201010-2 g++=4:10.2.0-1 g++-10=10.2.0-19 gcc=4:10.2.0-1 gcc-10=10.2.0-19 gcc-10-base=10.2.0-19 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 hostname=3.23 init-system-helpers=1.59 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libarchive-zip-perl=1.68-1 libarchive13=3.4.3-2 libasan6=10.2.0-19 libatomic1=10.2.0-19 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 libbamtools2.5.1=2.5.1+dfsg-7 libbinutils=2.35.1-3 libblkid1=2.36.1-1 libbrotli1=1.0.9-2+b1 libbz2-1.0=1.0.8-4 libc-bin=2.31-4 libc-dev-bin=2.31-4 libc6=2.31-4 libc6-dev=2.31-4 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.0-19 libcmark-gfm-extensions0=0.29.0.gfm.0-6 libcmark-gfm0=0.29.0.gfm.0-6 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=2.35.1-3 libctf0=2.35.1-3 libcurl4=7.72.0-1 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.255 libdebhelper-perl=13.2.1 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=10.2.0-19 libgcc-s1=10.2.0-19 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libglib2.0-0=2.66.3-1 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.6.15-4 libgomp1=10.2.0-19 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libhogweed6=3.6-2 libicu67=67.1-4 libidn2-0=2.3.0-4 libisl23=0.23-1 libitm1=10.2.0-19 libjsoncpp1=1.7.4-3.1 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 libldap-2.4-2=2.4.56+dfsg-1 liblsan0=10.2.0-19 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-1 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=1.41.0-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnss-nis=3.1-4 libnss-nisplus=1.3-4 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=10.34-7 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=10.2.0-19 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=2.36.1-1 libssh2-1=1.8.0-2.1 libssl1.1=1.1.1h-1 libstdc++-10-dev=10.2.0-19 libstdc++6=10.2.0-19 libsub-override-perl=0.09-2 libsystemd0=246.6-5 libtasn1-6=4.16.0-2 libtclap-dev=1.2.2-1+b1 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=10.2.0-19 libubsan1=10.2.0-19 libuchardet0=0.0.7-1 libudev1=246.6-5 libunistring2=0.9.10-4 libuuid1=2.36.1-1 libuv1=1.40.0-1 libxml2=2.9.10+dfsg-6.2 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.9.9-1 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 pandoc=2.9.2.1-1+b1 pandoc-data=2.9.2.1-1 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=1.30+dfsg-7 util-linux=2.36.1-1 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/20201219T145050Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201125T210657Z/ 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 sniffles=1.0.12b+ds-1 && mkdir -p /build/sniffles-cQT1WZ && dpkg-source --no-check -x /*.dsc /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds && chown -R builduser:builduser /build/sniffles-cQT1WZ" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1599072493" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/sniffles-cQT1WZ /tmp/sniffles-1.0.12b+ds-1_3txq2jv bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201125T210657Z 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.WnEI2Z8n5e 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.WnEI2Z8n5e Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-1). 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/20201125T210657Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201125T210657Z 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 (485 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 ... 4697 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 (2.31-4) ... 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/20201219T145050Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201125T210657Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.WnEI2Z8n5e Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201219T145050Z unstable InRelease [153 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20201125T210657Z 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/20201219T145050Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201219T145050Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201219T145050Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20201219T145050Z unstable/main amd64 Packages [11.6 MB] Fetched 34.3 MB in 29s (1192 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.WnEI2Z8n5e I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d sniffles=1.0.12b+ds-1 && mkdir -p /build/sniffles-cQT1WZ && dpkg-source --no-check -x /*.dsc /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds && chown -R builduser:builduser /build/sniffles-cQT1WZ"' exec /tmp/mmdebstrap.WnEI2Z8n5e Reading package lists... NOTICE: 'sniffles' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/sniffles.git Please use: git clone https://salsa.debian.org/med-team/sniffles.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 594 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main sniffles 1.0.12b+ds-1 (dsc) [2081 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main sniffles 1.0.12b+ds-1 (tar) [586 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main sniffles 1.0.12b+ds-1 (diff) [5760 B] Fetched 594 kB in 0s (1255 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'sniffles_1.0.12b+ds-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting sniffles in /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds dpkg-source: info: unpacking sniffles_1.0.12b+ds.orig.tar.xz dpkg-source: info: unpacking sniffles_1.0.12b+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying external-libs.patch dpkg-source: info: applying no-extra-binary.patch dpkg-source: info: applying stoppingRecursion.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1599072493" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.WnEI2Z8n5e dpkg-buildpackage: info: source package sniffles dpkg-buildpackage: info: source version 1.0.12b+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steffen Moeller dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds' dh_auto_clean find -name "*.mk" -delete rm -rf bin rm -f \ makefile \ debian/sniffles.1 \ test.vcf \ make[1]: Leaving directory '/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds' dh_auto_configure -- \ -DCMAKE_INCLUDE_PATH="/usr/include/bamtools" 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 -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DCMAKE_INCLUDE_PATH=/usr/include/bamtools .. -- The C compiler identification is GNU 10.2.0 -- The CXX compiler identification is GNU 10.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds' dh_auto_build -a cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds -B/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/CMakeFiles /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu' make -f src/CMakeFiles/sniffles.dir/build.make src/CMakeFiles/sniffles.dir/depend make[3]: Entering directory '/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu' cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src/CMakeFiles/sniffles.dir/DependInfo.cmake --color= Scanning dependencies of target sniffles make[3]: Leaving directory '/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu' make -f src/CMakeFiles/sniffles.dir/build.make src/CMakeFiles/sniffles.dir/build make[3]: Entering directory '/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu' [ 4%] Building CXX object src/CMakeFiles/sniffles.dir/tree/Breakpoint_Tree.cpp.o [ 13%] Building CXX object src/CMakeFiles/sniffles.dir/BamParser.cpp.o [ 13%] Building CXX object src/CMakeFiles/sniffles.dir/Alignment.cpp.o cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/tree/Breakpoint_Tree.cpp.o -c /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/tree/Breakpoint_Tree.cpp cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/Alignment.cpp.o -c /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/Alignment.cpp cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/BamParser.cpp.o -c /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/BamParser.cpp [ 17%] Building CXX object src/CMakeFiles/sniffles.dir/Genotyper/Genotyper.cpp.o cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/Genotyper/Genotyper.cpp.o -c /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp [ 21%] Building CXX object src/CMakeFiles/sniffles.dir/Sniffles.cpp.o cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/Sniffles.cpp.o -c /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/Sniffles.cpp [ 26%] Building CXX object src/CMakeFiles/sniffles.dir/Ignore_Regions.cpp.o cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/Ignore_Regions.cpp.o -c /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/Ignore_Regions.cpp /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp: In member function ‘void Genotyper::update_svs_output(std::map, std::vector >)’: /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp:343:8: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 343 | system(move.c_str()); | ~~~~~~^~~~~~~~~~~~~~ /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp: In member function ‘void Genotyper::update_SVs2()’: /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp:382:8: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 382 | system(del.c_str()); | ~~~~~~^~~~~~~~~~~~~ /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp: In member function ‘void Genotyper::update_file(Breakpoint_Tree&, breakpoint_node*&)’: /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp:719:8: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 719 | system(move.c_str()); | ~~~~~~^~~~~~~~~~~~~~ /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp: In member function ‘void Genotyper::update_SVs()’: /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp:858:8: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 858 | system(del.c_str()); | ~~~~~~^~~~~~~~~~~~~ [ 30%] Building CXX object src/CMakeFiles/sniffles.dir/tree/Intervall_bed.cpp.o cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/tree/Intervall_bed.cpp.o -c /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/tree/Intervall_bed.cpp [ 34%] Building CXX object src/CMakeFiles/sniffles.dir/sub/Detect_Breakpoints.cpp.o cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/sub/Detect_Breakpoints.cpp.o -c /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/sub/Detect_Breakpoints.cpp [ 39%] Building CXX object src/CMakeFiles/sniffles.dir/sub/Breakpoint.cpp.o cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/sub/Breakpoint.cpp.o -c /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/sub/Breakpoint.cpp [ 43%] Building CXX object src/CMakeFiles/sniffles.dir/tree/IntervallTree.cpp.o cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/tree/IntervallTree.cpp.o -c /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/tree/IntervallTree.cpp [ 47%] Building CXX object src/CMakeFiles/sniffles.dir/tree/IntervallList.cpp.o cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/tree/IntervallList.cpp.o -c /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/tree/IntervallList.cpp [ 52%] Building CXX object src/CMakeFiles/sniffles.dir/realign/SWCPU.cpp.o cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/realign/SWCPU.cpp.o -c /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/realign/SWCPU.cpp /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/realign/SWCPU.cpp: In constructor ‘SWCPUCor::SWCPUCor(int)’: /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/realign/SWCPU.cpp:30:35: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 30 | fprintf(stderr, "Allocationg: %llu\n", maxLen * sizeof(MatrixElement)); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | | long unsigned int | long long unsigned int | %lu [ 56%] Building CXX object src/CMakeFiles/sniffles.dir/realign/Realign.cpp.o cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/realign/Realign.cpp.o -c /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/realign/Realign.cpp [ 60%] Building CXX object src/CMakeFiles/sniffles.dir/print/VCFPrinter.cpp.o cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/print/VCFPrinter.cpp.o -c /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp [ 65%] Building CXX object src/CMakeFiles/sniffles.dir/print/BedpePrinter.cpp.o cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/print/BedpePrinter.cpp.o -c /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/BedpePrinter.cpp /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp: In member function ‘virtual void VCFPrinter::print_body(Breakpoint*&, BamTools::RefVector)’: /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp:369:22: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wformat=] 369 | fprintf(file, "%i", SV->get_sequence().size()); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int std::__cxx11::basic_string::size_type {aka long unsigned int} | %li /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp:376:21: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 376 | fprintf(file, "%i", SV->get_length() * -1); | ~^ ~~~~~~~~~~~~~~~~~~~~~ | | | | int long int | %li /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp:378:21: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 378 | fprintf(file, "%i", SV->get_length()); | ~^ ~~~~~~~~~~~~~~~~ | | | | int long int | %li /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp: In member function ‘virtual void VCFPrinter::print_body_recall(Breakpoint*&, BamTools::RefVector)’: /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp:510:19: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 510 | fprintf(file, "%i", SV->get_length()); | ~^ ~~~~~~~~~~~~~~~~ | | | | int long int | %li [ 69%] Building CXX object src/CMakeFiles/sniffles.dir/print/IPrinter.cpp.o cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/print/IPrinter.cpp.o -c /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/IPrinter.cpp [ 73%] Building CXX object src/CMakeFiles/sniffles.dir/tree/BinTree.cpp.o cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/tree/BinTree.cpp.o -c /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/tree/BinTree.cpp /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/BedpePrinter.cpp: In member function ‘virtual void BedpePrinter::print_body(Breakpoint*&, BamTools::RefVector)’: /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/BedpePrinter.cpp:99:21: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 99 | fprintf(file, "%i", SV->get_length()); | ~^ ~~~~~~~~~~~~~~~~ | | | | int long int | %li /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/BedpePrinter.cpp: In member function ‘virtual void BedpePrinter::print_body_recall(Breakpoint*&, BamTools::RefVector)’: /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/BedpePrinter.cpp:123:18: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 123 | fprintf(file, "%i", IPrinter::calc_pos(SV->get_coordinates().start.max_pos, ref, chr)); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long int | %li /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/BedpePrinter.cpp:130:18: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 130 | fprintf(file, "%i", IPrinter::calc_pos(SV->get_coordinates().stop.max_pos, ref, chr)); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long int | %li /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/BedpePrinter.cpp:158:19: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 158 | fprintf(file, "%i", SV->get_length()); | ~^ ~~~~~~~~~~~~~~~~ | | | | int long int | %li [ 78%] Building CXX object src/CMakeFiles/sniffles.dir/print/NGMPrinter.cpp.o cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/print/NGMPrinter.cpp.o -c /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/NGMPrinter.cpp /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/IPrinter.cpp: In function ‘void write_read(Alignment*, FILE*&)’: /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:21:29: warning: unknown conversion type character ‘r’ in format [-Wformat=] 21 | fprintf(ref_allel_reads, "%ref_plus", '\t'); | ^ /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:21:27: warning: too many arguments for format [-Wformat-extra-args] 21 | fprintf(ref_allel_reads, "%ref_plus", '\t'); | ^~~~~~~~~~~ /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:23:29: warning: unknown conversion type character ‘r’ in format [-Wformat=] 23 | fprintf(ref_allel_reads, "%ref_plus", '\t'); | ^ /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:23:27: warning: too many arguments for format [-Wformat-extra-args] 23 | fprintf(ref_allel_reads, "%ref_plus", '\t'); | ^~~~~~~~~~~ /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:24:29: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 24 | fprintf(ref_allel_reads, "%i", tmp_aln->getRefLength()); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | int size_t {aka long unsigned int} | %li /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:25:29: warning: unknown conversion type character ‘r’ in format [-Wformat=] 25 | fprintf(ref_allel_reads, "%ref_plus", '\t'); | ^ /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:25:27: warning: too many arguments for format [-Wformat-extra-args] 25 | fprintf(ref_allel_reads, "%ref_plus", '\t'); | ^~~~~~~~~~~ /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:27:30: warning: unknown conversion type character ‘r’ in format [-Wformat=] 27 | fprintf(ref_allel_reads, "%ref_plus", '1'); | ^ /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:27:28: warning: too many arguments for format [-Wformat-extra-args] 27 | fprintf(ref_allel_reads, "%ref_plus", '1'); | ^~~~~~~~~~~ /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:29:30: warning: unknown conversion type character ‘r’ in format [-Wformat=] 29 | fprintf(ref_allel_reads, "%ref_plus", '2'); | ^ /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:29:28: warning: too many arguments for format [-Wformat-extra-args] 29 | fprintf(ref_allel_reads, "%ref_plus", '2'); | ^~~~~~~~~~~ /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:31:29: warning: unknown conversion type character ‘r’ in format [-Wformat=] 31 | fprintf(ref_allel_reads, "%ref_plus", '\n'); | ^ /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:31:27: warning: too many arguments for format [-Wformat-extra-args] 31 | fprintf(ref_allel_reads, "%ref_plus", '\n'); | ^~~~~~~~~~~ [ 82%] Building CXX object src/CMakeFiles/sniffles.dir/plane-sweep/PlaneSweep_slim.cpp.o cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/plane-sweep/PlaneSweep_slim.cpp.o -c /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/plane-sweep/PlaneSweep_slim.cpp [ 86%] Building CXX object src/CMakeFiles/sniffles.dir/cluster/Cluster_SVs.cpp.o cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/cluster/Cluster_SVs.cpp.o -c /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/cluster/Cluster_SVs.cpp [ 91%] Building CXX object src/CMakeFiles/sniffles.dir/force_calling/Force_calling.cpp.o cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/force_calling/Force_calling.cpp.o -c /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/force_calling/Force_calling.cpp [ 95%] Building CXX object src/CMakeFiles/sniffles.dir/force_calling/VCF_parser.cpp.o cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/force_calling/VCF_parser.cpp.o -c /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/force_calling/VCF_parser.cpp /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/cluster/Cluster_SVs.cpp: In member function ‘void Cluster_SVS::update_SVs(std::vector&)’: /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/cluster/Cluster_SVs.cpp:84:8: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 84 | system(move.c_str()); | ~~~~~~^~~~~~~~~~~~~~ /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/cluster/Cluster_SVs.cpp: In member function ‘void Cluster_SVS::update_SVs()’: /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/src/cluster/Cluster_SVs.cpp:154:8: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 154 | system(del.c_str()); | ~~~~~~^~~~~~~~~~~~~ [100%] Linking CXX executable ../../bin/sniffles-core-1.0.12/sniffles cd /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/sniffles.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/sniffles.dir/tree/Breakpoint_Tree.cpp.o CMakeFiles/sniffles.dir/Genotyper/Genotyper.cpp.o CMakeFiles/sniffles.dir/Alignment.cpp.o CMakeFiles/sniffles.dir/BamParser.cpp.o CMakeFiles/sniffles.dir/Sniffles.cpp.o CMakeFiles/sniffles.dir/Ignore_Regions.cpp.o CMakeFiles/sniffles.dir/tree/Intervall_bed.cpp.o CMakeFiles/sniffles.dir/sub/Detect_Breakpoints.cpp.o CMakeFiles/sniffles.dir/sub/Breakpoint.cpp.o CMakeFiles/sniffles.dir/tree/IntervallTree.cpp.o CMakeFiles/sniffles.dir/tree/IntervallList.cpp.o CMakeFiles/sniffles.dir/realign/SWCPU.cpp.o CMakeFiles/sniffles.dir/realign/Realign.cpp.o CMakeFiles/sniffles.dir/print/VCFPrinter.cpp.o CMakeFiles/sniffles.dir/print/BedpePrinter.cpp.o CMakeFiles/sniffles.dir/print/IPrinter.cpp.o CMakeFiles/sniffles.dir/tree/BinTree.cpp.o CMakeFiles/sniffles.dir/print/NGMPrinter.cpp.o CMakeFiles/sniffles.dir/plane-sweep/PlaneSweep_slim.cpp.o CMakeFiles/sniffles.dir/cluster/Cluster_SVs.cpp.o CMakeFiles/sniffles.dir/force_calling/Force_calling.cpp.o CMakeFiles/sniffles.dir/force_calling/VCF_parser.cpp.o -o ../../bin/sniffles-core-1.0.12/sniffles -lbamtools -lz make[3]: Leaving directory '/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu' [100%] Built target sniffles make[2]: Leaving directory '/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds' bin/sniffles-*/sniffles -m test_set/reads_region.bam -v test.vcf Estimating parameter... Max dist between aln events: 4 Max diff in window: 50 Min score ratio: 2 Avg DEL ratio: 0.0432235 Avg INS ratio: 0.0740733 Start parsing... 21 Switch Chr 21 Reassessing breakpoints Continue parsing Finalizing .. Start genotype calling: Reopening Bam file for parsing coverage Finalizing .. make[1]: Leaving directory '/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds' create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a dh_auto_install -a dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a debian/rules override_dh_installman make[1]: Entering directory '/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds' pandoc --from markdown --to man -s debian/sniffles.1.md -o debian/sniffles.1 dh_installman debian/sniffles.1 make[1]: Leaving directory '/build/sniffles-cQT1WZ/sniffles-1.0.12b+ds' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a -a dh_strip -a -a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'sniffles-dbgsym' in '../sniffles-dbgsym_1.0.12b+ds-1_amd64.deb'. dpkg-deb: building package 'sniffles' in '../sniffles_1.0.12b+ds-1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../sniffles_1.0.12b+ds-1_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/sniffles-cQT1WZ /tmp/sniffles-1.0.12b+ds-1_3txq2jv I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.WnEI2Z8n5e... I: success in 605.5310 seconds md5: sniffles-dbgsym_1.0.12b+ds-1_amd64.deb: OK md5: sniffles_1.0.12b+ds-1_amd64.deb: OK sha1: sniffles-dbgsym_1.0.12b+ds-1_amd64.deb: OK sha1: sniffles_1.0.12b+ds-1_amd64.deb: OK sha256: sniffles-dbgsym_1.0.12b+ds-1_amd64.deb: OK sha256: sniffles_1.0.12b+ds-1_amd64.deb: OK Checksums: OK