Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/p/pbbam/pbbam_1.6.0+dfsg-2_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/pbbam-1.6.0+dfsg-26z4oq6kh/pbbam_1.6.0+dfsg-2_amd64.buildinfo Get source package info: pbbam=1.6.0+dfsg-2 Source URL: http://snapshot.notset.fr/mr/package/pbbam/1.6.0+dfsg-2/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 apt=2.1.11 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~rc2-1 binutils=2.35.1-2 binutils-common=2.35.1-2 binutils-x86-64-linux-gnu=2.35.1-2 bsdextrautils=2.36-3+b2 bsdutils=1:2.36-3+b2 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=10.2.0-16 d-shlibs=0.95 dash=0.5.10.2-7 debconf=1.5.74 debhelper=13.2.1 debian-archive-keyring=2019.1 debianutils=4.11.2 dh-autoreconf=19 dh-exec=0.23.2 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=1:5.38-5 findutils=4.7.0+git20201010-2 g++=4:10.2.0-1 g++-10=10.2.0-16 gcc=4:10.2.0-1 gcc-10=10.2.0-16 gcc-10-base=10.2.0-16 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 googletest=1.10.0.20201025-1 gpgv=2.2.20-1 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.58 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libapt-pkg6.0=2.1.11 libarchive-zip-perl=1.68-1 libarchive13=3.4.3-2 libasan6=10.2.0-16 libatomic1=10.2.0-16 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3.1 libaudit1=1:2.8.5-3.1 libbinutils=2.35.1-2 libblkid1=2.36-3+b2 libboost-dev=1.71.0.3 libboost1.71-dev=1.71.0-7+b1 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 libcc1-0=10.2.0-16 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=2.35.1-2 libctf0=2.35.1-2 libcurl3-gnutls=7.72.0-1 libcurl4=7.72.0-1 libcurl4-gnutls-dev=7.72.0-1 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.255 libdebhelper-perl=13.2.1 libdeflate-dev=1.6-1 libdeflate0=1.6-1 libdpkg-perl=1.20.5 libelf1=0.182-1 libexpat1=2.2.10-1 libffi7=3.3-4 libfile-stripnondeterminism-perl=1.9.0-1 libgcc-10-dev=10.2.0-16 libgcc-s1=10.2.0-16 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libglib2.0-0=2.66.2-1 libgmp10=2:6.2.0+dfsg-6 libgnutls30=3.6.15-4 libgomp1=10.2.0-16 libgpg-error0=1.38-2 libgssapi-krb5-2=1.17-10 libgtest-dev=1.10.0.20201025-1 libhogweed6=3.6-2 libhts-dev=1.11-2 libhts3=1.11-2 libicu67=67.1-4 libidn2-0=2.3.0-3 libisl22=0.22.1-1 libitm1=10.2.0-16 libjsoncpp1=1.7.4-3.1 libk5crypto3=1.17-10 libkeyutils1=1.6.1-2 libkrb5-3=1.17-10 libkrb5support0=1.17-10 libldap-2.4-2=2.4.56+dfsg-1 liblsan0=10.2.0-16 liblz4-1=1.9.2-2 liblzma-dev=5.2.4-1+b1 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-5 libmagic1=1:5.38-5 libmount1=2.36-3+b2 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libncurses6=6.2+20200918-1 libncursesw6=6.2+20200918-1 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 libpbcopper-dev=1.8.0+dfsg-2 libpbcopper1.8.0=1.8.0+dfsg-2 libpcre2-8-0=10.34-7 libpcre3=2:8.39-13 libperl5.32=5.32.0-4 libpipeline1=1.5.3-1 libprocps8=2:3.3.16-5 libpsl5=0.21.0-1.1 libpython3-stdlib=3.8.6-1 libpython3.8-minimal=3.8.6-1 libpython3.8-stdlib=3.8.6-1 libquadmath0=10.2.0-16 libreadline8=8.1~rc2-2 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 libsemanage-common=3.1-1 libsemanage1=3.1-1+b1 libsepol1=3.1-1 libsigsegv2=2.12-2 libsmartcols1=2.36-3+b2 libsqlite3-0=3.33.0-1 libssh2-1=1.8.0-2.1 libssl-dev=1.1.1h-1 libssl1.1=1.1.1h-1 libstdc++-10-dev=10.2.0-16 libstdc++6=10.2.0-16 libsub-override-perl=0.09-2 libsystemd0=246.6-2 libtasn1-6=4.16.0-2 libtinfo6=6.2+20200918-1 libtirpc-common=1.2.6-3 libtirpc-dev=1.2.6-3 libtirpc3=1.2.6-3 libtool=2.4.6-14 libtsan0=10.2.0-16 libubsan1=10.2.0-16 libuchardet0=0.0.7-1 libudev1=246.6-2 libunistring2=0.9.10-4 libuuid1=2.36-3+b2 libuv1=1.40.0-1 libxml2=2.9.10+dfsg-6.2 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.9.6-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 mailcap=3.67 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 media-types=1.0.1 meson=0.56.0-1 mime-support=3.66 ncurses-base=6.2+20200918-1 ncurses-bin=6.2+20200918-1 ninja-build=1.10.1-1 passwd=1:4.8.1-1 patch=2.7.6-6 perl=5.32.0-4 perl-base=5.32.0-4 perl-modules-5.32=5.32.0-4 pkg-config=0.29.2-1 po-debconf=1.0.21 procps=2:3.3.16-5 python3=3.8.6-1 python3-cram=0.7-4 python3-minimal=3.8.6-1 python3-pkg-resources=50.3.0-1 python3.8=3.8.6-1 python3.8-minimal=3.8.6-1 readline-common=8.1~rc2-2 samtools=1.11-1 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-5 tar=1.30+dfsg-7 util-linux=2.36-3+b2 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/20201226T204201Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201111T205648Z/ 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 pbbam=1.6.0+dfsg-2 && mkdir -p /build/pbbam-pQO2kN && dpkg-source --no-check -x /*.dsc /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg && chown -R builduser:builduser /build/pbbam-pQO2kN" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1605418281" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/pbbam-pQO2kN /tmp/pbbam-1.6.0+dfsg-26z4oq6kh bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201111T205648Z 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.3ZlYi0SkKv 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.3ZlYi0SkKv Reading package lists... Building dependency tree... util-linux is already the newest version (2.36-3+b2). 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/20201111T205648Z unstable/main amd64 libfakeroot amd64 1.25.3-1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201111T205648Z unstable/main amd64 fakeroot amd64 1.25.3-1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (634 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 ... 4694 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1_amd64.deb ... Unpacking fakeroot (1.25.3-1) ... Setting up libfakeroot:amd64 (1.25.3-1) ... Setting up fakeroot (1.25.3-1) ... 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/20201226T204201Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201111T205648Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.3ZlYi0SkKv Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201226T204201Z unstable InRelease [153 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20201111T205648Z 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/20201226T204201Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201226T204201Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201226T204201Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20201226T204201Z unstable/main amd64 Packages [11.6 MB] Fetched 34.3 MB in 29s (1171 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.3ZlYi0SkKv I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d pbbam=1.6.0+dfsg-2 && mkdir -p /build/pbbam-pQO2kN && dpkg-source --no-check -x /*.dsc /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg && chown -R builduser:builduser /build/pbbam-pQO2kN"' exec /tmp/mmdebstrap.3ZlYi0SkKv Reading package lists... NOTICE: 'pbbam' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/pbbam.git Please use: git clone https://salsa.debian.org/med-team/pbbam.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 7811 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main pbbam 1.6.0+dfsg-2 (dsc) [2320 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main pbbam 1.6.0+dfsg-2 (tar) [7800 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main pbbam 1.6.0+dfsg-2 (diff) [8564 B] Fetched 7811 kB in 7s (1142 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'pbbam_1.6.0+dfsg-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting pbbam in /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg dpkg-source: info: unpacking pbbam_1.6.0+dfsg.orig.tar.xz dpkg-source: info: unpacking pbbam_1.6.0+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_python3-cram.patch dpkg-source: info: applying python3.patch dpkg-source: info: applying results_with_latest_samtools.patch dpkg-source: info: applying boost_optional.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1605418281" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.3ZlYi0SkKv dpkg-buildpackage: info: source package pbbam dpkg-buildpackage: info: source version 1.6.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=meson debian/rules override_dh_auto_clean make[1]: Entering directory '/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg' dh_auto_clean find -name "*.deb.t" -delete rm -f -r /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/gendata make[1]: Leaving directory '/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg' dh_autoreconf_clean -O--buildsystem=meson dh_clean -O--buildsystem=meson debian/rules binary-arch dh binary-arch --buildsystem=meson dh_update_autotools_config -a -O--buildsystem=meson dh_autoreconf -a -O--buildsystem=meson dh_auto_configure -a -O--buildsystem=meson cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-linux-gnu The Meson build system Version: 0.56.0 Source dir: /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg Build dir: /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu Build type: native build Project name: PacBioBAM Project version: 1.6.0 Using 'CXXFLAGS' from environment with value: '-g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now' Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2' C++ compiler for the host machine: c++ (gcc 10.2.0 "c++ (Debian 10.2.0-16) 10.2.0") C++ linker for the host machine: c++ ld.bfd 2.35.1 Using 'CXXFLAGS' from environment with value: '-g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now' Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2' Host machine cpu family: x86_64 Host machine cpu: x86_64 Compiler for C++ supports arguments -Wduplicated-cond: YES Compiler for C++ supports arguments -Wduplicated-branches: YES Compiler for C++ supports arguments -Wlogical-op: YES Compiler for C++ supports arguments -Wrestrict: YES Compiler for C++ supports arguments -Wnull-dereference: YES Compiler for C++ supports arguments -Wuseless-cast: YES Compiler for C++ supports arguments -Wdouble-promotion: YES Compiler for C++ supports arguments -Wshadow: YES Compiler for C++ supports arguments -Wformat=1: YES Run-time dependency threads found: YES Found pkg-config: /usr/bin/pkg-config (0.29.2) Run-time dependency Boost found: YES 1.71.0 (/usr/include) Run-time dependency zlib found: YES 1.2.11 Run-time dependency htslib found: YES 1.11-2 Run-time dependency pbcopper found: YES 1.8.0 Configuring PbbamVersion.cpp using configuration Configuring LibraryVersion.h using configuration Program python3 found: YES (/usr/bin/python3) Program tools/check-formatting found: YES (/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/tools/check-formatting) Program tools/check-eof found: YES (/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/tools/check-eof) Program cram3 found: YES (/usr/bin/cram3) Run-time dependency GTest found: YES 1.10.0 Configuring group.fofn using configuration Configuring PbbamTestData.h using configuration Configuring synthetic_movie_all.subreadset.xml using configuration Configuring Bam2SamVersion.h using configuration Configuring bam2sam.t using configuration Configuring PbIndexVersion.h using configuration Configuring PbIndexDumpVersion.h using configuration Configuring pbindexdump_json.t using configuration Configuring pbindexdump_cpp.t using configuration Configuring PbMergeVersion.h using configuration Configuring pbmerge_pacbio_ordering.t using configuration Configuring pbmerge_aligned_ordering.t using configuration Configuring pbmerge_mixed_ordering.t using configuration Configuring pbmerge_dataset.t using configuration Configuring pbmerge_fofn.t using configuration Configuring PbBamifyVersion.h using configuration Program samtools found: YES (/usr/bin/samtools) Configuring pbbamify.t using configuration Configuring CcsKineticsBystrandifyVersion.h using configuration Build targets in project: 12 Option buildtype is: plain [default: release] Found ninja-1.10.1 at /usr/bin/ninja dh_auto_build -a -O--buildsystem=meson cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v [1/228] /usr/bin/meson --internal vcstagger ../src/LibraryGitHash.h.in src/LibraryGitHash.h 1.6.0 /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/src/git describe --always '--dirty=*' [2/228] /usr/bin/meson --internal vcstagger ../src/PbbamGitHash.cpp.in src/PbbamGitHash.cpp 1.6.0 /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/src/git describe --always '--dirty=*' [3/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/meson-generated_.._PbbamGitHash.cpp.o -MF src/libpbbam.so.1.6.0.p/meson-generated_.._PbbamGitHash.cpp.o.d -o src/libpbbam.so.1.6.0.p/meson-generated_.._PbbamGitHash.cpp.o -c src/PbbamGitHash.cpp [4/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/BaiIndexCache.cpp.o -MF src/libpbbam.so.1.6.0.p/BaiIndexCache.cpp.o.d -o src/libpbbam.so.1.6.0.p/BaiIndexCache.cpp.o -c ../src/BaiIndexCache.cpp [5/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/AlignmentPrinter.cpp.o -MF src/libpbbam.so.1.6.0.p/AlignmentPrinter.cpp.o.d -o src/libpbbam.so.1.6.0.p/AlignmentPrinter.cpp.o -c ../src/AlignmentPrinter.cpp [6/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/BamFile.cpp.o -MF src/libpbbam.so.1.6.0.p/BamFile.cpp.o.d -o src/libpbbam.so.1.6.0.p/BamFile.cpp.o -c ../src/BamFile.cpp [7/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/BaiIndexedBamReader.cpp.o -MF src/libpbbam.so.1.6.0.p/BaiIndexedBamReader.cpp.o.d -o src/libpbbam.so.1.6.0.p/BaiIndexedBamReader.cpp.o -c ../src/BaiIndexedBamReader.cpp [8/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/BamFileMerger.cpp.o -MF src/libpbbam.so.1.6.0.p/BamFileMerger.cpp.o.d -o src/libpbbam.so.1.6.0.p/BamFileMerger.cpp.o -c ../src/BamFileMerger.cpp [9/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/BamReader.cpp.o -MF src/libpbbam.so.1.6.0.p/BamReader.cpp.o.d -o src/libpbbam.so.1.6.0.p/BamReader.cpp.o -c ../src/BamReader.cpp [10/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/BamHeader.cpp.o -MF src/libpbbam.so.1.6.0.p/BamHeader.cpp.o.d -o src/libpbbam.so.1.6.0.p/BamHeader.cpp.o -c ../src/BamHeader.cpp [11/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/BamRecordImpl.cpp.o -MF src/libpbbam.so.1.6.0.p/BamRecordImpl.cpp.o.d -o src/libpbbam.so.1.6.0.p/BamRecordImpl.cpp.o -c ../src/BamRecordImpl.cpp [12/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/BamRecordTags.cpp.o -MF src/libpbbam.so.1.6.0.p/BamRecordTags.cpp.o.d -o src/libpbbam.so.1.6.0.p/BamRecordTags.cpp.o -c ../src/BamRecordTags.cpp [13/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/BamRecordView.cpp.o -MF src/libpbbam.so.1.6.0.p/BamRecordView.cpp.o.d -o src/libpbbam.so.1.6.0.p/BamRecordView.cpp.o -c ../src/BamRecordView.cpp [14/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/BamRecord.cpp.o -MF src/libpbbam.so.1.6.0.p/BamRecord.cpp.o.d -o src/libpbbam.so.1.6.0.p/BamRecord.cpp.o -c ../src/BamRecord.cpp [15/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/BamWriter.cpp.o -MF src/libpbbam.so.1.6.0.p/BamWriter.cpp.o.d -o src/libpbbam.so.1.6.0.p/BamWriter.cpp.o -c ../src/BamWriter.cpp [16/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/BamTagCodec.cpp.o -MF src/libpbbam.so.1.6.0.p/BamTagCodec.cpp.o.d -o src/libpbbam.so.1.6.0.p/BamTagCodec.cpp.o -c ../src/BamTagCodec.cpp [17/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/BgzipFastaWriter.cpp.o -MF src/libpbbam.so.1.6.0.p/BgzipFastaWriter.cpp.o.d -o src/libpbbam.so.1.6.0.p/BgzipFastaWriter.cpp.o -c ../src/BgzipFastaWriter.cpp [18/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/BgzipFastqWriter.cpp.o -MF src/libpbbam.so.1.6.0.p/BgzipFastqWriter.cpp.o.d -o src/libpbbam.so.1.6.0.p/BgzipFastqWriter.cpp.o -c ../src/BgzipFastqWriter.cpp [19/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/BgzipWriter.cpp.o -MF src/libpbbam.so.1.6.0.p/BgzipWriter.cpp.o.d -o src/libpbbam.so.1.6.0.p/BgzipWriter.cpp.o -c ../src/BgzipWriter.cpp [20/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 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src/libpbbam.so.1.6.0.p/MemoryUtils.cpp.o src/libpbbam.so.1.6.0.p/PbiBuilder.cpp.o src/libpbbam.so.1.6.0.p/PbiFile.cpp.o src/libpbbam.so.1.6.0.p/PbiFilter.cpp.o src/libpbbam.so.1.6.0.p/PbiFilterQuery.cpp.o src/libpbbam.so.1.6.0.p/PbiFilterTypes.cpp.o src/libpbbam.so.1.6.0.p/PbiIndexedBamReader.cpp.o src/libpbbam.so.1.6.0.p/PbiIndexIO.cpp.o src/libpbbam.so.1.6.0.p/PbiRawData.cpp.o src/libpbbam.so.1.6.0.p/ProgramInfo.cpp.o src/libpbbam.so.1.6.0.p/ReadGroupInfo.cpp.o src/libpbbam.so.1.6.0.p/RecordType.cpp.o src/libpbbam.so.1.6.0.p/RunMetadata.cpp.o src/libpbbam.so.1.6.0.p/RunMetadataParser.cpp.o src/libpbbam.so.1.6.0.p/SamReader.cpp.o src/libpbbam.so.1.6.0.p/SamTagCodec.cpp.o src/libpbbam.so.1.6.0.p/SamWriter.cpp.o src/libpbbam.so.1.6.0.p/SequenceInfo.cpp.o src/libpbbam.so.1.6.0.p/StringUtilities.cpp.o src/libpbbam.so.1.6.0.p/Tag.cpp.o src/libpbbam.so.1.6.0.p/TagCollection.cpp.o src/libpbbam.so.1.6.0.p/TextFileReader.cpp.o src/libpbbam.so.1.6.0.p/TextFileWriter.cpp.o src/libpbbam.so.1.6.0.p/Validator.cpp.o src/libpbbam.so.1.6.0.p/ValidationErrors.cpp.o src/libpbbam.so.1.6.0.p/ValidationException.cpp.o src/libpbbam.so.1.6.0.p/Version.cpp.o src/libpbbam.so.1.6.0.p/VirtualZmwBamRecord.cpp.o src/libpbbam.so.1.6.0.p/VirtualZmwCompositeReader.cpp.o src/libpbbam.so.1.6.0.p/VirtualZmwReader.cpp.o src/libpbbam.so.1.6.0.p/VirtualRegion.cpp.o src/libpbbam.so.1.6.0.p/VirtualRegionTypeMap.cpp.o src/libpbbam.so.1.6.0.p/XmlReader.cpp.o src/libpbbam.so.1.6.0.p/XmlWriter.cpp.o src/libpbbam.so.1.6.0.p/WhitelistedZmwReadStitcher.cpp.o src/libpbbam.so.1.6.0.p/ZmwChunkedFastaReader.cpp.o src/libpbbam.so.1.6.0.p/ZmwChunkedFastqReader.cpp.o src/libpbbam.so.1.6.0.p/ZmwChunkedFastxBgzfReader.cpp.o src/libpbbam.so.1.6.0.p/ZmwChunkedFastxReaderImpl.cpp.o src/libpbbam.so.1.6.0.p/ZmwChunkedFastxTextReader.cpp.o src/libpbbam.so.1.6.0.p/ZmwGroupQuery.cpp.o src/libpbbam.so.1.6.0.p/ZmwReadStitcher.cpp.o src/libpbbam.so.1.6.0.p/ZmwQuery.cpp.o src/libpbbam.so.1.6.0.p/ZmwTypeMap.cpp.o src/libpbbam.so.1.6.0.p/bed_BedReader.cpp.o src/libpbbam.so.1.6.0.p/bed_BedWriter.cpp.o src/libpbbam.so.1.6.0.p/ccs_CCSPbiBuilder.cpp.o src/libpbbam.so.1.6.0.p/ccs_CCSRecord.cpp.o src/libpbbam.so.1.6.0.p/ccs_CCSRecordFormat.cpp.o src/libpbbam.so.1.6.0.p/ccs_CCSRecordReader.cpp.o src/libpbbam.so.1.6.0.p/ccs_CCSRecordWriter.cpp.o src/libpbbam.so.1.6.0.p/vcf_VcfFile.cpp.o src/libpbbam.so.1.6.0.p/vcf_VcfFormat.cpp.o src/libpbbam.so.1.6.0.p/vcf_VcfHeader.cpp.o src/libpbbam.so.1.6.0.p/vcf_VcfHeaderTypes.cpp.o src/libpbbam.so.1.6.0.p/vcf_VcfQuery.cpp.o src/libpbbam.so.1.6.0.p/vcf_VcfReader.cpp.o src/libpbbam.so.1.6.0.p/vcf_VcfSort.cpp.o src/libpbbam.so.1.6.0.p/vcf_VcfVariant.cpp.o src/libpbbam.so.1.6.0.p/vcf_VcfWriter.cpp.o src/libpbbam.so.1.6.0.p/pugixml_pugixml.cpp.o src/libpbbam.so.1.6.0.p/meson-generated_.._PbbamVersion.cpp.o -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,--start-group -Wl,-soname,libpbbam.so.1.6.0 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -pthread /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group [129/228] /usr/bin/meson --internal symbolextractor /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu src/libpbbam.so.1.6.0 src/libpbbam.so.1.6.0 src/libpbbam.so.1.6.0.p/libpbbam.so.1.6.0.symbols [130/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast 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tests/pbbam_test.p/src_test_Tags.cpp.o.d -o tests/pbbam_test.p/src_test_Tags.cpp.o -c ../tests/src/test_Tags.cpp [191/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_VcfWriter.cpp.o -MF tests/pbbam_test.p/src_test_VcfWriter.cpp.o.d -o tests/pbbam_test.p/src_test_VcfWriter.cpp.o -c ../tests/src/test_VcfWriter.cpp [192/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall 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-Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_ZmwChunkedFastxReader.cpp.o -MF tests/pbbam_test.p/src_test_ZmwChunkedFastxReader.cpp.o.d -o tests/pbbam_test.p/src_test_ZmwChunkedFastxReader.cpp.o -c ../tests/src/test_ZmwChunkedFastxReader.cpp [194/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_WhitelistedZmwReadStitcher.cpp.o -MF tests/pbbam_test.p/src_test_WhitelistedZmwReadStitcher.cpp.o.d -o tests/pbbam_test.p/src_test_WhitelistedZmwReadStitcher.cpp.o -c ../tests/src/test_WhitelistedZmwReadStitcher.cpp [195/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_Version.cpp.o -MF tests/pbbam_test.p/src_test_Version.cpp.o.d -o tests/pbbam_test.p/src_test_Version.cpp.o -c ../tests/src/test_Version.cpp [196/228] /usr/bin/python3 ../tests/scripts/generate_data.py /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/tests/data /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/tests Generating test data in /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/tests - Creating file: truncated.bam...done. - Creating file: chunking_emptyfilters.subreadset.xml...done. - Creating file: chunking_missingfilters.subreadset.xml...done. - Creating file: normal.fa...done. - Creating file: normal.fq...done. - Creating symlink: aligned.bam...done. - Creating symlink: aligned.bam.bai...done. - Creating symlink: aligned.bam.pbi...done. - Creating symlink: aligned2.bam...done. - Creating symlink: aligned2.bam.bai...done. - Creating symlink: aligned2.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam.pbi...done. - Creating symlink: missing_pbi.bam...done. [197/228] c++ -Itools/ccs-kinetics-bystrandify.p -Itools -I../tools -Iinclude -I../include -I../tools/ccs-kinetics-bystrandify -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_main.cpp.o -MF tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_main.cpp.o.d -o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_main.cpp.o -c ../tools/ccs-kinetics-bystrandify/src/main.cpp [198/228] c++ -Itests/zero_byte_check/zero_byte_check.p -Itests/zero_byte_check -I../tests/zero_byte_check -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/zero_byte_check/zero_byte_check.p/main.cpp.o -MF tests/zero_byte_check/zero_byte_check.p/main.cpp.o.d -o tests/zero_byte_check/zero_byte_check.p/main.cpp.o -c ../tests/zero_byte_check/main.cpp [199/228] c++ -o tests/zero_byte_check/zero_byte_check tests/zero_byte_check/zero_byte_check.p/main.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.1.6.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../../src' -Wl,-rpath-link,/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/src [200/228] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/bam2sam.p/bam2sam_src_main.cpp.o -MF tools/bam2sam.p/bam2sam_src_main.cpp.o.d -o tools/bam2sam.p/bam2sam_src_main.cpp.o -c ../tools/bam2sam/src/main.cpp [201/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_ZmwQuery.cpp.o -MF tests/pbbam_test.p/src_test_ZmwQuery.cpp.o.d -o tests/pbbam_test.p/src_test_ZmwQuery.cpp.o -c ../tests/src/test_ZmwQuery.cpp [202/228] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o -MF tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o.d -o tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o -c ../tools/bam2sam/src/Bam2SamSettings.cpp [203/228] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o -MF tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o.d -o tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o -c ../tools/bam2sam/src/Bam2SamWorkflow.cpp [204/228] c++ -o tools/bam2sam tools/bam2sam.p/bam2sam_src_main.cpp.o tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group /usr/lib/x86_64-linux-gnu/libhts.so -pthread /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group [205/228] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindex.p/pbindex_src_main.cpp.o -MF tools/pbindex.p/pbindex_src_main.cpp.o.d -o tools/pbindex.p/pbindex_src_main.cpp.o -c ../tools/pbindex/src/main.cpp [206/228] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindex.p/pbindex_src_PbIndexSettings.cpp.o -MF tools/pbindex.p/pbindex_src_PbIndexSettings.cpp.o.d -o tools/pbindex.p/pbindex_src_PbIndexSettings.cpp.o -c ../tools/pbindex/src/PbIndexSettings.cpp [207/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o -MF tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o.d -o tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o -c ../tests/src/test_ZmwReadStitcher.cpp [208/228] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o -MF tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o.d -o tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o -c ../tools/pbindex/src/PbIndexWorkflow.cpp [209/228] c++ -o tools/pbindex tools/pbindex.p/pbindex_src_main.cpp.o tools/pbindex.p/pbindex_src_PbIndexSettings.cpp.o tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.1.6.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/src [210/228] c++ -o tests/pbbam_test tests/pbbam_test.p/src_test_AlignmentPrinter.cpp.o tests/pbbam_test.p/src_test_BamFile.cpp.o tests/pbbam_test.p/src_test_BamHeader.cpp.o tests/pbbam_test.p/src_test_BamReader.cpp.o tests/pbbam_test.p/src_test_BamRecord.cpp.o tests/pbbam_test.p/src_test_BamRecordClipping.cpp.o tests/pbbam_test.p/src_test_BamRecordImplCore.cpp.o tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o tests/pbbam_test.p/src_test_BamRecordImplVariableData.cpp.o tests/pbbam_test.p/src_test_BamRecordMapping.cpp.o tests/pbbam_test.p/src_test_BamWriter.cpp.o tests/pbbam_test.p/src_test_BedReader.cpp.o tests/pbbam_test.p/src_test_BedWriter.cpp.o tests/pbbam_test.p/src_test_BgzipFastaWriter.cpp.o tests/pbbam_test.p/src_test_BgzipFastqWriter.cpp.o tests/pbbam_test.p/src_test_BgzipWriter.cpp.o tests/pbbam_test.p/src_test_CCSPbiBuilder.cpp.o tests/pbbam_test.p/src_test_CCSRecord.cpp.o tests/pbbam_test.p/src_test_CCSRecordIO.cpp.o tests/pbbam_test.p/src_test_CollectionMetadata.cpp.o tests/pbbam_test.p/src_test_Compare.cpp.o tests/pbbam_test.p/src_test_CompositeBamReaders.cpp.o tests/pbbam_test.p/src_test_DataSetCore.cpp.o tests/pbbam_test.p/src_test_DataSetGenomicIntervals.cpp.o tests/pbbam_test.p/src_test_DataSetIO.cpp.o tests/pbbam_test.p/src_test_DataSetQuery.cpp.o tests/pbbam_test.p/src_test_DataSetXsd.cpp.o tests/pbbam_test.p/src_test_EndToEnd.cpp.o tests/pbbam_test.p/src_test_EntireFileQuery.cpp.o tests/pbbam_test.p/src_test_FaiIndex.cpp.o tests/pbbam_test.p/src_test_FaiZmwChunker.cpp.o tests/pbbam_test.p/src_test_FastaCache.cpp.o tests/pbbam_test.p/src_test_FastaReader.cpp.o tests/pbbam_test.p/src_test_FastaSequence.cpp.o tests/pbbam_test.p/src_test_FastaSequenceQuery.cpp.o tests/pbbam_test.p/src_test_FastaWriter.cpp.o tests/pbbam_test.p/src_test_FastqReader.cpp.o tests/pbbam_test.p/src_test_FastqSequence.cpp.o tests/pbbam_test.p/src_test_FastqWriter.cpp.o tests/pbbam_test.p/src_test_FileUtils.cpp.o tests/pbbam_test.p/src_test_GenomicIntervalQuery.cpp.o tests/pbbam_test.p/src_test_IndexedBamWriter.cpp.o tests/pbbam_test.p/src_test_IndexedFastaReader.cpp.o tests/pbbam_test.p/src_test_IndexedFastqReader.cpp.o tests/pbbam_test.p/src_test_LongCigar.cpp.o tests/pbbam_test.p/src_test_PacBioIndex.cpp.o tests/pbbam_test.p/src_test_PbiFilter.cpp.o tests/pbbam_test.p/src_test_PbiFilterQuery.cpp.o tests/pbbam_test.p/src_test_QualityValues.cpp.o tests/pbbam_test.p/src_test_Pulse2BaseCache.cpp.o tests/pbbam_test.p/src_test_ReadGroupInfo.cpp.o tests/pbbam_test.p/src_test_RunMetadata.cpp.o tests/pbbam_test.p/src_test_SamIO.cpp.o tests/pbbam_test.p/src_test_SequenceUtils.cpp.o tests/pbbam_test.p/src_test_StringUtils.cpp.o tests/pbbam_test.p/src_test_Tags.cpp.o tests/pbbam_test.p/src_test_TextFileReader.cpp.o tests/pbbam_test.p/src_test_TextFileWriter.cpp.o tests/pbbam_test.p/src_test_TimeUtils.cpp.o tests/pbbam_test.p/src_test_Validator.cpp.o tests/pbbam_test.p/src_test_VcfFile.cpp.o tests/pbbam_test.p/src_test_VcfFormat.cpp.o tests/pbbam_test.p/src_test_VcfHeader.cpp.o tests/pbbam_test.p/src_test_VcfReader.cpp.o tests/pbbam_test.p/src_test_VcfSort.cpp.o tests/pbbam_test.p/src_test_VcfQuery.cpp.o tests/pbbam_test.p/src_test_VcfVariant.cpp.o tests/pbbam_test.p/src_test_VcfWriter.cpp.o tests/pbbam_test.p/src_test_Version.cpp.o tests/pbbam_test.p/src_test_WhitelistedZmwReadStitcher.cpp.o tests/pbbam_test.p/src_test_ZmwChunkedFastxReader.cpp.o tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o tests/pbbam_test.p/src_test_ZmwQuery.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 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tools/pbmerge.p/pbmerge_src_PbMergeSettings.cpp.o tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.1.6.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/src [219/228] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond 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-Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/src [221/228] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_main.cpp.o -MF tools/pbbamify.p/pbbamify_src_main.cpp.o.d -o tools/pbbamify.p/pbbamify_src_main.cpp.o -c ../tools/pbbamify/src/main.cpp [222/228] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_PbBamifySettings.cpp.o -MF tools/pbbamify.p/pbbamify_src_PbBamifySettings.cpp.o.d -o tools/pbbamify.p/pbbamify_src_PbBamifySettings.cpp.o -c ../tools/pbbamify/src/PbBamifySettings.cpp [223/228] c++ -Itools/ccs-kinetics-bystrandify.p -Itools -I../tools -Iinclude -I../include -I../tools/ccs-kinetics-bystrandify -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o -c ../tools/pbbamify/src/PbBamifyWorkflow.cpp [226/228] c++ -o tools/pbbamify tools/pbbamify.p/pbbamify_src_main.cpp.o tools/pbbamify.p/pbbamify_src_PbBamifySettings.cpp.o tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.1.6.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/src [227/228] c++ -Itools/ccs-kinetics-bystrandify.p -Itools -I../tools -Iinclude -I../include -I../tools/ccs-kinetics-bystrandify -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -MF tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o.d -o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -c ../tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp [228/228] c++ -o tools/ccs-kinetics-bystrandify tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_main.cpp.o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifySettings.cpp.o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.1.6.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/src debian/rules override_dh_auto_test make[1]: Entering directory '/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg' sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbbamify.t.in > tests/src/cram/pbbamify.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbindexdump_cpp.t.in > tests/src/cram/pbindexdump_cpp.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbindexdump_json.t.in > tests/src/cram/pbindexdump_json.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_aligned_ordering.t.in > tests/src/cram/pbmerge_aligned_ordering.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_dataset.t.in > tests/src/cram/pbmerge_dataset.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_fofn.t.in > tests/src/cram/pbmerge_fofn.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_mixed_ordering.t.in > tests/src/cram/pbmerge_mixed_ordering.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_pacbio_ordering.t.in > tests/src/cram/pbmerge_pacbio_ordering.deb.t dh_auto_configure -O--buildsystem=meson cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-linux-gnu Directory already configured. Just run your build command (e.g. ninja) and Meson will regenerate as necessary. If ninja fails, run "ninja reconfigure" or "meson --reconfigure" to force Meson to regenerate. If build failures persist, run "meson setup --wipe" to rebuild from scratch using the same options as passed when configuring the build. To change option values, run "meson configure" instead. mkdir -p /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/gendata python3 tests/scripts/generate_data.py /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/tests/data /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/gendata Generating test data in /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/gendata - Creating file: truncated.bam...done. - Creating file: chunking_emptyfilters.subreadset.xml...done. - Creating file: chunking_missingfilters.subreadset.xml...done. - Creating file: normal.fa...done. - Creating file: normal.fq...done. - Creating symlink: aligned.bam...done. - Creating symlink: aligned.bam.bai...done. - Creating symlink: aligned.bam.pbi...done. - Creating symlink: aligned2.bam...done. - Creating symlink: aligned2.bam.bai...done. - Creating symlink: aligned2.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam.pbi...done. - Creating symlink: missing_pbi.bam...done. # Fix broken PATH synthetic_movie_all_path=`find $PWD -name synthetic_movie_all.subreadset.xml` ; \ sed -i -e "s?.GENERATEDDATADIR/synthetic_movie_all.subreadset.xml?${synthetic_movie_all_path}?" tests/src/cram/pbbamify* BINDIR=`dirname $(find $PWD -name pbmerge -type f -executable)`; \ LIBDIR=`find $PWD -name lib -type d`; \ PATH="$BINDIR:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin" LD_LIBRARY_PATH="$LIBDIR:" \ cram3 -v --preserve-env tests/src/cram/pbbamify.deb.t tests/src/cram/pbindexdump_cpp.deb.t tests/src/cram/pbindexdump_json.deb.t tests/src/cram/pbmerge_aligned_ordering.deb.t tests/src/cram/pbmerge_dataset.deb.t tests/src/cram/pbmerge_fofn.deb.t tests/src/cram/pbmerge_mixed_ordering.deb.t tests/src/cram/pbmerge_pacbio_ordering.deb.t tests/src/cram/pbbamify.deb.t: passed tests/src/cram/pbindexdump_cpp.deb.t: passed tests/src/cram/pbindexdump_json.deb.t: passed tests/src/cram/pbmerge_aligned_ordering.deb.t: passed tests/src/cram/pbmerge_dataset.deb.t: passed tests/src/cram/pbmerge_fofn.deb.t: passed tests/src/cram/pbmerge_mixed_ordering.deb.t: passed tests/src/cram/pbmerge_pacbio_ordering.deb.t: passed # Ran 8 tests, 0 skipped, 0 failed. make[1]: Leaving directory '/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=meson dh_prep -a -O--buildsystem=meson dh_auto_install -a -O--buildsystem=meson cd obj-x86_64-linux-gnu && DESTDIR=/build/pbbam-pQO2kN/pbbam-1.6.0\+dfsg/debian/tmp LC_ALL=C.UTF-8 ninja install [0/1] Regenerating build files. The Meson build system Version: 0.56.0 Source dir: /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg Build dir: /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu Build type: native build Project name: PacBioBAM Project version: 1.6.0 C++ compiler for the host machine: c++ (gcc 10.2.0 "c++ (Debian 10.2.0-16) 10.2.0") C++ linker for the host machine: c++ ld.bfd 2.35.1 Host machine cpu family: x86_64 Host machine cpu: x86_64 Compiler for C++ supports arguments -Wduplicated-cond: YES (cached) Compiler for C++ supports arguments -Wduplicated-branches: YES (cached) Compiler for C++ supports arguments -Wlogical-op: YES (cached) Compiler for C++ supports arguments -Wrestrict: YES (cached) Compiler for C++ supports arguments -Wnull-dereference: YES (cached) Compiler for C++ supports arguments -Wuseless-cast: YES (cached) Compiler for C++ supports arguments -Wdouble-promotion: YES (cached) Compiler for C++ supports arguments -Wshadow: YES (cached) Compiler for C++ supports arguments -Wformat=1: YES (cached) Dependency threads found: YES unknown (cached) Dependency boost found: YES 1.71.0 (cached) Dependency zlib found: YES 1.2.11 (cached) Dependency htslib found: YES 1.11-2 (cached) Dependency pbcopper found: YES 1.8.0 (cached) Configuring PbbamVersion.cpp using configuration Configuring LibraryVersion.h using configuration Program python3 found: YES (/usr/bin/python3) Program tools/check-formatting found: YES (/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/tools/check-formatting) Program tools/check-eof found: YES (/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/tools/check-eof) Program cram3 found: YES (/usr/bin/cram3) Dependency gtest found: YES 1.10.0 (cached) Configuring group.fofn using configuration Configuring PbbamTestData.h using configuration Configuring synthetic_movie_all.subreadset.xml using configuration Configuring Bam2SamVersion.h using configuration Configuring bam2sam.t using configuration Configuring PbIndexVersion.h using configuration Configuring PbIndexDumpVersion.h using configuration Configuring pbindexdump_json.t using configuration Configuring pbindexdump_cpp.t using configuration Configuring PbMergeVersion.h using configuration Configuring pbmerge_pacbio_ordering.t using configuration Configuring pbmerge_aligned_ordering.t using configuration Configuring pbmerge_mixed_ordering.t using configuration Configuring pbmerge_dataset.t using configuration Configuring pbmerge_fofn.t using configuration Configuring PbBamifyVersion.h using configuration Program samtools found: YES (/usr/bin/samtools) Configuring pbbamify.t using configuration Configuring CcsKineticsBystrandifyVersion.h using configuration Build targets in project: 12 Option buildtype is: plain [default: release] Found ninja-1.10.1 at /usr/bin/ninja [1/15] Generating pbbam_generate_data with a custom command [2/15] Generating PbbamGitHash.cpp with a custom command [3/14] Generating LibraryGitHash.h with a custom command [3/4] Installing files. Installing src/libpbbam.so.1.6.0 to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu Installing tools/bam2sam to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing tools/pbindex to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing tools/pbindexdump to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing tools/pbmerge to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing tools/pbbamify to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing tools/ccs-kinetics-bystrandify to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/Accuracy.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/AlignmentPrinter.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/BaiIndexCache.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/BaiIndexedBamReader.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/BamFile.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/BamFileMerger.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/BamHeader.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/BamReader.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/BamRecord.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/BamRecordImpl.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/BamRecordTag.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/BamRecordView.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/BamTagCodec.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/BamWriter.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/BgzipFastaWriter.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/BgzipFastqWriter.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/BgzipWriter.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/Cigar.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/CigarOperation.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/ClipType.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/CollectionMetadata.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/Compare.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/CompositeBamReader.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/CompositeFastaReader.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/Config.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/DataSet.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/DataSetTypes.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/DataSetXsd.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/Deleters.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/EntireFileQuery.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/FaiIndex.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/FastaCache.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/FastaReader.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/FastaSequence.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/FastaSequenceQuery.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/FastaWriter.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/FastqReader.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/FastqSequence.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/FastqWriter.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/FormatUtils.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/FrameEncodingType.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/Frames.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/GenomicInterval.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/GenomicIntervalQuery.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/IFastaWriter.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/IFastqWriter.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/IndexedBamWriter.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/IndexedFastaReader.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/IndexedFastqReader.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/Interval.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/IRecordWriter.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/LibraryInfo.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/LocalContextFlags.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/MD5.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/MoveAppend.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/Orientation.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/PbbamVersion.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/PbiBasicTypes.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/PbiBuilder.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/PbiFile.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/PbiFilter.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/PbiFilterQuery.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/PbiFilterTypes.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/PbiIndexedBamReader.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/PbiRawData.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/Position.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/ProgramInfo.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/PulseBehavior.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/PulseExclusionReason.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/QualityValue.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/QualityValues.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/ReadGroupInfo.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/RecordType.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/RunMetadata.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/SamReader.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/SamTagCodec.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/SamWriter.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/SequenceInfo.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/SNR.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/Strand.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/StringUtilities.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/Tag.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/TagCollection.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/TextFileReader.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/TextFileWriter.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/Validator.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/ZmwGroupQuery.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/ZmwQuery.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/ZmwType.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/ZmwTypeMap.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/bed/BedReader.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/bed Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/bed/BedWriter.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/bed Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSHeader.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSPbiBuilder.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSRecord.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSRecordFormat.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSRecordReader.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSRecordWriter.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/exception/BundleChemistryMappingException.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/exception Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/exception/InvalidSequencingChemistryException.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/exception Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/exception/ValidationException.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/exception Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/internal/Compare.inl to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/internal/CompositeBamReader.inl to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/internal/DataSetBaseTypes.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/internal/DataSetElement.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/internal/DataSetElement.inl to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/internal/PbiBasicTypes.inl to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/internal/PbiFilter.inl to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/internal/PbiFilterTypes.inl to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/internal/QueryBase.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/internal/QueryBase.inl to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfVariant.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfFile.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfFormat.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfHeader.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfHeaderTypes.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfReader.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfSort.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfQuery.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfWriter.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualPolymeraseBamRecord.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualPolymeraseCompositeReader.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualPolymeraseReader.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualRegion.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualRegionType.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualRegionTypeMap.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualZmwBamRecord.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/virtual/WhitelistedZmwReadStitcher.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/virtual/ZmwReadStitcher.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/include/pbbam/virtual/ZmwWhitelistVirtualReader.h to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/meson-private/pbbam.pc to /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig debian/rules override_dh_install make[1]: Entering directory '/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg' dh_install d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --exclude-a \ --override s/libhts2-dev/libhts-dev/ \ --override s/libpbcopper[0-9.]*-dev/libpbcopper-dev/ \ --movedev debian/tmp/usr/include/* usr/include \ --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/x86_64-linux-gnu/pkgconfig \ debian/tmp/usr/lib/*/*.so Library package automatic movement utility --> libhts-dev package exists. --> libpbcopper-dev package exists. --> zlib1g-dev package exists. set -e install -d -m 755 debian/libpbbam-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libpbbam1.6.0/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libpbbam.so debian/libpbbam-dev/usr/lib/x86_64-linux-gnu mv /build/pbbam-pQO2kN/pbbam-1.6.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libpbbam.so.1.6.0 debian/libpbbam1.6.0/usr/lib/x86_64-linux-gnu PKGDEV=libpbbam-dev PKGSHL=libpbbam1.6.0 install -d -m 755 debian/libpbbam-dev/usr/include mv debian/tmp/usr/include/pbbam debian/libpbbam-dev/usr/include install -d -m 755 debian/libpbbam-dev/usr/lib/x86_64-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libpbbam-dev/usr/lib/x86_64-linux-gnu/pkgconfig find debian -name "lib*.la" -delete make[1]: Leaving directory '/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg' dh_installdocs -a -O--buildsystem=meson debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg' dh_installchangelogs CHANGELOG.md make[1]: Leaving directory '/build/pbbam-pQO2kN/pbbam-1.6.0+dfsg' dh_installsystemduser -a -O--buildsystem=meson dh_perl -a -O--buildsystem=meson dh_link -a -O--buildsystem=meson dh_strip_nondeterminism -a -O--buildsystem=meson dh_compress -a -O--buildsystem=meson dh_fixperms -a -O--buildsystem=meson dh_missing -a -O--buildsystem=meson dh_dwz -a -a -O--buildsystem=meson dh_strip -a -a -O--buildsystem=meson dh_makeshlibs -a -a -O--buildsystem=meson dh_shlibdeps -a -a -O--buildsystem=meson dh_installdeb -a -O--buildsystem=meson dh_gencontrol -a -O--buildsystem=meson dpkg-gencontrol: warning: package libpbbam-dev: substitution variable ${devlibs:Depends} unused, but is defined dh_md5sums -a -O--buildsystem=meson dh_builddeb -a -O--buildsystem=meson dpkg-deb: building package 'pbbamtools' in '../pbbamtools_1.6.0+dfsg-2_amd64.deb'. dpkg-deb: building package 'libpbbam1.6.0' in '../libpbbam1.6.0_1.6.0+dfsg-2_amd64.deb'. dpkg-deb: building package 'libpbbam-dev' in '../libpbbam-dev_1.6.0+dfsg-2_amd64.deb'. dpkg-deb: building package 'pbbamtools-dbgsym' in '../pbbamtools-dbgsym_1.6.0+dfsg-2_amd64.deb'. dpkg-deb: building package 'libpbbam1.6.0-dbgsym' in '../libpbbam1.6.0-dbgsym_1.6.0+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../pbbam_1.6.0+dfsg-2_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/pbbam-pQO2kN /tmp/pbbam-1.6.0+dfsg-26z4oq6kh I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.3ZlYi0SkKv... I: success in 5725.0351 seconds md5: libpbbam-dev_1.6.0+dfsg-2_amd64.deb: OK md5: libpbbam1.6.0-dbgsym_1.6.0+dfsg-2_amd64.deb: OK md5: libpbbam1.6.0_1.6.0+dfsg-2_amd64.deb: OK md5: pbbamtools-dbgsym_1.6.0+dfsg-2_amd64.deb: OK md5: pbbamtools_1.6.0+dfsg-2_amd64.deb: OK sha1: libpbbam-dev_1.6.0+dfsg-2_amd64.deb: OK sha1: libpbbam1.6.0-dbgsym_1.6.0+dfsg-2_amd64.deb: OK sha1: libpbbam1.6.0_1.6.0+dfsg-2_amd64.deb: OK sha1: pbbamtools-dbgsym_1.6.0+dfsg-2_amd64.deb: OK sha1: pbbamtools_1.6.0+dfsg-2_amd64.deb: OK sha256: libpbbam-dev_1.6.0+dfsg-2_amd64.deb: OK sha256: libpbbam1.6.0-dbgsym_1.6.0+dfsg-2_amd64.deb: OK sha256: libpbbam1.6.0_1.6.0+dfsg-2_amd64.deb: OK sha256: pbbamtools-dbgsym_1.6.0+dfsg-2_amd64.deb: OK sha256: pbbamtools_1.6.0+dfsg-2_amd64.deb: OK Checksums: OK