Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/p/pbbam/pbbam_1.6.0+dfsg-2+b1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/pbbam-1.6.0+dfsg-2+b1o3otamvp/pbbam_1.6.0+dfsg-2+b1_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=2.3.13 autoconf=2.71-2 automake=1:1.16.5-1.1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-5 binutils=2.37-10 binutils-common=2.37-10 binutils-x86-64-linux-gnu=2.37-10 bsdextrautils=2.37.2-4 bsdutils=1:2.37.2-4 build-essential=12.9 bzip2=1.0.8-5 cmake=3.22.1-1 cmake-data=3.22.1-1 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-12 d-shlibs=0.104 dash=0.5.11+git20210903+057cd650a4ed-3 debconf=1.5.79 debhelper=13.5.2 debian-archive-keyring=2021.1.1 debianutils=5.5-1 dh-autoreconf=20 dh-elpa-helper=2.0.9 dh-exec=0.23.4 dh-strip-nondeterminism=1.12.1-1 diffutils=1:3.7-5 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 emacsen-common=3.0.4 file=1:5.41-2 findutils=4.8.0-1 g++=4:11.2.0-2 g++-11=11.2.0-12 gcc=4:11.2.0-2 gcc-11=11.2.0-12 gcc-11-base=11.2.0-12 gettext=0.21-4 gettext-base=0.21-4 googletest=1.11.0-3 gpgv=2.2.27-2 grep=3.7-1 groff-base=1.22.4-7 gzip=1.10-4 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libapt-pkg6.0=2.3.13 libarchive-zip-perl=1.68-1 libarchive13=3.4.3-2+b1 libasan6=11.2.0-12 libatomic1=11.2.0-12 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1+b1 libbinutils=2.37-10 libblkid1=2.37.2-4 libboost-dev=1.74.0.3 libboost1.74-dev=1.74.0-13 libbrotli1=1.0.9-2+b3 libbz2-1.0=1.0.8-5 libc-bin=2.32-5 libc-dev-bin=2.32-5 libc6=2.32-5 libc6-dev=2.32-5 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=11.2.0-12 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.26-1 libcrypt1=1:4.4.26-1 libctf-nobfd0=2.37-10 libctf0=2.37-10 libcurl3-gnutls=7.79.1-2 libcurl4=7.79.1-2 libcurl4-gnutls-dev=7.79.1-2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.5.2 libdeflate-dev=1.8-1 libdeflate0=1.8-1 libdpkg-perl=1.20.9 libelf1=0.186-1 libexpat1=2.4.1-3 libffi8=3.4.2-3 libfile-stripnondeterminism-perl=1.12.1-1 libgcc-11-dev=11.2.0-12 libgcc-s1=11.2.0-12 libgcrypt20=1.9.4-4 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libglib2.0-0=2.70.2-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.2-2 libgomp1=11.2.0-12 libgpg-error0=1.42-3 libgssapi-krb5-2=1.18.3-7 libgtest-dev=1.11.0-3 libhogweed6=3.7.3-1 libhts-dev=1.13+ds-2 libhts3=1.13+ds-2 libhtscodecs2=1.1.1-3+b1 libicu67=67.1-7 libidn2-0=2.3.2-2 libisl23=0.24-2 libitm1=11.2.0-12 libjsoncpp24=1.9.4-5 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 libldap-2.4-2=2.4.59+dfsg-1 liblsan0=11.2.0-12 liblz4-1=1.9.3-2 liblzma-dev=5.2.5-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-2 libmagic1=1:5.41-2 libmount1=2.37.2-4 libmpc3=1.2.1-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncurses6=6.3-1 libncursesw6=6.3-1 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.24.0-6 libpam-modules=1.4.0-10 libpam-modules-bin=1.4.0-10 libpam-runtime=1.4.0-10 libpam0g=1.4.0-10 libpbcopper-dev=1.9.3+dfsg-2 libpbcopper1.9.3=1.9.3+dfsg-2 libpcre2-8-0=10.39-3 libpcre3=2:8.39-13 libperl5.32=5.32.1-6 libpipeline1=1.5.4-1 libprocps8=2:3.3.17-5 libpsl5=0.21.0-1.2 libpython3-stdlib=3.9.8-1 libpython3.9-minimal=3.9.9-1 libpython3.9-stdlib=3.9.9-1 libquadmath0=11.2.0-12 libreadline8=8.1-2 librhash0=1.4.2-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg2-2 libsasl2-modules-db=2.1.27+dfsg2-2 libseccomp2=2.5.3-2 libselinux1=3.3-1+b1 libsemanage-common=3.3-1 libsemanage2=3.3-1+b1 libsepol2=3.3-1 libsigsegv2=2.13-1 libsmartcols1=2.37.2-4 libsqlite3-0=3.36.0-2 libssh2-1=1.10.0-2 libssl-dev=1.1.1l-1 libssl1.1=1.1.1l-1 libstdc++-11-dev=11.2.0-12 libstdc++6=11.2.0-12 libsub-override-perl=0.09-2 libsystemd0=249.7-1 libtasn1-6=4.18.0-4 libtinfo6=6.3-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-12 libubsan1=11.2.0-12 libuchardet0=0.0.7-1 libudev1=249.7-1 libunistring2=0.9.10-6 libuuid1=2.37.2-4 libuv1=1.42.0-1 libxml2=2.9.12+dfsg-5+b1 libxxhash0=0.8.0-2 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.15.5-1 login=1:4.8.1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 meson=0.60.2-1 ncurses-base=6.3-1 ncurses-bin=6.3-1 ninja-build=1.10.1-1 passwd=1:4.8.1-2 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 procps=2:3.3.17-5 python3=3.9.8-1 python3-cram=0.7-4 python3-distutils=3.9.9-3 python3-lib2to3=3.9.9-3 python3-minimal=3.9.8-1 python3-pkg-resources=59.4.0-1 python3.9=3.9.9-1 python3.9-minimal=3.9.9-1 readline-common=8.1-2 rpcsvc-proto=1.4.2-4 samtools=1.13-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.00-1 tar=1.34+dfsg-1 tzdata=2021e-1 util-linux=2.37.2-4 xz-utils=5.2.5-2 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/20211210T090303Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211205T210857Z/ 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-Bt274o && dpkg-source --no-check -x /*.dsc /build/pbbam-Bt274o/pbbam-1.6.0+dfsg && cd /build/pbbam-Bt274o/pbbam-1.6.0+dfsg && { printf '%s' 'pbbam (1.6.0+dfsg-2+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against libpbcopper1.9.3 -- all / amd64 / i386 Build Daemon (x86-conova-01) Wed, 08 Dec 2021 09:28:16 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/pbbam-Bt274o" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/pbbam-Bt274o/pbbam-1.6.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1638955696" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/pbbam-Bt274o /tmp/pbbam-1.6.0+dfsg-2+b1o3otamvp bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211205T210857Z 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.KivwwvDmTa 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.KivwwvDmTa Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-4). 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/20211205T210857Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211205T210857Z unstable/main amd64 fakeroot amd64 1.26-1 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1024 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 ... 4673 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1_amd64.deb ... Unpacking fakeroot (1.26-1) ... Setting up libfakeroot:amd64 (1.26-1) ... Setting up fakeroot (1.26-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.32-5) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211210T090303Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211205T210857Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.KivwwvDmTa Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211210T090303Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20211205T210857Z 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/20211210T090303Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20211210T090303Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20211210T090303Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20211210T090303Z unstable/main amd64 Packages [12.0 MB] Fetched 34.8 MB in 31s (1139 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.KivwwvDmTa 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-Bt274o && dpkg-source --no-check -x /*.dsc /build/pbbam-Bt274o/pbbam-1.6.0+dfsg && cd /build/pbbam-Bt274o/pbbam-1.6.0+dfsg && { printf '%s' 'pbbam (1.6.0+dfsg-2+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against libpbcopper1.9.3 -- all / amd64 / i386 Build Daemon (x86-conova-01) Wed, 08 Dec 2021 09:28:16 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/pbbam-Bt274o"' exec /tmp/mmdebstrap.KivwwvDmTa 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 6s (1220 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-Bt274o/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-Bt274o/pbbam-1.6.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1638955696" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.KivwwvDmTa dpkg-buildpackage: info: source package pbbam dpkg-buildpackage: info: source version 1.6.0+dfsg-2+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by all / amd64 / i386 Build Daemon (x86-conova-01) 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-Bt274o/pbbam-1.6.0+dfsg' dh_auto_clean find -name "*.deb.t" -delete rm -f -r /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/gendata make[1]: Leaving directory '/build/pbbam-Bt274o/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: 0.60.2 Source dir: /build/pbbam-Bt274o/pbbam-1.6.0+dfsg Build dir: /build/pbbam-Bt274o/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 11.2.0 "c++ (Debian 11.2.0-12) 11.2.0") C++ linker for the host machine: c++ ld.bfd 2.37 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 1.74.0 (/usr/include) Run-time dependency zlib found: YES 1.2.11 Run-time dependency htslib found: YES 1.13+ds Run-time dependency pbcopper found: YES 1.9.3 Program /usr/bin/meson found: YES (/usr/bin/meson) Configuring PbbamVersion.cpp using configuration Program /usr/bin/meson found: YES (/usr/bin/meson) Configuring LibraryVersion.h using configuration Program python3 found: YES (/usr/bin/python3) Program tools/check-formatting found: YES (/build/pbbam-Bt274o/pbbam-1.6.0+dfsg/tools/check-formatting) Program tools/check-eof found: YES (/build/pbbam-Bt274o/pbbam-1.6.0+dfsg/tools/check-eof) Program cram3 found: YES (/usr/bin/cram3) Run-time dependency GTest found: YES 1.11.0 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 PacBioBAM 1.6.0 User defined options buildtype : plain libdir : lib/x86_64-linux-gnu localstatedir: /var prefix : /usr sysconfdir : /etc wrap_mode : nodownload 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-Bt274o/pbbam-1.6.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' /build/pbbam-Bt274o/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-Bt274o/pbbam-1.6.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' /build/pbbam-Bt274o/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 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 [7/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 [8/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 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-ffile-prefix-map=/build/pbbam-Bt274o/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 [12/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 [13/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 [14/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 [15/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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_BamRecord.cpp.o -MF tests/pbbam_test.p/src_test_BamRecord.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecord.cpp.o -c ../tests/src/test_BamRecord.cpp [18/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 [19/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 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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 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 [130/228] /usr/bin/meson --internal symbolextractor /build/pbbam-Bt274o/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 [131/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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_BamHeader.cpp.o -MF tests/pbbam_test.p/src_test_BamHeader.cpp.o.d -o tests/pbbam_test.p/src_test_BamHeader.cpp.o -c ../tests/src/test_BamHeader.cpp [132/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 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c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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_BedReader.cpp.o -MF tests/pbbam_test.p/src_test_BedReader.cpp.o.d -o tests/pbbam_test.p/src_test_BedReader.cpp.o -c ../tests/src/test_BedReader.cpp [135/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/pbbam-1.6.0+dfsg=. 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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 [195/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 [196/228] /usr/bin/python3 ../tests/scripts/generate_data.py /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/tests/data /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/tests Generating test data in /build/pbbam-Bt274o/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 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../../src' -Wl,-rpath-link,/build/pbbam-Bt274o/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/src -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 [200/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 [201/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 [203/228] 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 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-Bt274o/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.1.6.0 /usr/lib/x86_64-linux-gnu/libgtest_main.a -lpthread /usr/lib/x86_64-linux-gnu/libgtest.a /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 [204/228] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 [205/228] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 [206/228] 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 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 [207/228] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 [208/228] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 [209/228] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 [210/228] 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 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-Bt274o/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/src -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 [211/228] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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 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/usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group [227/228] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/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_PbBamifyWorkflow.cpp.o -MF tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o.d -o tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o -c ../tools/pbbamify/src/PbBamifyWorkflow.cpp [228/228] 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 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/pbbam-Bt274o/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-Bt274o/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.1.6.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group debian/rules override_dh_auto_test make[1]: Entering directory '/build/pbbam-Bt274o/pbbam-1.6.0+dfsg' sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-Bt274o/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-Bt274o/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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-Bt274o/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-Bt274o/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|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-Bt274o/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-Bt274o/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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-Bt274o/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-Bt274o/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|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-Bt274o/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-Bt274o/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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-Bt274o/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-Bt274o/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|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-Bt274o/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-Bt274o/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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-Bt274o/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-Bt274o/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-Bt274o/pbbam-1.6.0+dfsg/gendata python3 tests/scripts/generate_data.py /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/tests/data /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/gendata Generating test data in /build/pbbam-Bt274o/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-Bt274o/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-Bt274o/pbbam-1.6.0\+dfsg/debian/tmp LC_ALL=C.UTF-8 ninja install [0/1] Regenerating build files. Cleaning... 0 files. The Meson build system Version: 0.60.2 Source dir: /build/pbbam-Bt274o/pbbam-1.6.0+dfsg Build dir: /build/pbbam-Bt274o/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 11.2.0 "c++ (Debian 11.2.0-12) 11.2.0") C++ linker for the host machine: c++ ld.bfd 2.37 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 1.74.0 (cached) Dependency zlib found: YES 1.2.11 (cached) Dependency htslib found: YES 1.13+ds (cached) Dependency pbcopper found: YES 1.9.3 (cached) Program /usr/bin/meson found: YES (/usr/bin/meson) Configuring PbbamVersion.cpp using configuration Program /usr/bin/meson found: YES (/usr/bin/meson) Configuring LibraryVersion.h using configuration Program python3 found: YES (/usr/bin/python3) Program tools/check-formatting found: YES (/build/pbbam-Bt274o/pbbam-1.6.0+dfsg/tools/check-formatting) Program tools/check-eof found: YES (/build/pbbam-Bt274o/pbbam-1.6.0+dfsg/tools/check-eof) Program cram3 found: YES (/usr/bin/cram3) Dependency gtest found: YES 1.11.0 (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 PacBioBAM 1.6.0 User defined options backend : ninja buildtype : plain libdir : lib/x86_64-linux-gnu localstatedir: /var prefix : /usr sysconfdir : /etc wrap_mode : nodownload Found ninja-1.10.1 at /usr/bin/ninja [1/15] Generating tests/pbbam_generate_data with a custom command [2/15] Generating src/PbbamGitHash.cpp with a custom command [3/14] Generating src/LibraryGitHash.h with a custom command [3/4] Installing files. Installing src/libpbbam.so.1.6.0 to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu Installing tools/bam2sam to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing tools/pbindex to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing tools/pbindexdump to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing tools/pbmerge to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing tools/pbbamify to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing tools/ccs-kinetics-bystrandify to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/Accuracy.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/AlignmentPrinter.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/BaiIndexCache.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/BaiIndexedBamReader.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/BamFile.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/BamFileMerger.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/BamHeader.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/BamReader.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/BamRecord.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/BamRecordImpl.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/BamRecordTag.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/BamRecordView.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/BamTagCodec.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/BamWriter.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/BgzipFastaWriter.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/BgzipFastqWriter.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/BgzipWriter.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/Cigar.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/CigarOperation.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/ClipType.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/CollectionMetadata.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/Compare.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/CompositeBamReader.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/CompositeFastaReader.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/Config.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/DataSet.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/DataSetTypes.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/DataSetXsd.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/Deleters.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/EntireFileQuery.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/FaiIndex.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/FastaCache.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/FastaReader.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/FastaSequence.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/FastaSequenceQuery.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/FastaWriter.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/FastqReader.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/FastqSequence.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/FastqWriter.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/FormatUtils.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/FrameEncodingType.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/Frames.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/GenomicInterval.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/GenomicIntervalQuery.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/IFastaWriter.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/IFastqWriter.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/IndexedBamWriter.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/IndexedFastaReader.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/IndexedFastqReader.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/Interval.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/IRecordWriter.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/LibraryInfo.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/LocalContextFlags.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/MD5.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/MoveAppend.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/Orientation.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/PbbamVersion.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/PbiBasicTypes.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/PbiBuilder.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/PbiFile.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/PbiFilter.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/PbiFilterQuery.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/PbiFilterTypes.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/PbiIndexedBamReader.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/PbiRawData.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/Position.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/ProgramInfo.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/PulseBehavior.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/PulseExclusionReason.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/QualityValue.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/QualityValues.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/ReadGroupInfo.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/RecordType.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/RunMetadata.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/SamReader.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/SamTagCodec.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/SamWriter.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/SequenceInfo.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/SNR.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/Strand.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/StringUtilities.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/Tag.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/TagCollection.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/TextFileReader.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/TextFileWriter.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/Validator.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/ZmwGroupQuery.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/ZmwQuery.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/ZmwType.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/ZmwTypeMap.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/bed/BedReader.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/bed Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/bed/BedWriter.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/bed Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSHeader.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSPbiBuilder.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSRecord.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSRecordFormat.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSRecordReader.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSRecordWriter.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/exception/BundleChemistryMappingException.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/exception Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/exception/InvalidSequencingChemistryException.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/exception Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/exception/ValidationException.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/exception Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/internal/Compare.inl to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/internal/CompositeBamReader.inl to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/internal/DataSetBaseTypes.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/internal/DataSetElement.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/internal/DataSetElement.inl to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/internal/PbiBasicTypes.inl to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/internal/PbiFilter.inl to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/internal/PbiFilterTypes.inl to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/internal/QueryBase.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/internal/QueryBase.inl to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfVariant.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfFile.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfFormat.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfHeader.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfHeaderTypes.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfReader.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfSort.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfQuery.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfWriter.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualPolymeraseBamRecord.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualPolymeraseCompositeReader.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualPolymeraseReader.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualRegion.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualRegionType.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualRegionTypeMap.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualZmwBamRecord.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/virtual/WhitelistedZmwReadStitcher.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/virtual/ZmwReadStitcher.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/include/pbbam/virtual/ZmwWhitelistVirtualReader.h to /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-Bt274o/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/meson-private/pbbam.pc to /build/pbbam-Bt274o/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-Bt274o/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-Bt274o/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-Bt274o/pbbam-1.6.0+dfsg' dh_installdocs -a -O--buildsystem=meson debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/pbbam-Bt274o/pbbam-1.6.0+dfsg' dh_installchangelogs CHANGELOG.md make[1]: Leaving directory '/build/pbbam-Bt274o/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 -O--buildsystem=meson dh_strip -a -O--buildsystem=meson dh_makeshlibs -a -O--buildsystem=meson dh_shlibdeps -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+b1_amd64.deb'. dpkg-deb: building package 'libpbbam1.6.0' in '../libpbbam1.6.0_1.6.0+dfsg-2+b1_amd64.deb'. dpkg-deb: building package 'libpbbam-dev' in '../libpbbam-dev_1.6.0+dfsg-2+b1_amd64.deb'. dpkg-deb: building package 'pbbamtools-dbgsym' in '../pbbamtools-dbgsym_1.6.0+dfsg-2+b1_amd64.deb'. dpkg-deb: building package 'libpbbam1.6.0-dbgsym' in '../libpbbam1.6.0-dbgsym_1.6.0+dfsg-2+b1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../pbbam_1.6.0+dfsg-2+b1_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-Bt274o /tmp/pbbam-1.6.0+dfsg-2+b1o3otamvp I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.KivwwvDmTa... I: success in 2642.7382 seconds md5: libpbbam-dev_1.6.0+dfsg-2+b1_amd64.deb: OK md5: libpbbam1.6.0-dbgsym_1.6.0+dfsg-2+b1_amd64.deb: OK md5: libpbbam1.6.0_1.6.0+dfsg-2+b1_amd64.deb: OK md5: pbbamtools-dbgsym_1.6.0+dfsg-2+b1_amd64.deb: OK md5: pbbamtools_1.6.0+dfsg-2+b1_amd64.deb: OK sha1: libpbbam-dev_1.6.0+dfsg-2+b1_amd64.deb: OK sha1: libpbbam1.6.0-dbgsym_1.6.0+dfsg-2+b1_amd64.deb: OK sha1: libpbbam1.6.0_1.6.0+dfsg-2+b1_amd64.deb: OK sha1: pbbamtools-dbgsym_1.6.0+dfsg-2+b1_amd64.deb: OK sha1: pbbamtools_1.6.0+dfsg-2+b1_amd64.deb: OK sha256: libpbbam-dev_1.6.0+dfsg-2+b1_amd64.deb: OK sha256: libpbbam1.6.0-dbgsym_1.6.0+dfsg-2+b1_amd64.deb: OK sha256: libpbbam1.6.0_1.6.0+dfsg-2+b1_amd64.deb: OK sha256: pbbamtools-dbgsym_1.6.0+dfsg-2+b1_amd64.deb: OK sha256: pbbamtools_1.6.0+dfsg-2+b1_amd64.deb: OK Checksums: OK