Sun Oct 12 06:49:01 UTC 2025 I: starting to build pbbam/forky/arm64 on jenkins on '2025-10-12 06:48' Sun Oct 12 06:49:01 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_6/122232/console.log Sun Oct 12 06:49:01 UTC 2025 I: Downloading source for forky/pbbam=2.4.0+dfsg-2 --2025-10-12 06:49:01-- http://deb.debian.org/debian/pool/main/p/pbbam/pbbam_2.4.0%2bdfsg-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2462 (2.4K) [text/prs.lines.tag] Saving to: ‘pbbam_2.4.0+dfsg-2.dsc’ 0K .. 100% 285M=0s 2025-10-12 06:49:01 (285 MB/s) - ‘pbbam_2.4.0+dfsg-2.dsc’ saved [2462/2462] Sun Oct 12 06:49:01 UTC 2025 I: pbbam_2.4.0+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: pbbam Binary: pbbamtools, libpbbam2.4.0, libpbbam-dev Architecture: any Version: 2.4.0+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://pbbam.readthedocs.org/en/latest/index.html Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/pbbam Vcs-Git: https://salsa.debian.org/med-team/pbbam.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@ Build-Depends: debhelper-compat (= 13), dh-exec, d-shlibs, meson, pkgconf, cmake, libboost-dev, libboost-iostreams-dev, zlib1g-dev, libssl-dev, libhts-dev, libpbcopper-dev (>> 2.2.0), python3-cram, libgtest-dev , samtools Package-List: libpbbam-dev deb libdevel optional arch=any libpbbam2.4.0 deb libs optional arch=any pbbamtools deb science optional arch=any Checksums-Sha1: c18a5477be1369d03c515bf59103d3233785d583 7826464 pbbam_2.4.0+dfsg.orig.tar.xz d14373206434f2d751086854be52b26f4b974df7 9152 pbbam_2.4.0+dfsg-2.debian.tar.xz Checksums-Sha256: e991e5f5470976f2ad0cca93658a273989738ca48cce4f024fd074cc1e8cbe2b 7826464 pbbam_2.4.0+dfsg.orig.tar.xz 8ee1208ec0048d271328fbfdedf4482108ecc4afa4909b7e361581751c8774fc 9152 pbbam_2.4.0+dfsg-2.debian.tar.xz Files: 315039ff474e762e609442ca84988512 7826464 pbbam_2.4.0+dfsg.orig.tar.xz 1f062fd9631add7836816da5a82eb615 9152 pbbam_2.4.0+dfsg-2.debian.tar.xz Dgit: aac2fb1e4ee9ed420d1b89975b183c345a9e515e debian archive/debian/2.4.0+dfsg-2 https://git.dgit.debian.org/pbbam -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmji7P4UHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqOMRAAhjlt9k0EyvIJKgSN7c+zj7Uf7M10 al0FK1u7gM/m/WioOOPz0Ug+I3HsIbVgnTvbmyOJ0TWSjpZcAaCnWw0/fJYMaDOk DfBiuggVENjNI/9MggKKiIqjSEg/pXGwXBAwF/EAd1h1uZUhO/X6PLwWVrXV2FJ+ DcsD+FFrFWYtu6/9ky2C3iwoFP4DrqNYlidg2/ARKz7ovY5176CjBmjll4bJdwHU NpJtaU3LuhfsMdpmmtody2S9UfsO9olLnqG7jkthSbo++N0Ie6pavM5SHw5kE9ky dvStUEeQukXDRurSs2Mm+McFd3T1W08ET/IZaUYlykZqdQujN91pmTGpvUDx1+Nw oHakYq/0q/4OGr4KcVIgR8q9FPxwPI+gITd+s/wGcMtTBzY87ttMhLdDabdvG7un 6m7aVlcBHQaxF/p/OQ3ElZBJw5fT1FKfkBPxrc/goa/DVqw2nzBYtvadCo9OoJRA /cub87bzCZfUYBS76n7B3iAMixQr6f1anpmCqxB+Tt9pYukHPinKWZjvznL+086d qnQofWb7/epjnF6Gi17XDKFmz3MeESS2s5CF9ShvObHM+pZyjeV3XxwNWAcpzwOX fC7srBP+BQLkDlM+j/LtM04Mx/qRQDTh0Y/rvjehDtNaKXnpr9CRbRTTEyM6plyB MBHjb4Axr0q2tHM= =Kmex -----END PGP SIGNATURE----- Sun Oct 12 06:49:01 UTC 2025 I: Checking whether the package is not for us Sun Oct 12 06:49:01 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net. Sun Oct 12 06:49:01 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Sun Oct 12 06:56:05 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. W: cgroups are not available on the host, not using them. I: pbuilder: network access will be disabled during build I: Current time: Sat Nov 14 01:12:02 -12 2026 I: pbuilder-time-stamp: 1794661922 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [pbbam_2.4.0+dfsg-2.dsc] I: copying [./pbbam_2.4.0+dfsg.orig.tar.xz] I: copying [./pbbam_2.4.0+dfsg-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./pbbam_2.4.0+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting pbbam in pbbam-2.4.0+dfsg dpkg-source: info: unpacking pbbam_2.4.0+dfsg.orig.tar.xz dpkg-source: info: unpacking pbbam_2.4.0+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 spelling I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1209296/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1209296' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.gjjlvic5/pbuilderrc_1yKF --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.gjjlvic5/b1 --logfile b1/build.log pbbam_2.4.0+dfsg-2.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/sbin/chroot' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1209296/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-exec, d-shlibs, meson, pkgconf, cmake, libboost-dev, libboost-iostreams-dev, zlib1g-dev, libssl-dev, libhts-dev, libpbcopper-dev (>> 2.2.0), python3-cram, libgtest-dev, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20000 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on meson; however: Package meson is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libpbcopper-dev (>> 2.2.0); however: Package libpbcopper-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-cram; however: Package python3-cram is not installed. pbuilder-satisfydepends-dummy depends on libgtest-dev; however: Package libgtest-dev is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} comerr-dev{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-strip-nondeterminism{a} dwz{a} file{a} gcc-14-base{a} gettext{a} gettext-base{a} googletest{a} groff-base{a} icu-devtools{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libarchive13t64{a} libboost-dev{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgcc-14-dev{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libgtest-dev{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu-dev{a} libicu76{a} libidn2-0{a} libidn2-dev{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-crypto-ossl0{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpbcopper-dev{a} libpbcopper2.3.0{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libstdc++-14-dev{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libuv1t64{a} libxml2-16{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} meson{a} netbase{a} nettle-dev{a} ninja-build{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-autocommand{a} python3-cram{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 150 newly installed, 0 to remove and 0 not upgraded. Need to get 93.5 MB of archives. After unpacking 526 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main arm64 libexpat1 arm64 2.7.3-1 [96.5 kB] Get: 2 http://deb.debian.org/debian forky/main arm64 libpython3.13-minimal arm64 3.13.7-1 [857 kB] Get: 3 http://deb.debian.org/debian forky/main arm64 python3.13-minimal arm64 3.13.7-1 [2001 kB] Get: 4 http://deb.debian.org/debian forky/main arm64 python3-minimal arm64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian forky/main arm64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian forky/main arm64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian forky/main arm64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian forky/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get: 9 http://deb.debian.org/debian forky/main arm64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian forky/main arm64 libreadline8t64 arm64 8.3-3 [169 kB] Get: 11 http://deb.debian.org/debian forky/main arm64 libpython3.13-stdlib arm64 3.13.7-1 [1895 kB] Get: 12 http://deb.debian.org/debian forky/main arm64 python3.13 arm64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian forky/main arm64 libpython3-stdlib arm64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian forky/main arm64 python3 arm64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian forky/main arm64 libproc2-0 arm64 2:4.0.4-9 [62.8 kB] Get: 16 http://deb.debian.org/debian forky/main arm64 procps arm64 2:4.0.4-9 [871 kB] Get: 17 http://deb.debian.org/debian forky/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 18 http://deb.debian.org/debian forky/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 19 http://deb.debian.org/debian forky/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 20 http://deb.debian.org/debian forky/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 21 http://deb.debian.org/debian forky/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 22 http://deb.debian.org/debian forky/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 23 http://deb.debian.org/debian forky/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 24 http://deb.debian.org/debian forky/main arm64 bsdextrautils arm64 2.41.2-1 [94.3 kB] Get: 25 http://deb.debian.org/debian forky/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 26 http://deb.debian.org/debian forky/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 27 http://deb.debian.org/debian forky/main arm64 m4 arm64 1.4.20-2 [315 kB] Get: 28 http://deb.debian.org/debian forky/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 29 http://deb.debian.org/debian forky/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 30 http://deb.debian.org/debian forky/main arm64 automake all 1:1.17-4 [862 kB] Get: 31 http://deb.debian.org/debian forky/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 32 http://deb.debian.org/debian forky/main arm64 cmake-data all 4.1.1+really3.31.6-2 [2268 kB] Get: 33 http://deb.debian.org/debian forky/main arm64 libxml2-16 arm64 2.14.6+dfsg-0.1 [601 kB] Get: 34 http://deb.debian.org/debian forky/main arm64 libarchive13t64 arm64 3.7.4-4+b1 [323 kB] Get: 35 http://deb.debian.org/debian forky/main arm64 libnghttp3-9 arm64 1.12.0-1 [63.6 kB] Get: 36 http://deb.debian.org/debian forky/main arm64 libngtcp2-16 arm64 1.16.0-1 [123 kB] Get: 37 http://deb.debian.org/debian forky/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 38 http://deb.debian.org/debian forky/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 39 http://deb.debian.org/debian forky/main arm64 libcom-err2 arm64 1.47.2-3+b3 [24.9 kB] Get: 40 http://deb.debian.org/debian forky/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 41 http://deb.debian.org/debian forky/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 42 http://deb.debian.org/debian forky/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 43 http://deb.debian.org/debian forky/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 44 http://deb.debian.org/debian forky/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 45 http://deb.debian.org/debian forky/main arm64 libidn2-0 arm64 2.3.8-4 [108 kB] Get: 46 http://deb.debian.org/debian forky/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-10 [19.8 kB] Get: 47 http://deb.debian.org/debian forky/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-10 [55.0 kB] Get: 48 http://deb.debian.org/debian forky/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Get: 49 http://deb.debian.org/debian forky/main arm64 libnghttp2-14 arm64 1.64.0-1.1+b1 [71.7 kB] Get: 50 http://deb.debian.org/debian forky/main arm64 libngtcp2-crypto-ossl0 arm64 1.16.0-1 [25.7 kB] Get: 51 http://deb.debian.org/debian forky/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 52 http://deb.debian.org/debian forky/main arm64 libp11-kit0 arm64 0.25.9-2 [420 kB] Get: 53 http://deb.debian.org/debian forky/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 54 http://deb.debian.org/debian forky/main arm64 libgnutls30t64 arm64 3.8.10-2 [1395 kB] Get: 55 http://deb.debian.org/debian forky/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-3 [56.3 kB] Get: 56 http://deb.debian.org/debian forky/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 57 http://deb.debian.org/debian forky/main arm64 libcurl4t64 arm64 8.16.0-4 [368 kB] Get: 58 http://deb.debian.org/debian forky/main arm64 libjsoncpp26 arm64 1.9.6-4 [73.2 kB] Get: 59 http://deb.debian.org/debian forky/main arm64 librhash1 arm64 1.4.6-1 [131 kB] Get: 60 http://deb.debian.org/debian forky/main arm64 libuv1t64 arm64 1.51.0-2 [150 kB] Get: 61 http://deb.debian.org/debian forky/main arm64 cmake arm64 4.1.1+really3.31.6-2 [10.1 MB] Get: 62 http://deb.debian.org/debian forky/main arm64 comerr-dev arm64 2.1-1.47.2-3+b3 [56.9 kB] Get: 63 http://deb.debian.org/debian forky/main arm64 d-shlibs all 0.109 [11.1 kB] Get: 64 http://deb.debian.org/debian forky/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get: 65 http://deb.debian.org/debian forky/main arm64 libtool all 2.5.4-5 [540 kB] Get: 66 http://deb.debian.org/debian forky/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 67 http://deb.debian.org/debian forky/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 68 http://deb.debian.org/debian forky/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 69 http://deb.debian.org/debian forky/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 70 http://deb.debian.org/debian forky/main arm64 libelf1t64 arm64 0.193-3 [189 kB] Get: 71 http://deb.debian.org/debian forky/main arm64 dwz arm64 0.16-2 [100 kB] Get: 72 http://deb.debian.org/debian forky/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 73 http://deb.debian.org/debian forky/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 74 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 75 http://deb.debian.org/debian forky/main arm64 debhelper all 13.28 [941 kB] Get: 76 http://deb.debian.org/debian forky/main arm64 dh-exec arm64 0.30+b1 [25.8 kB] Get: 77 http://deb.debian.org/debian forky/main arm64 gcc-14-base arm64 14.3.0-8 [52.1 kB] Get: 78 http://deb.debian.org/debian forky/main arm64 googletest all 1.17.0-1 [522 kB] Get: 79 http://deb.debian.org/debian forky/main arm64 libicu76 arm64 76.1-4 [9524 kB] Get: 80 http://deb.debian.org/debian forky/main arm64 icu-devtools arm64 76.1-4 [200 kB] Get: 81 http://deb.debian.org/debian forky/main arm64 libgssrpc4t64 arm64 1.21.3-5 [57.2 kB] Get: 82 http://deb.debian.org/debian forky/main arm64 libkadm5clnt-mit12 arm64 1.21.3-5 [41.1 kB] Get: 83 http://deb.debian.org/debian forky/main arm64 libkdb5-10t64 arm64 1.21.3-5 [41.3 kB] Get: 84 http://deb.debian.org/debian forky/main arm64 libkadm5srv-mit12 arm64 1.21.3-5 [53.0 kB] Get: 85 http://deb.debian.org/debian forky/main arm64 krb5-multidev arm64 1.21.3-5 [126 kB] Get: 86 http://deb.debian.org/debian forky/main arm64 libgcc-14-dev arm64 14.3.0-8 [2364 kB] Get: 87 http://deb.debian.org/debian forky/main arm64 libstdc++-14-dev arm64 14.3.0-8 [2567 kB] Get: 88 http://deb.debian.org/debian forky/main arm64 libboost1.83-dev arm64 1.83.0-5 [10.6 MB] Get: 89 http://deb.debian.org/debian forky/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 90 http://deb.debian.org/debian forky/main arm64 libboost-regex1.83.0 arm64 1.83.0-5 [314 kB] Get: 91 http://deb.debian.org/debian forky/main arm64 libicu-dev arm64 76.1-4 [10.6 MB] Get: 92 http://deb.debian.org/debian forky/main arm64 libboost-regex1.83-dev arm64 1.83.0-5 [335 kB] Get: 93 http://deb.debian.org/debian forky/main arm64 libboost-iostreams1.83-dev arm64 1.83.0-5 [261 kB] Get: 94 http://deb.debian.org/debian forky/main arm64 libboost-iostreams-dev arm64 1.83.0.2+b2 [3568 B] Get: 95 http://deb.debian.org/debian forky/main arm64 libbrotli-dev arm64 1.1.0-2+b7 [308 kB] Get: 96 http://deb.debian.org/debian forky/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 97 http://deb.debian.org/debian forky/main arm64 libngtcp2-crypto-gnutls8 arm64 1.16.0-1 [23.8 kB] Get: 98 http://deb.debian.org/debian forky/main arm64 libcurl3t64-gnutls arm64 8.16.0-4 [362 kB] Get: 99 http://deb.debian.org/debian forky/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 100 http://deb.debian.org/debian forky/main arm64 libunbound8 arm64 1.24.0-2 [559 kB] Get: 101 http://deb.debian.org/debian forky/main arm64 libgnutls-dane0t64 arm64 3.8.10-2 [456 kB] Get: 102 http://deb.debian.org/debian forky/main arm64 libgnutls-openssl27t64 arm64 3.8.10-2 [456 kB] Get: 103 http://deb.debian.org/debian forky/main arm64 libidn2-dev arm64 2.3.8-4 [102 kB] Get: 104 http://deb.debian.org/debian forky/main arm64 libp11-kit-dev arm64 0.25.9-2 [220 kB] Get: 105 http://deb.debian.org/debian forky/main arm64 libtasn1-6-dev arm64 4.20.0-2 [96.7 kB] Get: 106 http://deb.debian.org/debian forky/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-5 [329 kB] Get: 107 http://deb.debian.org/debian forky/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-5 [621 kB] Get: 108 http://deb.debian.org/debian forky/main arm64 nettle-dev arm64 3.10.2-1 [1319 kB] Get: 109 http://deb.debian.org/debian forky/main arm64 libgnutls28-dev arm64 3.8.10-2 [1438 kB] Get: 110 http://deb.debian.org/debian forky/main arm64 libkrb5-dev arm64 1.21.3-5 [16.1 kB] Get: 111 http://deb.debian.org/debian forky/main arm64 libldap-dev arm64 2.6.10+dfsg-1 [305 kB] Get: 112 http://deb.debian.org/debian forky/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 113 http://deb.debian.org/debian forky/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 114 http://deb.debian.org/debian forky/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 115 http://deb.debian.org/debian forky/main arm64 libnghttp2-dev arm64 1.64.0-1.1+b1 [112 kB] Get: 116 http://deb.debian.org/debian forky/main arm64 libnghttp3-dev arm64 1.12.0-1 [91.6 kB] Get: 117 http://deb.debian.org/debian forky/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.16.0-1 [24.6 kB] Get: 118 http://deb.debian.org/debian forky/main arm64 libngtcp2-dev arm64 1.16.0-1 [183 kB] Get: 119 http://deb.debian.org/debian forky/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 120 http://deb.debian.org/debian forky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 121 http://deb.debian.org/debian forky/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-3 [173 kB] Get: 122 http://deb.debian.org/debian forky/main arm64 libssl-dev arm64 3.5.4-1 [3377 kB] Get: 123 http://deb.debian.org/debian forky/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 124 http://deb.debian.org/debian forky/main arm64 libzstd-dev arm64 1.5.7+dfsg-2 [330 kB] Get: 125 http://deb.debian.org/debian forky/main arm64 libcurl4-gnutls-dev arm64 8.16.0-4 [498 kB] Get: 126 http://deb.debian.org/debian forky/main arm64 libdeflate0 arm64 1.23-2 [42.4 kB] Get: 127 http://deb.debian.org/debian forky/main arm64 libdeflate-dev arm64 1.23-2 [51.3 kB] Get: 128 http://deb.debian.org/debian forky/main arm64 libgtest-dev arm64 1.17.0-1 [247 kB] Get: 129 http://deb.debian.org/debian forky/main arm64 libhtscodecs2 arm64 1.6.1-2 [74.7 kB] Get: 130 http://deb.debian.org/debian forky/main arm64 libhts3t64 arm64 1.22.1+ds2-1 [434 kB] Get: 131 http://deb.debian.org/debian forky/main arm64 liblzma-dev arm64 5.8.1-2 [344 kB] Get: 132 http://deb.debian.org/debian forky/main arm64 libhts-dev arm64 1.22.1+ds2-1 [1684 kB] Get: 133 http://deb.debian.org/debian forky/main arm64 libncurses6 arm64 6.5+20250216-2 [96.1 kB] Get: 134 http://deb.debian.org/debian forky/main arm64 libpbcopper2.3.0 arm64 2.3.0+dfsg-4 [623 kB] Get: 135 http://deb.debian.org/debian forky/main arm64 libpbcopper-dev arm64 2.3.0+dfsg-4 [984 kB] Get: 136 http://deb.debian.org/debian forky/main arm64 ninja-build arm64 1.12.1-1+b1 [130 kB] Get: 137 http://deb.debian.org/debian forky/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 138 http://deb.debian.org/debian forky/main arm64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 139 http://deb.debian.org/debian forky/main arm64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 140 http://deb.debian.org/debian forky/main arm64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 141 http://deb.debian.org/debian forky/main arm64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 142 http://deb.debian.org/debian forky/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 143 http://deb.debian.org/debian forky/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 144 http://deb.debian.org/debian forky/main arm64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 145 http://deb.debian.org/debian forky/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 146 http://deb.debian.org/debian forky/main arm64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 147 http://deb.debian.org/debian forky/main arm64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 148 http://deb.debian.org/debian forky/main arm64 meson all 1.9.1-1 [665 kB] Get: 149 http://deb.debian.org/debian forky/main arm64 python3-cram all 0.7-6 [17.5 kB] Get: 150 http://deb.debian.org/debian forky/main arm64 samtools arm64 1.22.1-1 [666 kB] Fetched 93.5 MB in 1s (173 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (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 ... 20000 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.3-1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.7-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.7-1_arm64.deb ... Unpacking python3.13-minimal (3.13.7-1) ... Setting up libpython3.13-minimal:arm64 (3.13.7-1) ... Setting up libexpat1:arm64 (2.7.3-1) ... Setting up python3.13-minimal (3.13.7-1) ... Selecting previously unselected package python3-minimal. (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 ... 20334 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_arm64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-5_all.deb ... Unpacking tzdata (2025b-5) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../4-libffi8_3.5.2-2_arm64.deb ... Unpacking libffi8:arm64 (3.5.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../6-libreadline8t64_8.3-3_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_arm64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../9-libpython3-stdlib_3.13.7-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... Selecting previously unselected package python3. (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 ... 21349 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.7-1_arm64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-9_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-9) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-9_arm64.deb ... Unpacking procps (2:4.0.4-9) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../005-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.23.1-2+b1_arm64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../008-libuchardet0_0.0.8-2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.41.2-1_arm64.deb ... Unpacking bsdextrautils (2.41.2-1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../011-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../013-m4_1.4.20-2_arm64.deb ... Unpacking m4 (1.4.20-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../014-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../015-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../016-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../017-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package cmake-data. Preparing to unpack .../018-cmake-data_4.1.1+really3.31.6-2_all.deb ... Unpacking cmake-data (4.1.1+really3.31.6-2) ... Selecting previously unselected package libxml2-16:arm64. Preparing to unpack .../019-libxml2-16_2.14.6+dfsg-0.1_arm64.deb ... Unpacking libxml2-16:arm64 (2.14.6+dfsg-0.1) ... Selecting previously unselected package libarchive13t64:arm64. Preparing to unpack .../020-libarchive13t64_3.7.4-4+b1_arm64.deb ... Unpacking libarchive13t64:arm64 (3.7.4-4+b1) ... Selecting previously unselected package libnghttp3-9:arm64. Preparing to unpack .../021-libnghttp3-9_1.12.0-1_arm64.deb ... Unpacking libnghttp3-9:arm64 (1.12.0-1) ... Selecting previously unselected package libngtcp2-16:arm64. Preparing to unpack .../022-libngtcp2-16_1.16.0-1_arm64.deb ... Unpacking libngtcp2-16:arm64 (1.16.0-1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../023-libbrotli1_1.1.0-2+b7_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b7) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../024-libkrb5support0_1.21.3-5_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-5) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../025-libcom-err2_1.47.2-3+b3_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.2-3+b3) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../026-libk5crypto3_1.21.3-5_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../027-libkeyutils1_1.6.3-6_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../028-libkrb5-3_1.21.3-5_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../029-libgssapi-krb5-2_1.21.3-5_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-5) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../030-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libidn2-0:arm64. Preparing to unpack .../031-libidn2-0_2.3.8-4_arm64.deb ... Unpacking libidn2-0:arm64 (2.3.8-4) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../032-libsasl2-modules-db_2.1.28+dfsg1-10_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-10) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../033-libsasl2-2_2.1.28+dfsg1-10_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-10) ... Selecting previously unselected package libldap2:arm64. Preparing to unpack .../034-libldap2_2.6.10+dfsg-1_arm64.deb ... Unpacking libldap2:arm64 (2.6.10+dfsg-1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../035-libnghttp2-14_1.64.0-1.1+b1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.64.0-1.1+b1) ... Selecting previously unselected package libngtcp2-crypto-ossl0:arm64. Preparing to unpack .../036-libngtcp2-crypto-ossl0_1.16.0-1_arm64.deb ... Unpacking libngtcp2-crypto-ossl0:arm64 (1.16.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../037-libpsl5t64_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package libp11-kit0:arm64. Preparing to unpack .../038-libp11-kit0_0.25.9-2_arm64.deb ... Unpacking libp11-kit0:arm64 (0.25.9-2) ... Selecting previously unselected package libtasn1-6:arm64. Preparing to unpack .../039-libtasn1-6_4.20.0-2_arm64.deb ... Unpacking libtasn1-6:arm64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:arm64. Preparing to unpack .../040-libgnutls30t64_3.8.10-2_arm64.deb ... Unpacking libgnutls30t64:arm64 (3.8.10-2) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../041-librtmp1_2.4+20151223.gitfa8646d.1-3_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-3) ... Selecting previously unselected package libssh2-1t64:arm64. 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Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Nov 14 13:12:32 UTC 2026. Universal Time is now: Sat Nov 14 13:12:32 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libunbound8:arm64 (1.24.0-2) ... Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-5) ... Setting up libjsoncpp26:arm64 (1.9.6-4) ... Setting up libncurses6:arm64 (6.5+20250216-2) ... Setting up libproc2-0:arm64 (2:4.0.4-9) ... Setting up comerr-dev:arm64 (2.1-1.47.2-3+b3) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up libssl-dev:arm64 (3.5.4-1) ... Setting up autopoint (0.23.1-2) ... Setting up d-shlibs (0.109) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:arm64 (1.21.3-5) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-10) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:arm64 (1.12.0-1) ... 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Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.37.1.2-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/pbbam-2.4.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pbbam_2.4.0+dfsg-2_source.changes dpkg-buildpackage: info: source package pbbam dpkg-buildpackage: info: source version 2.4.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=meson debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/pbbam-2.4.0+dfsg' dh_auto_clean find -name "*.deb.t" -delete rm -f -r /build/reproducible-path/pbbam-2.4.0+dfsg/gendata make[1]: Leaving directory '/build/reproducible-path/pbbam-2.4.0+dfsg' dh_autoreconf_clean -O--buildsystem=meson dh_clean -O--buildsystem=meson debian/rules binary dh binary --buildsystem=meson dh_update_autotools_config -O--buildsystem=meson dh_autoreconf -O--buildsystem=meson dh_auto_configure -O--buildsystem=meson cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 meson setup .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/aarch64-linux-gnu -Dpython.bytecompile=-1 The Meson build system Version: 1.9.1 Source dir: /build/reproducible-path/pbbam-2.4.0+dfsg Build dir: /build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu Build type: native build Project name: PacBioBAM Project version: 2.4.0 C compiler for the host machine: cc (gcc 15.2.0 "cc (Debian 15.2.0-4) 15.2.0") C linker for the host machine: cc ld.bfd 2.45 C++ compiler for the host machine: c++ (gcc 15.2.0 "c++ (Debian 15.2.0-4) 15.2.0") C++ linker for the host machine: c++ ld.bfd 2.45 Host machine cpu family: aarch64 Host machine cpu: aarch64 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: YES (/usr/bin/pkg-config) 1.8.1 Run-time dependency Boost found: YES 1.83.0 (/usr) Run-time dependency zlib found: YES 1.3.1 Run-time dependency htslib found: YES 1.22.1 Run-time dependency pbcopper found: YES 2.3.0 Configuring PbbamVersion.cpp using configuration Configuring LibraryVersion.h using configuration Program tools/check-formatting found: YES (/build/reproducible-path/pbbam-2.4.0+dfsg/tools/check-formatting) Program python3 found: YES (/usr/bin/python3) Program cram3 found: YES (/usr/bin/cram3) Run-time dependency GTest found: YES 1.17.0 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 2.4.0 User defined options buildtype : plain libdir : lib/aarch64-linux-gnu localstatedir : /var prefix : /usr python.bytecompile: -1 sysconfdir : /etc wrap_mode : nodownload Found ninja-1.12.1 at /usr/bin/ninja dh_auto_build -O--buildsystem=meson cd obj-aarch64-linux-gnu && LC_ALL=C.UTF-8 ninja -j12 -v [1/226] /usr/bin/meson --internal vcstagger ../src/LibraryGitHash.h.in src/LibraryGitHash.h 2.4.0 /build/reproducible-path/pbbam-2.4.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' git describe --always '--dirty=*' [2/226] /usr/bin/meson --internal vcstagger ../src/PbbamGitHash.cpp.in src/PbbamGitHash.cpp 2.4.0 /build/reproducible-path/pbbam-2.4.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' git describe --always '--dirty=*' [3/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/meson-generated_.._PbbamGitHash.cpp.o -MF src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamGitHash.cpp.o.d -o src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamGitHash.cpp.o -c src/PbbamGitHash.cpp [4/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/BaiIndexCache.cpp.o -MF src/libpbbam.so.2.4.0.p/BaiIndexCache.cpp.o.d -o src/libpbbam.so.2.4.0.p/BaiIndexCache.cpp.o -c ../src/BaiIndexCache.cpp [5/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_AlignmentPrinter.cpp.o -MF tests/pbbam_test.p/src_test_AlignmentPrinter.cpp.o.d -o tests/pbbam_test.p/src_test_AlignmentPrinter.cpp.o -c ../tests/src/test_AlignmentPrinter.cpp [6/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/AlignmentPrinter.cpp.o -MF src/libpbbam.so.2.4.0.p/AlignmentPrinter.cpp.o.d -o src/libpbbam.so.2.4.0.p/AlignmentPrinter.cpp.o -c ../src/AlignmentPrinter.cpp [7/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_BamReader.cpp.o -MF tests/pbbam_test.p/src_test_BamReader.cpp.o.d -o tests/pbbam_test.p/src_test_BamReader.cpp.o -c ../tests/src/test_BamReader.cpp [8/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_BamFile.cpp.o -MF tests/pbbam_test.p/src_test_BamFile.cpp.o.d -o tests/pbbam_test.p/src_test_BamFile.cpp.o -c ../tests/src/test_BamFile.cpp [9/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_BamRecordImplTags.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o -c ../tests/src/test_BamRecordImplTags.cpp [10/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [11/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_BamRecordImplCore.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordImplCore.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordImplCore.cpp.o -c ../tests/src/test_BamRecordImplCore.cpp ../tests/src/test_BamRecordImplCore.cpp: In member function ‘virtual void BAM_BamRecordImplCore_can_be_move_constructed_Test::TestBody()’: ../tests/src/test_BamRecordImplCore.cpp:425:73: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 425 | BamRecordImpl bam(std::move(BamRecordImplCoreTests::CreateBamImpl())); | ^ ../tests/src/test_BamRecordImplCore.cpp:425:73: note: remove ‘std::move’ call [12/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/BamFile.cpp.o -MF 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-ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/IFastaWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/IFastaWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/IFastaWriter.cpp.o -c ../src/IFastaWriter.cpp [56/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/IndexedFastqBgzfReader.cpp.o -MF src/libpbbam.so.2.4.0.p/IndexedFastqBgzfReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/IndexedFastqBgzfReader.cpp.o -c ../src/IndexedFastqBgzfReader.cpp [57/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/IndexedFastqReaderImpl.cpp.o -MF src/libpbbam.so.2.4.0.p/IndexedFastqReaderImpl.cpp.o.d -o src/libpbbam.so.2.4.0.p/IndexedFastqReaderImpl.cpp.o -c ../src/IndexedFastqReaderImpl.cpp [58/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/IndexedFastqTextReader.cpp.o -MF src/libpbbam.so.2.4.0.p/IndexedFastqTextReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/IndexedFastqTextReader.cpp.o -c ../src/IndexedFastqTextReader.cpp [59/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/MD5.cpp.o -MF src/libpbbam.so.2.4.0.p/MD5.cpp.o.d -o src/libpbbam.so.2.4.0.p/MD5.cpp.o -c ../src/MD5.cpp [60/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/LibraryInfo.cpp.o -MF src/libpbbam.so.2.4.0.p/LibraryInfo.cpp.o.d -o src/libpbbam.so.2.4.0.p/LibraryInfo.cpp.o -c ../src/LibraryInfo.cpp [61/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/DataSetTypes.cpp.o -MF src/libpbbam.so.2.4.0.p/DataSetTypes.cpp.o.d -o src/libpbbam.so.2.4.0.p/DataSetTypes.cpp.o -c ../src/DataSetTypes.cpp In file included from /usr/include/c++/15/map:64, from ../include/pbbam/ProgramInfo.h:6, from ../include/pbbam/BamHeader.h:6, from ../include/pbbam/BamFile.h:6, from ../include/pbbam/DataSetTypes.h:6, from ../src/DataSetTypes.cpp:3: In constructor ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_Reuse_or_alloc_node::_Reuse_or_alloc_node(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::operator=(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/15/bits/stl_tree.h:2449:25, inlined from ‘std::map<_Key, _Tp, _Compare, _Alloc>& std::map<_Key, _Tp, _Compare, _Alloc>::operator=(const std::map<_Key, _Tp, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Tp = PacBio::BAM::NamespaceInfo; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/15/bits/stl_map.h:354:7, inlined from ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/15/bits/stl_tree.h:1047:11: warning: array subscript 25 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 1047 | : _M_root(__t._M_root()), _M_nodes(__t._M_rightmost()), _M_t(__t) | ^~~~~~~~~~~~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 200 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In constructor ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_Reuse_or_alloc_node::_Reuse_or_alloc_node(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::operator=(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/15/bits/stl_tree.h:2449:25, inlined from ‘std::map<_Key, _Tp, _Compare, _Alloc>& std::map<_Key, _Tp, _Compare, _Alloc>::operator=(const std::map<_Key, _Tp, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Tp = PacBio::BAM::NamespaceInfo; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/15/bits/stl_map.h:354:7, inlined from ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/15/bits/stl_tree.h:1047:35: warning: array subscript 27 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 1047 | : _M_root(__t._M_root()), _M_nodes(__t._M_rightmost()), _M_t(__t) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 216 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘void std::_Rb_tree_header::_M_reset()’, inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::operator=(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/15/bits/stl_tree.h:2450:20, inlined from ‘std::map<_Key, _Tp, _Compare, _Alloc>& std::map<_Key, _Tp, _Compare, _Alloc>::operator=(const std::map<_Key, _Tp, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Tp = PacBio::BAM::NamespaceInfo; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/15/bits/stl_map.h:354:7, inlined from ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/15/bits/stl_tree.h:206:27: warning: array subscript 4 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 206 | _M_header._M_parent = 0; | ~~~~~~~~~~~~~~~~~~~~^~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 192 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘void std::_Rb_tree_header::_M_reset()’, inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::operator=(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/15/bits/stl_tree.h:2450:20, inlined from ‘std::map<_Key, _Tp, _Compare, _Alloc>& std::map<_Key, _Tp, _Compare, _Alloc>::operator=(const std::map<_Key, _Tp, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Tp = PacBio::BAM::NamespaceInfo; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/15/bits/stl_map.h:354:7, inlined from ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/15/bits/stl_tree.h:207:27: warning: array subscript 4 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 207 | _M_header._M_left = &_M_header; | ^~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 192 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘void std::_Rb_tree_header::_M_reset()’, inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::operator=(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/15/bits/stl_tree.h:2450:20, inlined from ‘std::map<_Key, _Tp, _Compare, _Alloc>& std::map<_Key, _Tp, _Compare, _Alloc>::operator=(const std::map<_Key, _Tp, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Tp = PacBio::BAM::NamespaceInfo; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/15/bits/stl_map.h:354:7, inlined from ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/15/bits/stl_tree.h:207:25: warning: array subscript 4 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 207 | _M_header._M_left = &_M_header; | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 192 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘void std::_Rb_tree_header::_M_reset()’, inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::operator=(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/15/bits/stl_tree.h:2450:20, inlined from ‘std::map<_Key, _Tp, _Compare, _Alloc>& std::map<_Key, _Tp, _Compare, _Alloc>::operator=(const std::map<_Key, _Tp, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Tp = PacBio::BAM::NamespaceInfo; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/15/bits/stl_map.h:354:7, inlined from ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/15/bits/stl_tree.h:208:26: warning: array subscript 4 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 208 | _M_header._M_right = &_M_header; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 192 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘void std::_Rb_tree_header::_M_reset()’, inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::operator=(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/15/bits/stl_tree.h:2450:20, inlined from ‘std::map<_Key, _Tp, _Compare, _Alloc>& std::map<_Key, _Tp, _Compare, _Alloc>::operator=(const std::map<_Key, _Tp, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Tp = PacBio::BAM::NamespaceInfo; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/15/bits/stl_map.h:354:7, inlined from ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/15/bits/stl_tree.h:209:21: warning: array subscript 4 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 209 | _M_node_count = 0; | ~~~~~~~~~~~~~~^~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 192 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_Base_ptr std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_copy(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&, _NodeGen&) [with bool _MoveValues = false; _NodeGen = std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Reuse_or_alloc_node; _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::operator=(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/15/bits/stl_tree.h:2453:38, inlined from ‘std::map<_Key, _Tp, _Compare, _Alloc>& std::map<_Key, _Tp, _Compare, _Alloc>::operator=(const std::map<_Key, _Tp, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Tp = PacBio::BAM::NamespaceInfo; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/15/bits/stl_map.h:354:7, inlined from ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/15/bits/stl_tree.h:1524:25: warning: array subscript 26 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 1524 | _M_leftmost() = _Node_base::_S_minimum(__root); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 208 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_Base_ptr std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_copy(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&, _NodeGen&) [with bool _MoveValues = false; _NodeGen = std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Reuse_or_alloc_node; _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::operator=(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/15/bits/stl_tree.h:2453:38, inlined from ‘std::map<_Key, _Tp, _Compare, _Alloc>& std::map<_Key, _Tp, _Compare, _Alloc>::operator=(const std::map<_Key, _Tp, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Tp = PacBio::BAM::NamespaceInfo; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/15/bits/stl_map.h:354:7, inlined from ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/15/bits/stl_tree.h:1525:26: warning: array subscript 27 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 1525 | _M_rightmost() = _Node_base::_S_maximum(__root); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 216 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_Base_ptr std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_copy(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&, _NodeGen&) [with bool _MoveValues = false; _NodeGen = std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Reuse_or_alloc_node; _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::operator=(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/15/bits/stl_tree.h:2453:38, inlined from ‘std::map<_Key, _Tp, _Compare, _Alloc>& std::map<_Key, _Tp, _Compare, _Alloc>::operator=(const std::map<_Key, _Tp, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Tp = PacBio::BAM::NamespaceInfo; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/15/bits/stl_map.h:354:7, inlined from ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/15/bits/stl_tree.h:1526:33: warning: array subscript 3 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 1526 | _M_impl._M_node_count = __x._M_impl._M_node_count; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 184 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::operator=(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::map<_Key, _Tp, _Compare, _Alloc>& std::map<_Key, _Tp, _Compare, _Alloc>::operator=(const std::map<_Key, _Tp, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Tp = PacBio::BAM::NamespaceInfo; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/15/bits/stl_map.h:354:7, inlined from ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/15/bits/stl_tree.h:2453:23: warning: array subscript 25 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 2453 | _M_root() = _M_copy<__as_lvalue>(__x, __roan); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 200 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In file included from ../include/pbbam/internal/DataSetElement.h:6, from ../include/pbbam/internal/DataSetBaseTypes.h:6, from ../include/pbbam/CollectionMetadata.h:6, from ../include/pbbam/DataSetTypes.h:7: In member function ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: ../include/pbbam/DataSetXsd.h:65:20: warning: array subscript 3 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 65 | class PBBAM_EXPORT NamespaceRegistry | ^~~~~~~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 184 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ [62/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/KSeqReader.cpp.o -MF src/libpbbam.so.2.4.0.p/KSeqReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/KSeqReader.cpp.o -c ../src/KSeqReader.cpp [63/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/GenomicIntervalQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/GenomicIntervalQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/GenomicIntervalQuery.cpp.o -c ../src/GenomicIntervalQuery.cpp [64/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/IndexedFastaReader.cpp.o -MF src/libpbbam.so.2.4.0.p/IndexedFastaReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/IndexedFastaReader.cpp.o -c ../src/IndexedFastaReader.cpp [65/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/IRecordWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/IRecordWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/IRecordWriter.cpp.o -c ../src/IRecordWriter.cpp [66/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/IndexedFastqReader.cpp.o -MF src/libpbbam.so.2.4.0.p/IndexedFastqReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/IndexedFastqReader.cpp.o -c ../src/IndexedFastqReader.cpp [67/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../tests/src/test_BamRecord.cpp: In member function ‘virtual void BAM_BamRecord_can_be_constructed_from_bamrecordimpl_Test::TestBody()’: ../tests/src/test_BamRecord.cpp:771:29: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 771 | BamRecord bam3(std::move(BamRecordTests::CreateBamImpl())); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/src/test_BamRecord.cpp:771:29: note: remove ‘std::move’ call ../tests/src/test_BamRecord.cpp:797:21: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 797 | bam4 = std::move(BamRecordTests::CreateBamImpl()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/src/test_BamRecord.cpp:797:21: note: remove ‘std::move’ call [68/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_BamRecordImplVariableData.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordImplVariableData.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordImplVariableData.cpp.o -c ../tests/src/test_BamRecordImplVariableData.cpp [69/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/IndexedBamWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/IndexedBamWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/IndexedBamWriter.cpp.o -c ../src/IndexedBamWriter.cpp [70/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/MemoryUtils.cpp.o -MF src/libpbbam.so.2.4.0.p/MemoryUtils.cpp.o.d -o src/libpbbam.so.2.4.0.p/MemoryUtils.cpp.o -c ../src/MemoryUtils.cpp [71/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/PbiBuilder.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiBuilder.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiBuilder.cpp.o -c ../src/PbiBuilder.cpp [72/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/PbiFile.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiFile.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiFile.cpp.o -c ../src/PbiFile.cpp [73/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/RunMetadata.cpp.o -MF src/libpbbam.so.2.4.0.p/RunMetadata.cpp.o.d -o src/libpbbam.so.2.4.0.p/RunMetadata.cpp.o -c ../src/RunMetadata.cpp [74/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/RecordType.cpp.o -MF src/libpbbam.so.2.4.0.p/RecordType.cpp.o.d -o src/libpbbam.so.2.4.0.p/RecordType.cpp.o -c ../src/RecordType.cpp [75/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/ProgramInfo.cpp.o -MF src/libpbbam.so.2.4.0.p/ProgramInfo.cpp.o.d -o src/libpbbam.so.2.4.0.p/ProgramInfo.cpp.o -c ../src/ProgramInfo.cpp [76/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond 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-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.2.4.0.p/PbiIndexIO.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiIndexIO.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiIndexIO.cpp.o -c ../src/PbiIndexIO.cpp [85/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/SamReader.cpp.o -MF src/libpbbam.so.2.4.0.p/SamReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/SamReader.cpp.o -c ../src/SamReader.cpp [86/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/ValidationErrors.cpp.o -MF src/libpbbam.so.2.4.0.p/ValidationErrors.cpp.o.d -o src/libpbbam.so.2.4.0.p/ValidationErrors.cpp.o -c ../src/ValidationErrors.cpp [87/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/SamTagCodec.cpp.o -MF src/libpbbam.so.2.4.0.p/SamTagCodec.cpp.o.d -o src/libpbbam.so.2.4.0.p/SamTagCodec.cpp.o -c ../src/SamTagCodec.cpp ../src/SamTagCodec.cpp: In static member function ‘static PacBio::BAM::TagCollection PacBio::BAM::SamTagCodec::Decode(const std::string&)’: ../src/SamTagCodec.cpp:79:63: warning: ignoring return value of ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::const_reference std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator[](size_type) const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; const_reference = const char&; size_type = long unsigned int]’, declared with attribute ‘nodiscard’ [-Wunused-result] 79 | tags[name] = Tag{static_cast(remainder[0], TagModifier::ASCII_CHAR)}; | ^ In file included from /usr/include/c++/15/string:56, from ../include/pbbam/Tag.h:7, from ../include/pbbam/TagCollection.h:6, from ../include/pbbam/SamTagCodec.h:6, from ../src/SamTagCodec.cpp:3: /usr/include/c++/15/bits/basic_string.h:1347:7: note: declared here 1347 | operator[] (size_type __pos) const _GLIBCXX_NOEXCEPT | ^~~~~~~~ [88/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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-fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/Tag.cpp.o -MF src/libpbbam.so.2.4.0.p/Tag.cpp.o.d -o src/libpbbam.so.2.4.0.p/Tag.cpp.o -c ../src/Tag.cpp [100/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/ZmwChunkedFastxBgzfReader.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastxBgzfReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxBgzfReader.cpp.o -c ../src/ZmwChunkedFastxBgzfReader.cpp [101/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/ZmwChunkedFastxReaderImpl.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastxReaderImpl.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxReaderImpl.cpp.o -c ../src/ZmwChunkedFastxReaderImpl.cpp [102/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/XmlWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/XmlWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/XmlWriter.cpp.o -c ../src/XmlWriter.cpp [103/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/VirtualZmwBamRecord.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualZmwBamRecord.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualZmwBamRecord.cpp.o -c ../src/VirtualZmwBamRecord.cpp [104/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/ZmwChunkedFastxTextReader.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastxTextReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxTextReader.cpp.o -c ../src/ZmwChunkedFastxTextReader.cpp [105/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/ZmwTypeMap.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwTypeMap.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwTypeMap.cpp.o -c ../src/ZmwTypeMap.cpp [106/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/ZmwChunkedFastqReader.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastqReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastqReader.cpp.o -c ../src/ZmwChunkedFastqReader.cpp ../src/ZmwChunkedFastqReader.cpp: In constructor ‘PacBio::BAM::ZmwChunkedFastqReader::ZmwChunkedFastqReaderPrivate::ZmwChunkedFastqReaderPrivate(const std::string&, size_t)’: ../src/ZmwChunkedFastqReader.cpp:78:48: warning: redundant move in initialization [-Wredundant-move] 78 | : reader_{MakeFastqReaderImpl(std::move(fn), numChunks)} | ~~~~~~~~~^~~~ ../src/ZmwChunkedFastqReader.cpp:78:48: note: remove ‘std::move’ call [107/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/VirtualZmwCompositeReader.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualZmwCompositeReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualZmwCompositeReader.cpp.o -c ../src/VirtualZmwCompositeReader.cpp [108/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/Validator.cpp.o -MF src/libpbbam.so.2.4.0.p/Validator.cpp.o.d -o src/libpbbam.so.2.4.0.p/Validator.cpp.o -c ../src/Validator.cpp [109/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/ZmwChunkedFastaReader.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastaReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastaReader.cpp.o -c ../src/ZmwChunkedFastaReader.cpp ../src/ZmwChunkedFastaReader.cpp: In constructor ‘PacBio::BAM::ZmwChunkedFastaReader::ZmwChunkedFastaReaderPrivate::ZmwChunkedFastaReaderPrivate(const std::string&, size_t)’: ../src/ZmwChunkedFastaReader.cpp:78:48: warning: redundant move in initialization [-Wredundant-move] 78 | : reader_{MakeFastaReaderImpl(std::move(fn), numChunks)} | ~~~~~~~~~^~~~ ../src/ZmwChunkedFastaReader.cpp:78:48: note: remove ‘std::move’ call [110/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/VirtualZmwReader.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualZmwReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualZmwReader.cpp.o -c ../src/VirtualZmwReader.cpp [111/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/vcf_VcfFile.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfFile.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfFile.cpp.o -c ../src/vcf/VcfFile.cpp [112/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/bed_BedWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/bed_BedWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/bed_BedWriter.cpp.o -c ../src/bed/BedWriter.cpp [113/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/XmlReader.cpp.o -MF src/libpbbam.so.2.4.0.p/XmlReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/XmlReader.cpp.o -c ../src/XmlReader.cpp [114/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/csv_CsvWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/csv_CsvWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/csv_CsvWriter.cpp.o -c ../src/csv/CsvWriter.cpp [115/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/vcf_VcfHeaderTypes.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfHeaderTypes.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfHeaderTypes.cpp.o -c ../src/vcf/VcfHeaderTypes.cpp [116/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/WhitelistedZmwReadStitcher.cpp.o -MF src/libpbbam.so.2.4.0.p/WhitelistedZmwReadStitcher.cpp.o.d -o src/libpbbam.so.2.4.0.p/WhitelistedZmwReadStitcher.cpp.o -c ../src/WhitelistedZmwReadStitcher.cpp [117/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_BamRecordClipping.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordClipping.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordClipping.cpp.o -c ../tests/src/test_BamRecordClipping.cpp [118/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/bed_BedReader.cpp.o -MF src/libpbbam.so.2.4.0.p/bed_BedReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/bed_BedReader.cpp.o -c ../src/bed/BedReader.cpp [119/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/vcf_VcfWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfWriter.cpp.o -c ../src/vcf/VcfWriter.cpp [120/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/meson-generated_.._PbbamVersion.cpp.o -MF src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamVersion.cpp.o.d -o src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamVersion.cpp.o -c src/PbbamVersion.cpp [121/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/vcf_VcfReader.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfReader.cpp.o -c ../src/vcf/VcfReader.cpp [122/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/ZmwReadStitcher.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwReadStitcher.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwReadStitcher.cpp.o -c ../src/ZmwReadStitcher.cpp [123/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/vcf_VcfHeader.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfHeader.cpp.o.d -o 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-ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/vcf_VcfQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfQuery.cpp.o -c ../src/vcf/VcfQuery.cpp [126/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/vcf_VcfVariant.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfVariant.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfVariant.cpp.o -c ../src/vcf/VcfVariant.cpp ../src/vcf/VcfVariant.cpp: In member function ‘PacBio::VCF::VcfVariant& PacBio::VCF::VcfVariant::RemoveInfoField(const std::string&)’: ../src/vcf/VcfVariant.cpp:250:35: warning: redundant move in initialization [-Wredundant-move] 250 | AddInfoField(std::move(field)); | ~~~~~~~~~^~~~~~~ ../src/vcf/VcfVariant.cpp:250:35: note: remove ‘std::move’ call [127/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/vcf_VcfFormat.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfFormat.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfFormat.cpp.o -c ../src/vcf/VcfFormat.cpp [128/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/ZmwGroupQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwGroupQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwGroupQuery.cpp.o -c ../src/ZmwGroupQuery.cpp [129/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/csv_CsvReader.cpp.o -MF src/libpbbam.so.2.4.0.p/csv_CsvReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/csv_CsvReader.cpp.o -c ../src/csv/CsvReader.cpp [130/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/vcf_VcfSort.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfSort.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfSort.cpp.o -c ../src/vcf/VcfSort.cpp [132/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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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-ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_BgzipFastqWriter.cpp.o -MF tests/pbbam_test.p/src_test_BgzipFastqWriter.cpp.o.d -o tests/pbbam_test.p/src_test_BgzipFastqWriter.cpp.o -c ../tests/src/test_BgzipFastqWriter.cpp [136/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_CollectionMetadata.cpp.o -MF tests/pbbam_test.p/src_test_CollectionMetadata.cpp.o.d -o tests/pbbam_test.p/src_test_CollectionMetadata.cpp.o -c ../tests/src/test_CollectionMetadata.cpp [137/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_BamWriter.cpp.o -MF tests/pbbam_test.p/src_test_BamWriter.cpp.o.d -o tests/pbbam_test.p/src_test_BamWriter.cpp.o -c ../tests/src/test_BamWriter.cpp [138/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.2.4.0.p/pugixml_pugixml.cpp.o -MF src/libpbbam.so.2.4.0.p/pugixml_pugixml.cpp.o.d -o src/libpbbam.so.2.4.0.p/pugixml_pugixml.cpp.o -c ../src/pugixml/pugixml.cpp [139/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_DataSetGenomicIntervals.cpp.o -MF tests/pbbam_test.p/src_test_DataSetGenomicIntervals.cpp.o.d -o tests/pbbam_test.p/src_test_DataSetGenomicIntervals.cpp.o -c ../tests/src/test_DataSetGenomicIntervals.cpp [140/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 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src/libpbbam.so.2.4.0.p/BamRecordImpl.cpp.o src/libpbbam.so.2.4.0.p/BamRecordTags.cpp.o src/libpbbam.so.2.4.0.p/BamRecordView.cpp.o src/libpbbam.so.2.4.0.p/BamTagCodec.cpp.o src/libpbbam.so.2.4.0.p/BamWriter.cpp.o src/libpbbam.so.2.4.0.p/BgzipFastaWriter.cpp.o src/libpbbam.so.2.4.0.p/BgzipFastqWriter.cpp.o src/libpbbam.so.2.4.0.p/BgzipWriter.cpp.o src/libpbbam.so.2.4.0.p/ChemistryTable.cpp.o src/libpbbam.so.2.4.0.p/CollectionMetadata.cpp.o src/libpbbam.so.2.4.0.p/Compare.cpp.o src/libpbbam.so.2.4.0.p/CompositeBamReader.cpp.o src/libpbbam.so.2.4.0.p/CompositeFastaReader.cpp.o src/libpbbam.so.2.4.0.p/Config.cpp.o src/libpbbam.so.2.4.0.p/DataSet.cpp.o src/libpbbam.so.2.4.0.p/DataSetBaseTypes.cpp.o src/libpbbam.so.2.4.0.p/DataSetElement.cpp.o src/libpbbam.so.2.4.0.p/DataSetIO.cpp.o src/libpbbam.so.2.4.0.p/DataSetTypes.cpp.o src/libpbbam.so.2.4.0.p/DataSetXsd.cpp.o src/libpbbam.so.2.4.0.p/EntireFileQuery.cpp.o src/libpbbam.so.2.4.0.p/ErrnoReason.cpp.o src/libpbbam.so.2.4.0.p/FaiIndex.cpp.o src/libpbbam.so.2.4.0.p/FaiZmwChunker.cpp.o src/libpbbam.so.2.4.0.p/FastaCache.cpp.o src/libpbbam.so.2.4.0.p/FastaReader.cpp.o src/libpbbam.so.2.4.0.p/FastaSequence.cpp.o src/libpbbam.so.2.4.0.p/FastaSequenceQuery.cpp.o src/libpbbam.so.2.4.0.p/FastaWriter.cpp.o src/libpbbam.so.2.4.0.p/FastqReader.cpp.o src/libpbbam.so.2.4.0.p/FastqSequence.cpp.o src/libpbbam.so.2.4.0.p/FastqWriter.cpp.o src/libpbbam.so.2.4.0.p/FileProducer.cpp.o src/libpbbam.so.2.4.0.p/FileUtils.cpp.o src/libpbbam.so.2.4.0.p/FofnReader.cpp.o src/libpbbam.so.2.4.0.p/FormatUtils.cpp.o src/libpbbam.so.2.4.0.p/GenomicIntervalQuery.cpp.o src/libpbbam.so.2.4.0.p/IFastaWriter.cpp.o src/libpbbam.so.2.4.0.p/IFastqWriter.cpp.o src/libpbbam.so.2.4.0.p/IndexedBamWriter.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastaReader.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastqBgzfReader.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastqReader.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastqTextReader.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastqReaderImpl.cpp.o src/libpbbam.so.2.4.0.p/IRecordWriter.cpp.o src/libpbbam.so.2.4.0.p/KSeqReader.cpp.o src/libpbbam.so.2.4.0.p/LibraryInfo.cpp.o src/libpbbam.so.2.4.0.p/MD5.cpp.o src/libpbbam.so.2.4.0.p/MemoryUtils.cpp.o src/libpbbam.so.2.4.0.p/PbiBuilder.cpp.o src/libpbbam.so.2.4.0.p/PbiBuilderBase.cpp.o src/libpbbam.so.2.4.0.p/PbiFile.cpp.o src/libpbbam.so.2.4.0.p/PbiFilter.cpp.o src/libpbbam.so.2.4.0.p/PbiFilterQuery.cpp.o src/libpbbam.so.2.4.0.p/PbiFilterTypes.cpp.o src/libpbbam.so.2.4.0.p/PbiIndexedBamReader.cpp.o src/libpbbam.so.2.4.0.p/PbiIndexIO.cpp.o src/libpbbam.so.2.4.0.p/PbiRawData.cpp.o src/libpbbam.so.2.4.0.p/ProgramInfo.cpp.o src/libpbbam.so.2.4.0.p/ReadGroupInfo.cpp.o src/libpbbam.so.2.4.0.p/RecordType.cpp.o src/libpbbam.so.2.4.0.p/RunMetadata.cpp.o src/libpbbam.so.2.4.0.p/RunMetadataParser.cpp.o src/libpbbam.so.2.4.0.p/SamReader.cpp.o src/libpbbam.so.2.4.0.p/SamTagCodec.cpp.o src/libpbbam.so.2.4.0.p/SamWriter.cpp.o src/libpbbam.so.2.4.0.p/SequenceInfo.cpp.o src/libpbbam.so.2.4.0.p/StringUtilities.cpp.o src/libpbbam.so.2.4.0.p/Tag.cpp.o src/libpbbam.so.2.4.0.p/TagCollection.cpp.o src/libpbbam.so.2.4.0.p/TextFileReader.cpp.o src/libpbbam.so.2.4.0.p/TextFileWriter.cpp.o src/libpbbam.so.2.4.0.p/TimeUtils.cpp.o src/libpbbam.so.2.4.0.p/Validator.cpp.o src/libpbbam.so.2.4.0.p/ValidationErrors.cpp.o src/libpbbam.so.2.4.0.p/ValidationException.cpp.o src/libpbbam.so.2.4.0.p/Version.cpp.o src/libpbbam.so.2.4.0.p/VirtualZmwBamRecord.cpp.o src/libpbbam.so.2.4.0.p/VirtualZmwCompositeReader.cpp.o src/libpbbam.so.2.4.0.p/VirtualZmwReader.cpp.o src/libpbbam.so.2.4.0.p/VirtualRegion.cpp.o src/libpbbam.so.2.4.0.p/VirtualRegionTypeMap.cpp.o src/libpbbam.so.2.4.0.p/XmlReader.cpp.o src/libpbbam.so.2.4.0.p/XmlWriter.cpp.o src/libpbbam.so.2.4.0.p/WhitelistedZmwReadStitcher.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastaReader.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastqReader.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxBgzfReader.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxReaderImpl.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxTextReader.cpp.o src/libpbbam.so.2.4.0.p/ZmwGroupQuery.cpp.o src/libpbbam.so.2.4.0.p/ZmwReadStitcher.cpp.o src/libpbbam.so.2.4.0.p/ZmwQuery.cpp.o src/libpbbam.so.2.4.0.p/ZmwTypeMap.cpp.o src/libpbbam.so.2.4.0.p/bed_BedReader.cpp.o src/libpbbam.so.2.4.0.p/bed_BedWriter.cpp.o src/libpbbam.so.2.4.0.p/csv_CsvReader.cpp.o src/libpbbam.so.2.4.0.p/csv_CsvWriter.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfFile.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfFormat.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfHeader.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfHeaderTypes.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfQuery.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfReader.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfSort.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfVariant.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfWriter.cpp.o src/libpbbam.so.2.4.0.p/pugixml_pugixml.cpp.o src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamVersion.cpp.o -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,-soname,libpbbam.so.2.4.0 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wl,--start-group /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group /usr/lib/aarch64-linux-gnu/libz.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libhts.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. 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-fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_TimeUtils.cpp.o -MF tests/pbbam_test.p/src_test_TimeUtils.cpp.o.d -o tests/pbbam_test.p/src_test_TimeUtils.cpp.o -c ../tests/src/test_TimeUtils.cpp [173/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_ReadGroupHashing.cpp.o -MF tests/pbbam_test.p/src_test_ReadGroupHashing.cpp.o.d -o tests/pbbam_test.p/src_test_ReadGroupHashing.cpp.o -c ../tests/src/test_ReadGroupHashing.cpp [174/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_SamIO.cpp.o -MF tests/pbbam_test.p/src_test_SamIO.cpp.o.d -o tests/pbbam_test.p/src_test_SamIO.cpp.o -c ../tests/src/test_SamIO.cpp In file included from /usr/include/c++/15/ios:47, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/sstream:42, from ../include/pbbam/exception/InvalidSequencingChemistryException.h:7, from ../include/pbbam/ReadGroupInfo.h:6, from ../include/pbbam/BamHeader.h:7, from ../include/pbbam/SamReader.h:6, from ../tests/src/test_SamIO.cpp:1: In member function ‘std::basic_streambuf<_CharT, _Traits>::char_type* std::basic_streambuf<_CharT, _Traits>::egptr() const [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘std::basic_streambuf<_CharT, _Traits>::int_type std::basic_streambuf<_CharT, _Traits>::sbumpc() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/15/streambuf:328:49, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>& std::istreambuf_iterator<_CharT, _Traits>::operator++() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/15/bits/streambuf_iterator.h:175:17, inlined from ‘constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_construct(_InIterator, _InIterator, std::input_iterator_tag) [with _InIterator = std::istreambuf_iterator >; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/basic_string.tcc:187:6, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(_InputIterator, _InputIterator, const _Alloc&) [with _InputIterator = std::istreambuf_iterator >; = void; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/basic_string.h:857:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/15/streambuf:497:30: warning: potential null pointer dereference [-Wnull-dereference] 497 | egptr() const { return _M_in_end; } | ^~~~~~~~~ In member function ‘std::basic_streambuf<_CharT, _Traits>::char_type* std::basic_streambuf<_CharT, _Traits>::gptr() const [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘std::basic_streambuf<_CharT, _Traits>::int_type std::basic_streambuf<_CharT, _Traits>::sbumpc() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/15/streambuf:328:33, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>& std::istreambuf_iterator<_CharT, _Traits>::operator++() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/15/bits/streambuf_iterator.h:175:17, inlined from ‘constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_construct(_InIterator, _InIterator, std::input_iterator_tag) [with _InIterator = std::istreambuf_iterator >; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/basic_string.tcc:187:6, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(_InputIterator, _InputIterator, const _Alloc&) [with _InputIterator = std::istreambuf_iterator >; = void; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/basic_string.h:857:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/15/streambuf:494:30: warning: potential null pointer dereference [-Wnull-dereference] 494 | gptr() const { return _M_in_cur; } | ^~~~~~~~~ In member function ‘std::basic_streambuf<_CharT, _Traits>::char_type* std::basic_streambuf<_CharT, _Traits>::gptr() const [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘std::basic_streambuf<_CharT, _Traits>::int_type std::basic_streambuf<_CharT, _Traits>::sbumpc() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/15/streambuf:328:33, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>& std::istreambuf_iterator<_CharT, _Traits>::operator++() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/15/bits/streambuf_iterator.h:175:17, inlined from ‘constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_construct(_InIterator, _InIterator, std::input_iterator_tag) [with _InIterator = std::istreambuf_iterator >; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/basic_string.tcc:215:6, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(_InputIterator, _InputIterator, const _Alloc&) [with _InputIterator = std::istreambuf_iterator >; = void; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/basic_string.h:857:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/15/streambuf:494:30: warning: null pointer dereference [-Wnull-dereference] 494 | gptr() const { return _M_in_cur; } | ^~~~~~~~~ In member function ‘std::basic_streambuf<_CharT, _Traits>::char_type* std::basic_streambuf<_CharT, _Traits>::egptr() const [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘std::basic_streambuf<_CharT, _Traits>::int_type std::basic_streambuf<_CharT, _Traits>::sbumpc() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/15/streambuf:328:49, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>& std::istreambuf_iterator<_CharT, _Traits>::operator++() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/15/bits/streambuf_iterator.h:175:17, inlined from ‘constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_construct(_InIterator, _InIterator, std::input_iterator_tag) [with _InIterator = std::istreambuf_iterator >; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/basic_string.tcc:215:6, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(_InputIterator, _InputIterator, const _Alloc&) [with _InputIterator = std::istreambuf_iterator >; = void; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/basic_string.h:857:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/15/streambuf:497:30: warning: null pointer dereference [-Wnull-dereference] 497 | egptr() const { return _M_in_end; } | ^~~~~~~~~ In member function ‘void std::basic_streambuf<_CharT, _Traits>::gbump(int) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘std::basic_streambuf<_CharT, _Traits>::int_type std::basic_streambuf<_CharT, _Traits>::sbumpc() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/15/streambuf:331:17, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>& std::istreambuf_iterator<_CharT, _Traits>::operator++() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/15/bits/streambuf_iterator.h:175:17, inlined from ‘constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_construct(_InIterator, _InIterator, std::input_iterator_tag) [with _InIterator = std::istreambuf_iterator >; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/basic_string.tcc:215:6, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(_InputIterator, _InputIterator, const _Alloc&) [with _InputIterator = std::istreambuf_iterator >; = void; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/15/bits/basic_string.h:857:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/15/streambuf:507:34: warning: null pointer dereference [-Wnull-dereference] 507 | gbump(int __n) { _M_in_cur += __n; } | ~~~~~~~~~~^~~~~~ [175/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_VcfFile.cpp.o -MF tests/pbbam_test.p/src_test_VcfFile.cpp.o.d -o tests/pbbam_test.p/src_test_VcfFile.cpp.o -c ../tests/src/test_VcfFile.cpp [176/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_TextFileReader.cpp.o -MF tests/pbbam_test.p/src_test_TextFileReader.cpp.o.d -o tests/pbbam_test.p/src_test_TextFileReader.cpp.o -c ../tests/src/test_TextFileReader.cpp [177/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_TextFileWriter.cpp.o -MF tests/pbbam_test.p/src_test_TextFileWriter.cpp.o.d -o tests/pbbam_test.p/src_test_TextFileWriter.cpp.o -c ../tests/src/test_TextFileWriter.cpp [178/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_VcfReader.cpp.o -MF tests/pbbam_test.p/src_test_VcfReader.cpp.o.d -o tests/pbbam_test.p/src_test_VcfReader.cpp.o -c ../tests/src/test_VcfReader.cpp [179/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_DataSetIO.cpp.o -MF tests/pbbam_test.p/src_test_DataSetIO.cpp.o.d -o tests/pbbam_test.p/src_test_DataSetIO.cpp.o -c ../tests/src/test_DataSetIO.cpp [180/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_VcfSort.cpp.o -MF tests/pbbam_test.p/src_test_VcfSort.cpp.o.d -o tests/pbbam_test.p/src_test_VcfSort.cpp.o -c ../tests/src/test_VcfSort.cpp [181/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_SegmentReads.cpp.o -MF tests/pbbam_test.p/src_test_SegmentReads.cpp.o.d -o tests/pbbam_test.p/src_test_SegmentReads.cpp.o -c ../tests/src/test_SegmentReads.cpp [182/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_VcfHeader.cpp.o -MF tests/pbbam_test.p/src_test_VcfHeader.cpp.o.d -o tests/pbbam_test.p/src_test_VcfHeader.cpp.o -c ../tests/src/test_VcfHeader.cpp [183/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_VcfFormat.cpp.o -MF tests/pbbam_test.p/src_test_VcfFormat.cpp.o.d -o tests/pbbam_test.p/src_test_VcfFormat.cpp.o -c ../tests/src/test_VcfFormat.cpp [184/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_VcfQuery.cpp.o -MF tests/pbbam_test.p/src_test_VcfQuery.cpp.o.d -o tests/pbbam_test.p/src_test_VcfQuery.cpp.o -c ../tests/src/test_VcfQuery.cpp [185/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_PbiFilterQuery.cpp.o -MF tests/pbbam_test.p/src_test_PbiFilterQuery.cpp.o.d -o tests/pbbam_test.p/src_test_PbiFilterQuery.cpp.o -c ../tests/src/test_PbiFilterQuery.cpp [186/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_VcfVariant.cpp.o -MF tests/pbbam_test.p/src_test_VcfVariant.cpp.o.d -o tests/pbbam_test.p/src_test_VcfVariant.cpp.o -c ../tests/src/test_VcfVariant.cpp [187/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [188/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_Validator.cpp.o -MF tests/pbbam_test.p/src_test_Validator.cpp.o.d -o tests/pbbam_test.p/src_test_Validator.cpp.o -c ../tests/src/test_Validator.cpp [189/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [190/226] 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 -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [191/226] 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 -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [192/226] 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 -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [193/226] 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 -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [194/226] 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 -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [195/226] 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 -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [196/226] 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 -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [197/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_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 [198/226] 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 -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o -c ../tools/pbindexdump/src/PbIndexDumpWorkflow.cpp [199/226] 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 -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/pbindexdump.p/pbindexdump_src_main.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_main.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_main.cpp.o -c ../tools/pbindexdump/src/main.cpp [200/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_PbiFilter.cpp.o -MF tests/pbbam_test.p/src_test_PbiFilter.cpp.o.d -o tests/pbbam_test.p/src_test_PbiFilter.cpp.o -c ../tests/src/test_PbiFilter.cpp [201/226] 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 -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/pbindexdump.p/pbindexdump_src_PbIndexDumpSettings.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_PbIndexDumpSettings.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpSettings.cpp.o -c ../tools/pbindexdump/src/PbIndexDumpSettings.cpp [202/226] 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 -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o -c ../tools/pbindexdump/src/CppFormatter.cpp [203/226] c++ -Itools/pbmerge.p -Itools -I../tools -Iinclude -I../include -I../tools/pbmerge -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/pbmerge.p/pbmerge_src_main.cpp.o -MF tools/pbmerge.p/pbmerge_src_main.cpp.o.d -o tools/pbmerge.p/pbmerge_src_main.cpp.o -c ../tools/pbmerge/src/main.cpp [204/226] c++ -Itools/pbmerge.p -Itools -I../tools -Iinclude -I../include -I../tools/pbmerge -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/pbmerge.p/pbmerge_src_PbMergeSettings.cpp.o -MF tools/pbmerge.p/pbmerge_src_PbMergeSettings.cpp.o.d -o tools/pbmerge.p/pbmerge_src_PbMergeSettings.cpp.o -c ../tools/pbmerge/src/PbMergeSettings.cpp [205/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [206/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_Tags.cpp.o -MF 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 [207/226] /usr/bin/python3 ../tests/scripts/generate_data.py /build/reproducible-path/pbbam-2.4.0+dfsg/tests/data /build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu/tests Generating test data in /build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-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. [208/226] 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 -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [209/226] 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/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../../src' -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group [210/226] 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/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libhts.so -pthread /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group [211/226] 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/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group [212/226] 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 -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [213/226] 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 -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_CcsKineticsBystrandifySettings.cpp.o -MF tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifySettings.cpp.o.d -o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifySettings.cpp.o -c ../tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifySettings.cpp [214/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [215/226] c++ -Itools/pbmerge.p -Itools -I../tools -Iinclude -I../include -I../tools/pbmerge -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -MF tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o.d -o tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -c ../tools/pbmerge/src/PbMergeWorkflow.cpp [216/226] c++ -o tools/pbmerge tools/pbmerge.p/pbmerge_src_main.cpp.o tools/pbmerge.p/pbmerge_src_PbMergeSettings.cpp.o tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group [217/226] 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 -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_QueryLookup.cpp.o -MF tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o.d -o tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -c ../tools/pbbamify/src/QueryLookup.cpp [218/226] 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 -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [219/226] 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 -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o -c ../tools/pbindexdump/src/JsonFormatter.cpp [220/226] c++ -o tools/pbindexdump tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpSettings.cpp.o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o tools/pbindexdump.p/pbindexdump_src_main.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group [221/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [222/226] 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 -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 [223/226] 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/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group [224/226] 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_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_Csv.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_Pulse2BaseCache.cpp.o tests/pbbam_test.p/src_test_ReadGroupHashing.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_SegmentReads.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/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/aarch64-linux-gnu/libgtest_main.a /usr/lib/aarch64-linux-gnu/libgtest.a /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group [225/226] c++ -Itools/ccs-kinetics-bystrandify.p -Itools -I../tools -Iinclude -I../include -I../tools/ccs-kinetics-bystrandify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -MF tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o.d -o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -c ../tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp [226/226] c++ -o tools/ccs-kinetics-bystrandify tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_main.cpp.o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifySettings.cpp.o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/pbbam-2.4.0+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/reproducible-path/pbbam-2.4.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/reproducible-path/pbbam-2.4.0+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|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/reproducible-path/pbbam-2.4.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/reproducible-path/pbbam-2.4.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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/reproducible-path/pbbam-2.4.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/reproducible-path/pbbam-2.4.0+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|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/reproducible-path/pbbam-2.4.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/reproducible-path/pbbam-2.4.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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/reproducible-path/pbbam-2.4.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/reproducible-path/pbbam-2.4.0+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|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/reproducible-path/pbbam-2.4.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/reproducible-path/pbbam-2.4.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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/reproducible-path/pbbam-2.4.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/reproducible-path/pbbam-2.4.0+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|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/reproducible-path/pbbam-2.4.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/reproducible-path/pbbam-2.4.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 meson setup .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/aarch64-linux-gnu -Dpython.bytecompile=-1 Directory already configured. Just run your build command (e.g. ninja) and Meson will regenerate as necessary. Run "meson setup --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. mkdir -p /build/reproducible-path/pbbam-2.4.0+dfsg/gendata python3 tests/scripts/generate_data.py /build/reproducible-path/pbbam-2.4.0+dfsg/tests/data /build/reproducible-path/pbbam-2.4.0+dfsg/gendata Generating test data in /build/reproducible-path/pbbam-2.4.0+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/games" 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/reproducible-path/pbbam-2.4.0+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=meson dh_prep -O--buildsystem=meson dh_auto_install -O--buildsystem=meson cd obj-aarch64-linux-gnu && DESTDIR=/build/reproducible-path/pbbam-2.4.0\+dfsg/debian/tmp LC_ALL=C.UTF-8 ninja install [0/1] Regenerating build files Cleaning... 0 files. The Meson build system Version: 1.9.1 Source dir: /build/reproducible-path/pbbam-2.4.0+dfsg Build dir: /build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu Build type: native build Project name: PacBioBAM Project version: 2.4.0 C compiler for the host machine: cc (gcc 15.2.0 "cc (Debian 15.2.0-4) 15.2.0") C linker for the host machine: cc ld.bfd 2.45 C++ compiler for the host machine: c++ (gcc 15.2.0 "c++ (Debian 15.2.0-4) 15.2.0") C++ linker for the host machine: c++ ld.bfd 2.45 Host machine cpu family: aarch64 Host machine cpu: aarch64 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 1.83.0 (cached) Dependency zlib found: YES 1.3.1 (cached) Dependency htslib found: YES 1.22.1 (cached) Dependency pbcopper found: YES 2.3.0 (cached) Configuring PbbamVersion.cpp using configuration Configuring LibraryVersion.h using configuration Program tools/check-formatting found: YES (/build/reproducible-path/pbbam-2.4.0+dfsg/tools/check-formatting) Program python3 found: YES (/usr/bin/python3) Program cram3 found: YES (/usr/bin/cram3) Dependency gtest found: YES 1.17.0 (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 Found pkg-config: YES (/usr/bin/pkg-config) 1.8.1 Build targets in project: 12 PacBioBAM 2.4.0 User defined options buildtype : plain libdir : lib/aarch64-linux-gnu localstatedir : /var prefix : /usr python.bytecompile: -1 sysconfdir : /etc wrap_mode : nodownload Found ninja-1.12.1 at /usr/bin/ninja [1/16] Generating tests/pbbam_generate_data with a custom command [2/16] Generating src/PbbamGitHash.cpp with a custom command [3/15] Generating src/LibraryGitHash.h with a custom command [3/5] Installing files Installing src/libpbbam.so.2.4.0 to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu Installing tools/bam2sam to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/bin Installing tools/pbindex to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/bin Installing tools/pbindexdump to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/bin Installing tools/pbmerge to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/bin Installing tools/pbbamify to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/bin Installing tools/ccs-kinetics-bystrandify to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/bin Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/AlignmentPrinter.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/BaiIndexCache.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/BaiIndexedBamReader.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/BamFile.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/BamFileMerger.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/BamHeader.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/BamReader.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/BamRecord.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/BamRecordImpl.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/BamRecordTag.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/BamRecordView.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/BamTagCodec.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/BamWriter.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/BgzipFastaWriter.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/BgzipFastqWriter.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/BgzipWriter.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/ClipType.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/CollectionMetadata.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/Compare.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/CompositeBamReader.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/CompositeFastaReader.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/Config.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/DataSet.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/DataSetTypes.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/DataSetXsd.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/Deleters.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/EntireFileQuery.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/FaiIndex.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/FastaCache.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/FastaReader.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/FastaSequence.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/FastaSequenceQuery.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/FastaWriter.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/FastqReader.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/FastqSequence.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/FastqWriter.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/FormatUtils.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/FrameEncodingType.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/GenomicIntervalQuery.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/IFastaWriter.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/IFastqWriter.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/IndexedBamWriter.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/IndexedFastaReader.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/IndexedFastqReader.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/IRecordWriter.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/LibraryInfo.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/MD5.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/MoveAppend.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/PbbamVersion.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/PbiBasicTypes.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/PbiBuilder.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/PbiFile.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/PbiFilter.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/PbiFilterQuery.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/PbiFilterTypes.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/PbiIndexedBamReader.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/PbiRawData.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/ProgramInfo.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/PulseBehavior.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/PulseExclusionReason.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/ReadGroupInfo.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/RecordType.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/RunMetadata.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/SamReader.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/SamTagCodec.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/SamWriter.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/SequenceInfo.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/StringUtilities.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/Tag.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/TagCollection.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/TextFileReader.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/TextFileWriter.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/Validator.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/ZmwGroupQuery.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/ZmwQuery.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/ZmwType.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/ZmwTypeMap.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/bed/BedReader.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/bed Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/bed/BedWriter.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/bed Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/csv/CsvReader.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/csv Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/csv/CsvTypes.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/csv Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/csv/CsvWriter.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/csv Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/exception/BundleChemistryMappingException.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/exception Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/exception/InvalidSequencingChemistryException.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/exception Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/exception/ValidationException.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/exception Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/internal/Compare.inl to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/internal/CompositeBamReader.inl to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/internal/DataSetBaseTypes.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/internal/DataSetElement.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/internal/DataSetElement.inl to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/internal/PbiBasicTypes.inl to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/internal/PbiFilter.inl to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/internal/PbiFilterTypes.inl to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/internal/QueryBase.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/internal/QueryBase.inl to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/vcf/VcfVariant.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/vcf/VcfFile.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/vcf/VcfFormat.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/vcf/VcfHeader.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/vcf/VcfHeaderTypes.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/vcf/VcfReader.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/vcf/VcfSort.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/vcf/VcfQuery.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/vcf/VcfWriter.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/virtual/VirtualPolymeraseBamRecord.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/virtual/VirtualPolymeraseCompositeReader.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/virtual/VirtualPolymeraseReader.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/virtual/VirtualRegion.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/virtual/VirtualRegionType.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/virtual/VirtualRegionTypeMap.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/virtual/VirtualZmwBamRecord.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/virtual/WhitelistedZmwReadStitcher.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/virtual/ZmwReadStitcher.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/reproducible-path/pbbam-2.4.0+dfsg/include/pbbam/virtual/ZmwWhitelistVirtualReader.h to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu/meson-private/pbbam.pc to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig Installing symlink pointing to libpbbam.so.2.4.0 to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libpbbam.so debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/pbbam-2.4.0+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/aarch64-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/aarch64-linux-gnu install -d -m 755 debian/libpbbam2.4.0/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libpbbam.so debian/libpbbam-dev/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libpbbam.so.2.4.0 debian/libpbbam2.4.0/usr/lib/aarch64-linux-gnu PKGDEV=libpbbam-dev PKGSHL=libpbbam2.4.0 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/aarch64-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libpbbam-dev/usr/lib/aarch64-linux-gnu/pkgconfig find debian -name "lib*.la" -delete make[1]: Leaving directory '/build/reproducible-path/pbbam-2.4.0+dfsg' dh_installdocs -O--buildsystem=meson debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/pbbam-2.4.0+dfsg' dh_installchangelogs CHANGELOG.md make[1]: Leaving directory '/build/reproducible-path/pbbam-2.4.0+dfsg' dh_installsystemduser -O--buildsystem=meson dh_perl -O--buildsystem=meson dh_link -O--buildsystem=meson dh_strip_nondeterminism -O--buildsystem=meson dh_compress -O--buildsystem=meson dh_fixperms -O--buildsystem=meson dh_missing -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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -O--buildsystem=meson dh_gencontrol -O--buildsystem=meson dh_md5sums -O--buildsystem=meson dh_builddeb -O--buildsystem=meson dpkg-deb: building package 'pbbamtools-dbgsym' in '../pbbamtools-dbgsym_2.4.0+dfsg-2_arm64.deb'. dpkg-deb: building package 'pbbamtools' in '../pbbamtools_2.4.0+dfsg-2_arm64.deb'. dpkg-deb: building package 'libpbbam2.4.0-dbgsym' in '../libpbbam2.4.0-dbgsym_2.4.0+dfsg-2_arm64.deb'. dpkg-deb: building package 'libpbbam2.4.0' in '../libpbbam2.4.0_2.4.0+dfsg-2_arm64.deb'. dpkg-deb: building package 'libpbbam-dev' in '../libpbbam-dev_2.4.0+dfsg-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../pbbam_2.4.0+dfsg-2_arm64.buildinfo dpkg-genchanges --build=binary -O../pbbam_2.4.0+dfsg-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1209296 and its subdirectories I: Current time: Sat Nov 14 01:19:01 -12 2026 I: pbuilder-time-stamp: 1794662341 Sun Oct 12 06:56:05 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Sun Oct 12 06:56:05 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Sun Oct 12 06:59:31 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Sun Oct 12 06:59:31 UTC 2025 I: pbbam_2.4.0+dfsg-2_arm64.changes: Format: 1.8 Date: Sun, 05 Oct 2025 23:56:29 +0200 Source: pbbam Binary: libpbbam-dev libpbbam2.4.0 libpbbam2.4.0-dbgsym pbbamtools pbbamtools-dbgsym Architecture: arm64 Version: 2.4.0+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: libpbbam-dev - Pacific Biosciences binary alignment/map (BAM) library (headers) libpbbam2.4.0 - Pacific Biosciences binary alignment/map (BAM) library pbbamtools - processing Pacific Biosciences binary alignment/map files Closes: 1117414 Changes: pbbam (2.4.0+dfsg-2) unstable; urgency=medium . * Team upload. * d/control: build depends on libboost-iostreams-dev. (Closes: #1117414) * d/control: build depends on pkgconf. * d/patches/*: normalize Last-Update timestamp. * d/watch: convert to watch file version 5. * d/control: declare compliance to standards version 4.7.2. * d/control: drop redundant Rules-Requires-Root: no. Checksums-Sha1: cc67820fb9868d096430ec28c71aedbbf0757b28 88240 libpbbam-dev_2.4.0+dfsg-2_arm64.deb 8288b44b57f5b0964e2b61950cef2b57aae8e44c 17675340 libpbbam2.4.0-dbgsym_2.4.0+dfsg-2_arm64.deb 494885da0470fb128c166b2b6b13dd93af1b0b00 692800 libpbbam2.4.0_2.4.0+dfsg-2_arm64.deb c959752a82e07f473417aca5eeeef25924144788 9899 pbbam_2.4.0+dfsg-2_arm64.buildinfo 2c79c863e927637ce79a7913e2dd5943c6ee7c21 3027848 pbbamtools-dbgsym_2.4.0+dfsg-2_arm64.deb 1b9b58538a9fd5d2c5608e8741847bce32e1b24c 114228 pbbamtools_2.4.0+dfsg-2_arm64.deb Checksums-Sha256: 532aac8abe3005c7a279563c6fd5076c2d30a1b7f33a043bfb2bf9c7eed74a3e 88240 libpbbam-dev_2.4.0+dfsg-2_arm64.deb f303330e5fbf23e077a1eda94a846c7d7dce933ccb6cfd8bacd1f3b8def94145 17675340 libpbbam2.4.0-dbgsym_2.4.0+dfsg-2_arm64.deb d30fcd4e76a7b41a511bad80b05008aad466b8f737ab4c34db6715206acb33d8 692800 libpbbam2.4.0_2.4.0+dfsg-2_arm64.deb 95ec2c0cda0bd46fee8e11a63e7dd3dd19ee581d30b9d590b9537b3821a2c136 9899 pbbam_2.4.0+dfsg-2_arm64.buildinfo 33290de3c00f96767c0821b723826d5ad5c2d10aec5ef8546bcfcfe420ba7e9e 3027848 pbbamtools-dbgsym_2.4.0+dfsg-2_arm64.deb b06971b373ce7b3d0c77b8e3533615b6ea339d7a42b7051894b071f417eedde8 114228 pbbamtools_2.4.0+dfsg-2_arm64.deb Files: a0f50f4463674646594c12c6fcd6de9a 88240 libdevel optional libpbbam-dev_2.4.0+dfsg-2_arm64.deb eaf303f0923d06f0e692daaa51694b41 17675340 debug optional libpbbam2.4.0-dbgsym_2.4.0+dfsg-2_arm64.deb e571f300d9c5ddcc2a5a2b3dfc319ab3 692800 libs optional libpbbam2.4.0_2.4.0+dfsg-2_arm64.deb 5dbdb55ef560aa7bac8510d20f312f03 9899 science optional pbbam_2.4.0+dfsg-2_arm64.buildinfo 573513f3b72054b543674a4ab4192694 3027848 debug optional pbbamtools-dbgsym_2.4.0+dfsg-2_arm64.deb 09777c0ea43862c2cc88a77e55bfd1ac 114228 science optional pbbamtools_2.4.0+dfsg-2_arm64.deb Sun Oct 12 06:59:32 UTC 2025 I: diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_6-122232.service; invocation ID: d24dee3295ee44c6b75b51509413fc6b # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.gjjlvic5/pbbam_2.4.0+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.gjjlvic5/pbbam_2.4.0+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.gjjlvic5/pbbam_2.4.0+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.gjjlvic5/b1/pbbam_2.4.0+dfsg-2_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.gjjlvic5/b2/pbbam_2.4.0+dfsg-2_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 223ms CPU time consumed: 173ms Memory peak: 18M (swap: 0B) Sun Oct 12 06:59:32 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Sun Oct 12 06:59:32 UTC 2025 I: pbbam from forky built successfully and reproducibly on arm64. Sun Oct 12 06:59:33 UTC 2025 I: Removing signed pbbam_2.4.0+dfsg-2_arm64.buildinfo.asc files: removed './b1/pbbam_2.4.0+dfsg-2_arm64.buildinfo.asc' removed './b2/pbbam_2.4.0+dfsg-2_arm64.buildinfo.asc'