Sat Mar 1 01:36:36 UTC 2025 I: starting to build pbbam/trixie/arm64 on jenkins on '2025-03-01 01:36' Sat Mar 1 01:36:36 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_7/59158/console.log Sat Mar 1 01:36:36 UTC 2025 I: Downloading source for trixie/pbbam=2.4.0+dfsg-1 --2025-03-01 01:36:36-- http://deb.debian.org/debian/pool/main/p/pbbam/pbbam_2.4.0%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2321 (2.3K) [text/prs.lines.tag] Saving to: ‘pbbam_2.4.0+dfsg-1.dsc’ 0K .. 100% 380M=0s 2025-03-01 01:36:36 (380 MB/s) - ‘pbbam_2.4.0+dfsg-1.dsc’ saved [2321/2321] Sat Mar 1 01:36:36 UTC 2025 I: pbbam_2.4.0+dfsg-1.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-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://pbbam.readthedocs.org/en/latest/index.html Standards-Version: 4.6.2 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, pkg-config, cmake, libboost-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 72dd9934d4f507818c2f0314db588e13d78102c0 8980 pbbam_2.4.0+dfsg-1.debian.tar.xz Checksums-Sha256: e991e5f5470976f2ad0cca93658a273989738ca48cce4f024fd074cc1e8cbe2b 7826464 pbbam_2.4.0+dfsg.orig.tar.xz 598bb22aaaab6c7b2ea2faf7a1a31431c78c223f9464a63e3a90c5a2f5f21f1b 8980 pbbam_2.4.0+dfsg-1.debian.tar.xz Files: 315039ff474e762e609442ca84988512 7826464 pbbam_2.4.0+dfsg.orig.tar.xz 8a3ee5bde31a061b9aa0d9b90769671f 8980 pbbam_2.4.0+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmVL0gQRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFqzhAAjj9eYBapnecg3wapHEEL3ZFRf1ZvJRKB Uv3i95KA25Rw4nr8pVn4+rAjTxtxhuA1CIrGVxILsY1dicgN6YtZvwgs+UTActuB HBjGBpuh8yus8gdWmA0KXK4W03LYLAdvp+1GTApWhOa/jDngePdkIc7f/ZbYVdR0 UpPL7OX9xHMbRLWOo8wEj9mioWdK/I6CuKzGA00ffuyvLluopquQ2rDCChdLJLR8 mu4cU/Nnm5EQpHVPw2qz6d4eJngnv6bjEa2AJpte8+WxPYzUFoWy3ojrVGyF2f3R tWwk7j22mHUUkPuueLco3oHMzj7SGOTInf+QdkhRGCqe65+MILpdkgnBj/AaLGuF jLTa/Dv2oX8w7JJP9U1ht5GdGxCb8qMviLZMjeV6n8Xm2M7hnGLVNPR8a3eV+RGB tB3XL+Q1kfpYxLJVkjeSBFun524YH/uAQiaO73diavSraIi9oJXh9Bh7RgLRJmSg EvFLvEWq3g/h1TUlnWsKIzIpuybaX8XC2d8eIc+JWr+OWhBLjPspTVJNrpTgsake qwClK0Mo/8cUK78YCWlfS6m6SYc1JbO0SUH+SweId1r0bTZw+brDJ2mAXTJojCi+ 84ehZMWCdKFlUQLNuJgu1a5oLX1oHDVYtkLkHHTuI0CSsH/O1grQ8WQokYrmoa+B S4tQL20deRo= =OT0g -----END PGP SIGNATURE----- Sat Mar 1 01:36:36 UTC 2025 I: Checking whether the package is not for us Sat Mar 1 01:36:36 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Sat Mar 1 01:36:36 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Sat Mar 1 01:40:28 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Feb 28 13:36:39 -12 2025 I: pbuilder-time-stamp: 1740792999 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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-1.dsc] I: copying [./pbbam_2.4.0+dfsg.orig.tar.xz] I: copying [./pbbam_2.4.0+dfsg-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./pbbam_2.4.0+dfsg-1.dsc: unsupported subcommand 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-1.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: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3083744/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='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='6d769548d8a34df9ba5532efccda423f' 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='3083744' 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.9o4blbWp/pbuilderrc_cYh4 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9o4blbWp/b1 --logfile b1/build.log pbbam_2.4.0+dfsg-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3083744/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, pkg-config, cmake, libboost-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 ... 19916 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 pkg-config; however: Package pkg-config 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 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} gettext{a} gettext-base{a} googletest{a} groff-base{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libarchive13t64{a} libboost-dev{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} 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} libicu72{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-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} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libuv1t64{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} meson{a} netbase{a} nettle-dev{a} ninja-build{a} pkg-config{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, 141 newly installed, 0 to remove and 0 not upgraded. Need to get 75.5 MB of archives. After unpacking 418 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.13-minimal arm64 3.13.2-1 [853 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 python3.13-minimal arm64 3.13.2-1 [1997 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.13.2-1 [27.1 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 media-types all 12.0.0 [28.9 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 tzdata all 2025a-2 [259 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.7-1 [21.2 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libpython3.13-stdlib arm64 3.13.2-1 [1914 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 python3.13 arm64 3.13.2-1 [745 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.13.2-1 [10.0 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.13.2-1 [28.1 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-7 [62.4 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-7 [868 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-5 [92.0 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-3 [862 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 cmake-data all 3.31.5-2 [2267 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b2 [630 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libarchive13t64 arm64 3.7.4-1.1 [323 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-4 [32.2 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-4 [81.5 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 41 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-4 [308 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-4 [127 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8+b1 [20.3 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8+b1 [55.7 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.6.0-2 [60.5 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libgnutls30t64 arm64 3.8.9-2 [1374 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libcurl4t64 arm64 8.12.1-2 [340 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 librhash1 arm64 1.4.5-1 [129 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libuv1t64 arm64 1.50.0-2 [148 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 cmake arm64 3.31.5-2 [9907 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 comerr-dev arm64 2.1-1.47.2-1 [55.9 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 d-shlibs all 0.109 [11.1 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-3 [539 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 69 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 dh-exec arm64 0.30+b1 [25.8 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 googletest all 1.16.0-1 [517 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libgssrpc4t64 arm64 1.21.3-4 [56.9 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libkadm5clnt-mit12 arm64 1.21.3-4 [41.0 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libkdb5-10t64 arm64 1.21.3-4 [41.0 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libkadm5srv-mit12 arm64 1.21.3-4 [53.1 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 krb5-multidev arm64 1.21.3-4 [126 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libboost1.83-dev arm64 1.83.0-4.1 [10.6 MB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 84 http://deb.debian.org/debian trixie/main arm64 libbrotli-dev arm64 1.1.0-2+b7 [308 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.9.1-1 [109 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.9.1-1 [17.3 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.12.1-2 [336 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libunbound8 arm64 1.22.0-1+b1 [553 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libgnutls-dane0t64 arm64 3.8.9-2 [452 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libgnutls-openssl27t64 arm64 3.8.9-2 [452 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libp11-kit-dev arm64 0.25.5-3 [208 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libtasn1-6-dev arm64 4.20.0-2 [96.7 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-3 [329 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-3 [621 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 nettle-dev arm64 3.10.1-1 [1325 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libgnutls28-dev arm64 3.8.9-2 [1419 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libkrb5-dev arm64 1.21.3-4 [15.9 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libldap-dev arm64 2.6.9+dfsg-1 [305 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libnghttp3-dev arm64 1.6.0-2 [86.5 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.9.1-1 [23.0 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libngtcp2-dev arm64 1.9.1-1 [162 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libssl-dev arm64 3.4.1-1 [3232 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libzstd-dev arm64 1.5.6+dfsg-2 [329 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libcurl4-gnutls-dev arm64 8.12.1-2 [465 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libdeflate-dev arm64 1.23-1+b1 [51.4 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libgtest-dev arm64 1.16.0-1 [246 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.1-2 [74.7 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.21+ds-1 [426 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 liblzma-dev arm64 5.6.3-1+b1 [312 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 libhts-dev arm64 1.21+ds-1 [1658 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5+20250216-1 [96.1 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libpbcopper2.3.0 arm64 2.3.0+dfsg-2+b2 [626 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 libpbcopper-dev arm64 2.3.0+dfsg-2+b2 [994 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 ninja-build arm64 1.12.1-1+b1 [130 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 133 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 75.8.0-1 [222 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 75.8.0-1 [724 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 meson all 1.7.0-1 [639 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 pkg-config arm64 1.8.1-4 [14.0 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 python3-cram all 0.7-6 [17.5 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 samtools arm64 1.21-1 [637 kB] Fetched 75.5 MB in 0s (183 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal: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 ... 19916 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.2-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-1_arm64.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:arm64 (3.13.2-1) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... 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 ... 20250 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.2-1_arm64.deb ... Unpacking python3-minimal (3.13.2-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_12.0.0_all.deb ... Unpacking media-types (12.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025a-2_all.deb ... Unpacking tzdata (2025a-2) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../4-libffi8_3.4.7-1_arm64.deb ... Unpacking libffi8:arm64 (3.4.7-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../6-libreadline8t64_8.2-6_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 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_arm64.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../9-libpython3-stdlib_3.13.2-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.13.2-1) ... Setting up python3-minimal (3.13.2-1) ... 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 ... 21260 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.2-1_arm64.deb ... Unpacking python3 (3.13.2-1) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-7_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-7) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-7_arm64.deb ... Unpacking procps (2:4.0.4-7) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../005-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../008-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.40.4-5_arm64.deb ... Unpacking bsdextrautils (2.40.4-5) ... 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_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../013-m4_1.4.19-5_arm64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../014-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../015-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../016-automake_1%3a1.17-3_all.deb ... Unpacking automake (1:1.17-3) ... Selecting previously unselected package autopoint. Preparing to unpack .../017-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package cmake-data. Preparing to unpack .../018-cmake-data_3.31.5-2_all.deb ... Unpacking cmake-data (3.31.5-2) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../019-libicu72_72.1-6_arm64.deb ... Unpacking libicu72:arm64 (72.1-6) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../020-libxml2_2.12.7+dfsg+really2.9.14-0.2+b2_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b2) ... Selecting previously unselected package libarchive13t64:arm64. Preparing to unpack .../021-libarchive13t64_3.7.4-1.1_arm64.deb ... Unpacking libarchive13t64:arm64 (3.7.4-1.1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../022-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 .../023-libkrb5support0_1.21.3-4_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-4) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../024-libcom-err2_1.47.2-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.2-1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../025-libk5crypto3_1.21.3-4_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-4) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../026-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../027-libkrb5-3_1.21.3-4_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-4) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../028-libgssapi-krb5-2_1.21.3-4_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-4) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../029-libunistring5_1.3-1_arm64.deb ... Unpacking libunistring5:arm64 (1.3-1) ... Selecting previously unselected package libidn2-0:arm64. Preparing to unpack .../030-libidn2-0_2.3.7-2+b1_arm64.deb ... Unpacking libidn2-0:arm64 (2.3.7-2+b1) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../031-libsasl2-modules-db_2.1.28+dfsg1-8+b1_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-8+b1) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../032-libsasl2-2_2.1.28+dfsg1-8+b1_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-8+b1) ... Selecting previously unselected package libldap2:arm64. Preparing to unpack .../033-libldap2_2.6.9+dfsg-1_arm64.deb ... Unpacking libldap2:arm64 (2.6.9+dfsg-1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../034-libnghttp2-14_1.64.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.64.0-1) ... Selecting previously unselected package libnghttp3-9:arm64. Preparing to unpack .../035-libnghttp3-9_1.6.0-2_arm64.deb ... Unpacking libnghttp3-9:arm64 (1.6.0-2) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../036-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 .../037-libp11-kit0_0.25.5-3_arm64.deb ... Unpacking libp11-kit0:arm64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:arm64. Preparing to unpack .../038-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 .../039-libgnutls30t64_3.8.9-2_arm64.deb ... Unpacking libgnutls30t64:arm64 (3.8.9-2) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../040-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../041-libssh2-1t64_1.11.1-1_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:arm64. Preparing to unpack .../042-libcurl4t64_8.12.1-2_arm64.deb ... Unpacking libcurl4t64:arm64 (8.12.1-2) ... Selecting previously unselected package libjsoncpp26:arm64. Preparing to unpack .../043-libjsoncpp26_1.9.6-3_arm64.deb ... Unpacking libjsoncpp26:arm64 (1.9.6-3) ... Selecting previously unselected package librhash1:arm64. Preparing to unpack .../044-librhash1_1.4.5-1_arm64.deb ... Unpacking librhash1:arm64 (1.4.5-1) ... Selecting previously unselected package libuv1t64:arm64. Preparing to unpack .../045-libuv1t64_1.50.0-2_arm64.deb ... Unpacking libuv1t64:arm64 (1.50.0-2) ... Selecting previously unselected package cmake. Preparing to unpack .../046-cmake_3.31.5-2_arm64.deb ... Unpacking cmake (3.31.5-2) ... Selecting previously unselected package comerr-dev:arm64. Preparing to unpack .../047-comerr-dev_2.1-1.47.2-1_arm64.deb ... Unpacking comerr-dev:arm64 (2.1-1.47.2-1) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../048-d-shlibs_0.109_all.deb ... Unpacking d-shlibs (0.109) ... Selecting previously unselected package libdebhelper-perl. 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Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8+b1) ... Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Mar 1 01:37:05 UTC 2025. Universal Time is now: Sat Mar 1 01:37:05 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libunbound8:arm64 (1.22.0-1+b1) ... Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-3) ... Setting up libjsoncpp26:arm64 (1.9.6-3) ... Setting up libncurses6:arm64 (6.5+20250216-1) ... Setting up libproc2-0:arm64 (2:4.0.4-7) ... Setting up comerr-dev:arm64 (2.1-1.47.2-1) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up libssl-dev:arm64 (3.4.1-1) ... Setting up autopoint (0.23.1-1) ... Setting up d-shlibs (0.109) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:arm64 (1.21.3-4) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8+b1) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:arm64 (1.6.0-2) ... Setting up libnghttp3-dev:arm64 (1.6.0-2) ... Setting up liblzma-dev:arm64 (5.6.3-1+b1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.4.7-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-7) ... Setting up libtasn1-6:arm64 (4.20.0-2) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:arm64 (1.9.1-1) ... Setting up cmake-data (3.31.5-2) ... Setting up librhash1:arm64 (1.4.5-1) ... Setting up libkrb5-3:arm64 (1.21.3-4) ... Setting up libboost-dev:arm64 (1.83.0.2+b2) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libtasn1-6-dev:arm64 (4.20.0-2) ... Setting up libdeflate-dev:arm64 (1.23-1+b1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b2) ... Setting up libldap2:arm64 (2.6.9+dfsg-1) ... Setting up libbrotli-dev:arm64 (1.1.0-2+b7) ... Setting up libpbcopper2.3.0:arm64 (2.3.0+dfsg-2+b2) ... Setting up libbz2-dev:arm64 (1.0.8-6) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-1) ... Setting up libgmp-dev:arm64 (2:6.3.0+dfsg-3) ... Setting up libgtest-dev:arm64 (1.16.0-1) ... Setting up nettle-dev:arm64 (3.10.1-1) ... Setting up libtool (2.5.4-3) ... Setting up libidn2-0:arm64 (2.3.7-2+b1) ... Setting up libngtcp2-dev:arm64 (1.9.1-1) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libldap-dev:arm64 (2.6.9+dfsg-1) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-4) ... Setting up pkg-config:arm64 (1.8.1-4) ... Setting up libpbcopper-dev:arm64 (2.3.0+dfsg-2+b2) ... Setting up libssh2-1-dev:arm64 (1.11.1-1) ... Setting up libidn2-dev:arm64 (2.3.7-2+b1) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up libarchive13t64:arm64 (3.7.4-1.1) ... Setting up libpython3.13-stdlib:arm64 (3.13.2-1) ... Setting up libp11-kit-dev:arm64 (0.25.5-3) ... Setting up libpython3-stdlib:arm64 (3.13.2-1) ... Setting up libgnutls30t64:arm64 (3.8.9-2) ... Setting up libgnutls-openssl27t64:arm64 (3.8.9-2) ... Setting up libnghttp2-dev:arm64 (1.64.0-1) ... Setting up python3.13 (3.13.2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.2-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpsl-dev:arm64 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:arm64 (3.8.9-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libgssrpc4t64:arm64 (1.21.3-4) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-cram (0.7-6) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.9.1-1) ... Setting up libkadm5clnt-mit12:arm64 (1.21.3-4) ... Setting up libgnutls28-dev:arm64 (3.8.9-2) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up libcurl4t64:arm64 (8.12.1-2) ... Setting up libkdb5-10t64:arm64 (1.21.3-4) ... Setting up python3-typeguard (4.4.1-1) ... Setting up libcurl3t64-gnutls:arm64 (8.12.1-2) ... Setting up debhelper (13.24.1) ... Setting up dh-exec (0.30+b1) ... Setting up libngtcp2-crypto-gnutls-dev:arm64 (1.9.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libkadm5srv-mit12:arm64 (1.21.3-4) ... Setting up cmake (3.31.5-2) ... Setting up libhts3t64:arm64 (1.21+ds-1) ... Setting up krb5-multidev:arm64 (1.21.3-4) ... Setting up python3-pkg-resources (75.8.0-1) ... Setting up python3-setuptools (75.8.0-1) ... Setting up meson (1.7.0-1) ... Setting up samtools (1.21-1) ... Setting up libkrb5-dev:arm64 (1.21.3-4) ... Setting up libcurl4-gnutls-dev:arm64 (8.12.1-2) ... Setting up libhts-dev:arm64 (1.21+ds-1) ... Processing triggers for libc-bin (2.40-7) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps 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-1_source.changes dpkg-buildpackage: info: source package pbbam dpkg-buildpackage: info: source version 2.4.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille 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: 1.7.0 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 14.2.0 "cc (Debian 14.2.0-16) 14.2.0") C linker for the host machine: cc ld.bfd 2.44 C++ compiler for the host machine: c++ (gcc 14.2.0 "c++ (Debian 14.2.0-16) 14.2.0") C++ linker for the host machine: c++ ld.bfd 2.44 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/include) Run-time dependency zlib found: YES 1.3.1 Run-time dependency htslib found: YES 1.21 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 1.15.0 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/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=*' [2/226] /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=*' [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++ -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 [5/226] 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 [6/226] 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 [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_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 [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_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 [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_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 [10/226] 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 [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_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 [12/226] 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 [13/226] 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 src/libpbbam.so.2.4.0.p/BamFile.cpp.o.d -o src/libpbbam.so.2.4.0.p/BamFile.cpp.o -c ../src/BamFile.cpp [14/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude 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-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/FastaCache.cpp.o -MF src/libpbbam.so.2.4.0.p/FastaCache.cpp.o.d -o src/libpbbam.so.2.4.0.p/FastaCache.cpp.o -c ../src/FastaCache.cpp [48/226] 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()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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src/libpbbam.so.2.4.0.p/IFastqWriter.cpp.o -c ../src/IFastqWriter.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/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 [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/FastqReader.cpp.o -MF src/libpbbam.so.2.4.0.p/FastqReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/FastqReader.cpp.o -c ../src/FastqReader.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/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 [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/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 [61/226] 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 [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/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 [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/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++/14/map:62, 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++/14/bits/stl_tree.h:1796:25, 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++/14/bits/stl_map.h:331:7, 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++/14/bits/stl_tree.h:442:11: warning: array subscript 25 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 442 | : _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++/14/bits/stl_tree.h:1796:25, 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++/14/bits/stl_map.h:331:7, 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++/14/bits/stl_tree.h:442:35: warning: array subscript 27 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 442 | : _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++/14/bits/stl_tree.h:1797:20, 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++/14/bits/stl_map.h:331:7, 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++/14/bits/stl_tree.h:204:27: warning: array subscript 4 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 204 | _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++/14/bits/stl_tree.h:1797:20, 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++/14/bits/stl_map.h:331:7, 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++/14/bits/stl_tree.h:205:27: warning: array subscript 4 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 205 | _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++/14/bits/stl_tree.h:1797:20, 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++/14/bits/stl_map.h:331:7, 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++/14/bits/stl_tree.h:205:25: warning: array subscript 4 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 205 | _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++/14/bits/stl_tree.h:1797:20, 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++/14/bits/stl_map.h:331:7, 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++/14/bits/stl_tree.h:206:26: warning: array subscript 4 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 206 | _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++/14/bits/stl_tree.h:1797:20, 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++/14/bits/stl_map.h:331:7, 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++/14/bits/stl_tree.h:207:21: warning: array subscript 4 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 207 | _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_node<_Val>* 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++/14/bits/stl_tree.h:1800:38, 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++/14/bits/stl_map.h:331:7, 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++/14/bits/stl_tree.h:889:25: warning: array subscript 26 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 889 | _M_leftmost() = _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_node<_Val>* 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++/14/bits/stl_tree.h:1800:38, 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++/14/bits/stl_map.h:331:7, 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++/14/bits/stl_tree.h:890:26: warning: array subscript 27 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 890 | _M_rightmost() = _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_node<_Val>* 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++/14/bits/stl_tree.h:1800:38, 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++/14/bits/stl_map.h:331:7, 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++/14/bits/stl_tree.h:891:33: warning: array subscript 3 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 891 | _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++/14/bits/stl_map.h:331:7, 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++/14/bits/stl_tree.h:1800:23: warning: array subscript 25 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 1800 | _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); | ^ [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/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 [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/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 [67/226] 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 [68/226] 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 [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/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 [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/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 [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/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 [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/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 [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 -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiFilterQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiFilterQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiFilterQuery.cpp.o -c ../src/PbiFilterQuery.cpp In file included from /usr/include/c++/14/memory:78, from /usr/include/pbcopper/data/FrameEncoders.h:8, from ../include/pbbam/ReadGroupInfo.h:9, from ../include/pbbam/BamHeader.h:7, from ../include/pbbam/BamFile.h:6, from ../include/pbbam/DataSet.h:6, from ../include/pbbam/PbiFilter.h:6, from ../include/pbbam/PbiFilterQuery.h:6, from ../src/PbiFilterQuery.cpp:3: In destructor ‘std::unique_ptr<_Tp, _Dp>::~unique_ptr() [with _Tp = PacBio::BAM::internal::FilterWrapper::WrapperInterface; _Dp = std::default_delete]’, inlined from ‘PacBio::BAM::internal::FilterWrapper::~FilterWrapper()’ at ../include/pbbam/internal/PbiFilter.inl:38:8, inlined from ‘constexpr void std::destroy_at(_Tp*) [with _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/14/bits/stl_construct.h:88:18, inlined from ‘constexpr void std::_Destroy(_Tp*) [with _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/14/bits/stl_construct.h:149:22, inlined from ‘static constexpr void std::_Destroy_aux< >::__destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; bool = false]’ at /usr/include/c++/14/bits/stl_construct.h:163:19, inlined from ‘constexpr void std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_construct.h:196:11, inlined from ‘constexpr void std::_Destroy(_ForwardIterator, _ForwardIterator, allocator<_T2>&) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/14/bits/alloc_traits.h:993:20, inlined from ‘constexpr std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = PacBio::BAM::internal::FilterWrapper; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:250:21, inlined from ‘std::unique_ptr PacBio::BAM::internal::PbiFilterPrivate::DeepCopy()’ at ../include/pbbam/internal/PbiFilter.inl:143:32, inlined from ‘PacBio::BAM::PbiFilter::PbiFilter(const PacBio::BAM::PbiFilter&)’ at ../include/pbbam/internal/PbiFilter.inl:199:55, inlined from ‘PacBio::BAM::PbiFilterCompositeBamReader& PacBio::BAM::PbiFilterCompositeBamReader::Filter(const PacBio::BAM::PbiFilter&) [with OrderByType = PacBio::BAM::Compare::None]’ at ../include/pbbam/internal/CompositeBamReader.inl:147:17: /usr/include/c++/14/bits/unique_ptr.h:398:19: warning: potential null pointer dereference [-Wnull-dereference] 398 | if (__ptr != nullptr) | ~~~~~~^~~~~~~~~~ [77/226] 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 [78/226] 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/PbiBuilderBase.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiBuilderBase.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiBuilderBase.cpp.o -c ../src/PbiBuilderBase.cpp [79/226] 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/PbiIndexedBamReader.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiIndexedBamReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiIndexedBamReader.cpp.o -c ../src/PbiIndexedBamReader.cpp In file included from /usr/include/c++/14/memory:78, from /usr/include/pbcopper/data/FrameEncoders.h:8, from ../include/pbbam/ReadGroupInfo.h:9, from ../include/pbbam/BamHeader.h:7, from ../include/pbbam/BamFile.h:6, from ../include/pbbam/PbiIndexedBamReader.h:6, from ../src/PbiIndexedBamReader.cpp:3: In destructor ‘std::unique_ptr<_Tp, _Dp>::~unique_ptr() [with _Tp = PacBio::BAM::internal::FilterWrapper::WrapperInterface; _Dp = std::default_delete]’, inlined from ‘PacBio::BAM::internal::FilterWrapper::~FilterWrapper()’ at ../include/pbbam/internal/PbiFilter.inl:38:8, inlined from ‘constexpr void std::destroy_at(_Tp*) [with _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/14/bits/stl_construct.h:88:18, inlined from ‘constexpr void std::_Destroy(_Tp*) [with _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/14/bits/stl_construct.h:149:22, inlined from ‘static constexpr void std::_Destroy_aux< >::__destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; bool = false]’ at /usr/include/c++/14/bits/stl_construct.h:163:19, inlined from ‘constexpr void std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_construct.h:196:11, inlined from ‘constexpr void std::_Destroy(_ForwardIterator, _ForwardIterator, allocator<_T2>&) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/14/bits/alloc_traits.h:993:20, inlined from ‘constexpr std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = PacBio::BAM::internal::FilterWrapper; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:250:21, inlined from ‘std::unique_ptr PacBio::BAM::internal::PbiFilterPrivate::DeepCopy()’ at ../include/pbbam/internal/PbiFilter.inl:143:32, inlined from ‘PacBio::BAM::PbiFilter& PacBio::BAM::PbiFilter::operator=(const PacBio::BAM::PbiFilter&)’ at ../include/pbbam/internal/PbiFilter.inl:203:28, inlined from ‘void PacBio::BAM::PbiIndexedBamReader::PbiIndexedBamReaderPrivate::Filter(PacBio::BAM::PbiFilter)’ at ../src/PbiIndexedBamReader.cpp:36:35: /usr/include/c++/14/bits/unique_ptr.h:398:19: warning: potential null pointer dereference [-Wnull-dereference] 398 | if (__ptr != nullptr) | ~~~~~~^~~~~~~~~~ [80/226] 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/PbiRawData.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiRawData.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiRawData.cpp.o -c ../src/PbiRawData.cpp [81/226] 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/SequenceInfo.cpp.o -MF src/libpbbam.so.2.4.0.p/SequenceInfo.cpp.o.d -o src/libpbbam.so.2.4.0.p/SequenceInfo.cpp.o -c ../src/SequenceInfo.cpp [82/226] 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/SamWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/SamWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/SamWriter.cpp.o -c ../src/SamWriter.cpp [83/226] 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/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 [84/226] 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/StringUtilities.cpp.o -MF src/libpbbam.so.2.4.0.p/StringUtilities.cpp.o.d -o src/libpbbam.so.2.4.0.p/StringUtilities.cpp.o -c ../src/StringUtilities.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/RunMetadataParser.cpp.o -MF src/libpbbam.so.2.4.0.p/RunMetadataParser.cpp.o.d -o src/libpbbam.so.2.4.0.p/RunMetadataParser.cpp.o -c ../src/RunMetadataParser.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/TagCollection.cpp.o -MF src/libpbbam.so.2.4.0.p/TagCollection.cpp.o.d -o src/libpbbam.so.2.4.0.p/TagCollection.cpp.o -c ../src/TagCollection.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++/14/string:54, 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++/14/bits/basic_string.h:1247:7: note: declared here 1247 | 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 -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 [89/226] 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 [90/226] 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/Version.cpp.o -MF src/libpbbam.so.2.4.0.p/Version.cpp.o.d -o src/libpbbam.so.2.4.0.p/Version.cpp.o -c ../src/Version.cpp [91/226] 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/ValidationException.cpp.o -MF src/libpbbam.so.2.4.0.p/ValidationException.cpp.o.d -o src/libpbbam.so.2.4.0.p/ValidationException.cpp.o -c ../src/ValidationException.cpp [92/226] 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/TimeUtils.cpp.o -MF src/libpbbam.so.2.4.0.p/TimeUtils.cpp.o.d -o src/libpbbam.so.2.4.0.p/TimeUtils.cpp.o -c ../src/TimeUtils.cpp [93/226] 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/TextFileWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/TextFileWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/TextFileWriter.cpp.o -c ../src/TextFileWriter.cpp [94/226] 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/VirtualRegion.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualRegion.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualRegion.cpp.o -c ../src/VirtualRegion.cpp [95/226] 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/PbiFilterTypes.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiFilterTypes.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiFilterTypes.cpp.o -c ../src/PbiFilterTypes.cpp [96/226] 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/VirtualRegionTypeMap.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualRegionTypeMap.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualRegionTypeMap.cpp.o -c ../src/VirtualRegionTypeMap.cpp [97/226] 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/ReadGroupInfo.cpp.o -MF src/libpbbam.so.2.4.0.p/ReadGroupInfo.cpp.o.d -o src/libpbbam.so.2.4.0.p/ReadGroupInfo.cpp.o -c ../src/ReadGroupInfo.cpp [98/226] 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/PbiFilter.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiFilter.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiFilter.cpp.o -c ../src/PbiFilter.cpp [99/226] 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/TextFileReader.cpp.o -MF src/libpbbam.so.2.4.0.p/TextFileReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/TextFileReader.cpp.o -c ../src/TextFileReader.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/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 [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/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 [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/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 [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/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 [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/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 [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/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 [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/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 [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/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 [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/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 [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/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 [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/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 [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/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 [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/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 [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/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 [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/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 [117/226] 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 [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/vcf_VcfHeader.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfHeader.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfHeader.cpp.o -c ../src/vcf/VcfHeader.cpp [119/226] 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 [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/ZmwQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwQuery.cpp.o -c ../src/ZmwQuery.cpp In file included from /usr/include/c++/14/memory:78, from /usr/include/pbcopper/data/FrameEncoders.h:8, from ../include/pbbam/ReadGroupInfo.h:9, from ../include/pbbam/BamHeader.h:7, from ../include/pbbam/BamFile.h:6, from ../include/pbbam/internal/QueryBase.h:6, from ../include/pbbam/ZmwQuery.h:6, from ../src/ZmwQuery.cpp:3: In destructor ‘std::unique_ptr<_Tp, _Dp>::~unique_ptr() [with _Tp = PacBio::BAM::internal::FilterWrapper::WrapperInterface; _Dp = std::default_delete]’, inlined from ‘PacBio::BAM::internal::FilterWrapper::~FilterWrapper()’ at ../include/pbbam/internal/PbiFilter.inl:38:8, inlined from ‘constexpr void std::destroy_at(_Tp*) [with _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/14/bits/stl_construct.h:88:18, inlined from ‘constexpr void std::_Destroy(_Tp*) [with _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/14/bits/stl_construct.h:149:22, inlined from ‘static constexpr void std::_Destroy_aux< >::__destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; bool = false]’ at /usr/include/c++/14/bits/stl_construct.h:163:19, inlined from ‘constexpr void std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_construct.h:196:11, inlined from ‘constexpr void std::_Destroy(_ForwardIterator, _ForwardIterator, allocator<_T2>&) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/14/bits/alloc_traits.h:993:20, inlined from ‘constexpr std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = PacBio::BAM::internal::FilterWrapper; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:250:21, inlined from ‘std::unique_ptr PacBio::BAM::internal::PbiFilterPrivate::DeepCopy()’ at ../include/pbbam/internal/PbiFilter.inl:143:32, inlined from ‘PacBio::BAM::PbiFilter::PbiFilter(const PacBio::BAM::PbiFilter&)’ at ../include/pbbam/internal/PbiFilter.inl:199:55, inlined from ‘PacBio::BAM::PbiFilterCompositeBamReader& PacBio::BAM::PbiFilterCompositeBamReader::Filter(const PacBio::BAM::PbiFilter&) [with OrderByType = PacBio::BAM::Compare::Zmw]’ at ../include/pbbam/internal/CompositeBamReader.inl:147:17: /usr/include/c++/14/bits/unique_ptr.h:398:19: warning: potential null pointer dereference [-Wnull-dereference] 398 | if (__ptr != nullptr) | ~~~~~~^~~~~~~~~~ [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/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 [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/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 [124/226] 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 [125/226] 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 [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/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 [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/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 [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/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 [130/226] 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_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 [131/226] 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_BgzipWriter.cpp.o -MF tests/pbbam_test.p/src_test_BgzipWriter.cpp.o.d -o tests/pbbam_test.p/src_test_BgzipWriter.cpp.o -c ../tests/src/test_BgzipWriter.cpp [132/226] 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_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 [133/226] 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 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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 [140/226] /usr/bin/meson --internal symbolextractor /build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu src/libpbbam.so.2.4.0 src/libpbbam.so.2.4.0 src/libpbbam.so.2.4.0.p/libpbbam.so.2.4.0.symbols [141/226] 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_Csv.cpp.o -MF 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tests/pbbam_test.p/src_test_ReadGroupInfo.cpp.o -c ../tests/src/test_ReadGroupInfo.cpp [170/226] 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_PacBioIndex.cpp.o -MF tests/pbbam_test.p/src_test_PacBioIndex.cpp.o.d -o tests/pbbam_test.p/src_test_PacBioIndex.cpp.o -c ../tests/src/test_PacBioIndex.cpp [171/226] 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 [172/226] 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++/14/ios:45, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, 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++/14/streambuf:326:49, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>& std::istreambuf_iterator<_CharT, _Traits>::operator++() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/14/bits/streambuf_iterator.h:173:17, 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++/14/bits/basic_string.tcc:182:6, 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++/14/bits/basic_string.h:770:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/14/streambuf:495:30: warning: potential null pointer dereference [-Wnull-dereference] 495 | 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++/14/streambuf:326:33, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>& std::istreambuf_iterator<_CharT, _Traits>::operator++() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/14/bits/streambuf_iterator.h:173:17, 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++/14/bits/basic_string.tcc:182:6, 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++/14/bits/basic_string.h:770:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/14/streambuf:492:30: warning: potential null pointer dereference [-Wnull-dereference] 492 | 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++/14/streambuf:326:33, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>& std::istreambuf_iterator<_CharT, _Traits>::operator++() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/14/bits/streambuf_iterator.h:173:17, 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++/14/bits/basic_string.tcc:209:6, 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++/14/bits/basic_string.h:770:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/14/streambuf:492:30: warning: null pointer dereference [-Wnull-dereference] 492 | 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++/14/streambuf:326:49, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>& std::istreambuf_iterator<_CharT, _Traits>::operator++() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/14/bits/streambuf_iterator.h:173:17, 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++/14/bits/basic_string.tcc:209:6, 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++/14/bits/basic_string.h:770:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/14/streambuf:495:30: warning: null pointer dereference [-Wnull-dereference] 495 | 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++/14/streambuf:329:17, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>& std::istreambuf_iterator<_CharT, _Traits>::operator++() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/14/bits/streambuf_iterator.h:173:17, 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++/14/bits/basic_string.tcc:209:6, 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++/14/bits/basic_string.h:770:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/14/streambuf:505:34: warning: null pointer dereference [-Wnull-dereference] 505 | gbump(int __n) { _M_in_cur += __n; } | ~~~~~~~~~~^~~~~~ [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_RunMetadata.cpp.o -MF tests/pbbam_test.p/src_test_RunMetadata.cpp.o.d -o tests/pbbam_test.p/src_test_RunMetadata.cpp.o -c ../tests/src/test_RunMetadata.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_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 [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_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 [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_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 [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_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 [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_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 [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_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 [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_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 [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_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 [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_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 [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_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 [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_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 [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_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 [189/226] 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 [190/226] 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 [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_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 [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_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 [193/226] 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 [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_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 [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/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 [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/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 [199/226] 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 [200/226] 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 [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_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 [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_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 [203/226] 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 [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_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 [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++ -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 [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++ -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,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu/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 [209/226] 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 [210/226] 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 [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,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu/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_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 [214/226] 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 [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++ -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 [217/226] 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,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu/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 [218/226] 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 [219/226] 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,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu/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 [220/226] 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 [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 In file included from /usr/include/c++/14/memory:78, from /usr/include/pbcopper/data/FrameEncoders.h:8, from ../include/pbbam/ReadGroupInfo.h:9, from ../include/pbbam/BamHeader.h:7, from ../include/pbbam/BamRecord.h:6, from ../include/pbbam/virtual/ZmwReadStitcher.h:6, from ../tests/src/test_ZmwReadStitcher.cpp:1: In destructor ‘std::unique_ptr<_Tp, _Dp>::~unique_ptr() [with _Tp = PacBio::BAM::internal::FilterWrapper::WrapperInterface; _Dp = std::default_delete]’, inlined from ‘PacBio::BAM::internal::FilterWrapper::~FilterWrapper()’ at ../include/pbbam/internal/PbiFilter.inl:38:8, inlined from ‘constexpr void std::destroy_at(_Tp*) [with _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/14/bits/stl_construct.h:88:18, inlined from ‘constexpr void std::_Destroy(_Tp*) [with _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/14/bits/stl_construct.h:149:22, inlined from ‘static constexpr void std::_Destroy_aux< >::__destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; bool = false]’ at /usr/include/c++/14/bits/stl_construct.h:163:19, inlined from ‘constexpr void std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_construct.h:196:11, inlined from ‘constexpr void std::_Destroy(_ForwardIterator, _ForwardIterator, allocator<_T2>&) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/14/bits/alloc_traits.h:993:20, inlined from ‘constexpr std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = PacBio::BAM::internal::FilterWrapper; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:250:21, inlined from ‘std::unique_ptr PacBio::BAM::internal::PbiFilterPrivate::DeepCopy()’ at ../include/pbbam/internal/PbiFilter.inl:143:32, inlined from ‘PacBio::BAM::PbiFilter::PbiFilter(const PacBio::BAM::PbiFilter&)’ at ../include/pbbam/internal/PbiFilter.inl:199:55, inlined from ‘virtual void BAM_ZmwReadStitcher_can_stitch_from_filtered_bams_Test::TestBody()’ at ../tests/src/test_ZmwReadStitcher.cpp:115:36: /usr/include/c++/14/bits/unique_ptr.h:398:19: warning: potential null pointer dereference [-Wnull-dereference] 398 | if (__ptr != nullptr) | ~~~~~~^~~~~~~~~~ [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,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu/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,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu/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 In file included from /usr/include/c++/14/memory:78, from /usr/include/pbcopper/logging/LogMessage.h:8, from /usr/include/pbcopper/logging/Logging.h:8, from /usr/include/pbcopper/cli2/Results.h:12, from ../tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.h:4, from ../tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp:1: In destructor ‘std::unique_ptr<_Tp, _Dp>::~unique_ptr() [with _Tp = PacBio::BAM::internal::FilterWrapper::WrapperInterface; _Dp = std::default_delete]’, inlined from ‘PacBio::BAM::internal::FilterWrapper::~FilterWrapper()’ at ../include/pbbam/internal/PbiFilter.inl:38:8, inlined from ‘constexpr void std::destroy_at(_Tp*) [with _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/14/bits/stl_construct.h:88:18, inlined from ‘constexpr void std::_Destroy(_Tp*) [with _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/14/bits/stl_construct.h:149:22, inlined from ‘static constexpr void std::_Destroy_aux< >::__destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; bool = false]’ at /usr/include/c++/14/bits/stl_construct.h:163:19, inlined from ‘constexpr void std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_construct.h:196:11, inlined from ‘constexpr void std::_Destroy(_ForwardIterator, _ForwardIterator, allocator<_T2>&) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/14/bits/alloc_traits.h:993:20, inlined from ‘constexpr std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = PacBio::BAM::internal::FilterWrapper; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/vector.tcc:250:21, inlined from ‘std::unique_ptr PacBio::BAM::internal::PbiFilterPrivate::DeepCopy()’ at ../include/pbbam/internal/PbiFilter.inl:143:32, inlined from ‘PacBio::BAM::PbiFilter::PbiFilter(const PacBio::BAM::PbiFilter&)’ at ../include/pbbam/internal/PbiFilter.inl:199:55, inlined from ‘std::__detail::__unique_ptr_t<_Tp> std::make_unique(_Args&& ...) [with _Tp = PacBio::BAM::PbiIndexedBamReader; _Args = {const PacBio::BAM::PbiFilter&, PacBio::BAM::BamFile}]’ at /usr/include/c++/14/bits/unique_ptr.h:1077:30: /usr/include/c++/14/bits/unique_ptr.h:398:19: warning: potential null pointer dereference [-Wnull-dereference] 398 | if (__ptr != nullptr) | ~~~~~~^~~~~~~~~~ [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,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu/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: 1.7.0 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 14.2.0 "cc (Debian 14.2.0-16) 14.2.0") C linker for the host machine: cc ld.bfd 2.44 C++ compiler for the host machine: c++ (gcc 14.2.0 "c++ (Debian 14.2.0-16) 14.2.0") C++ linker for the host machine: c++ ld.bfd 2.44 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 1.21 (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 1.15.0 (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/LibraryGitHash.h with a custom command [3/15] Generating src/PbbamGitHash.cpp 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' in '../pbbamtools_2.4.0+dfsg-1_arm64.deb'. dpkg-deb: building package 'pbbamtools-dbgsym' in '../pbbamtools-dbgsym_2.4.0+dfsg-1_arm64.deb'. dpkg-deb: building package 'libpbbam2.4.0' in '../libpbbam2.4.0_2.4.0+dfsg-1_arm64.deb'. dpkg-deb: building package 'libpbbam2.4.0-dbgsym' in '../libpbbam2.4.0-dbgsym_2.4.0+dfsg-1_arm64.deb'. dpkg-deb: building package 'libpbbam-dev' in '../libpbbam-dev_2.4.0+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../pbbam_2.4.0+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../pbbam_2.4.0+dfsg-1_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: including full 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/3083744 and its subdirectories I: Current time: Fri Feb 28 13:40:26 -12 2025 I: pbuilder-time-stamp: 1740793226 Sat Mar 1 01:40:29 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Sat Mar 1 01:40:29 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Sat Mar 1 01:46:35 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Sat Mar 1 01:46:35 UTC 2025 I: pbbam_2.4.0+dfsg-1_arm64.changes: Format: 1.8 Date: Wed, 08 Nov 2023 17:24:23 +0100 Source: pbbam Binary: libpbbam-dev libpbbam2.4.0 libpbbam2.4.0-dbgsym pbbamtools pbbamtools-dbgsym Architecture: arm64 Version: 2.4.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille 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 Changes: pbbam (2.4.0+dfsg-1) unstable; urgency=medium . * New upstream version * Bump SOVERSION as upstream does in any new version Checksums-Sha1: 8e624118e14b98541cae2a0064f29927ccd175bd 88072 libpbbam-dev_2.4.0+dfsg-1_arm64.deb fa19b9e38895b7f1f419457ef07973431fd404a9 17831192 libpbbam2.4.0-dbgsym_2.4.0+dfsg-1_arm64.deb f36bd541bef8e511ebaa6e8c390e293e23eca542 712680 libpbbam2.4.0_2.4.0+dfsg-1_arm64.deb 2273e2813ea2489cdc4fff5bef7f9cbf26947c9c 9591 pbbam_2.4.0+dfsg-1_arm64.buildinfo cfa5b15bf1e5ccb2be9ea78ff3ab0f79a45286a9 3068140 pbbamtools-dbgsym_2.4.0+dfsg-1_arm64.deb c6a4b2445dffd6146c57f0d646896056a095331c 119700 pbbamtools_2.4.0+dfsg-1_arm64.deb Checksums-Sha256: 738849e2c403b596d419e812f2d85cd5275cd469cb173d6987e12cae1986473a 88072 libpbbam-dev_2.4.0+dfsg-1_arm64.deb f6af32fbd2988ec7c9bcd486d1d8b204c1486ed9768345c775a6ff85f9e069b1 17831192 libpbbam2.4.0-dbgsym_2.4.0+dfsg-1_arm64.deb 10939e9e9d9ae65b06e536773fc66dbfc9982d259e2be87394ca36bbe484c0cc 712680 libpbbam2.4.0_2.4.0+dfsg-1_arm64.deb 611dfe8895085f46304a5f23559d211bd32ffb834bb328e9adcadca9470eb8fc 9591 pbbam_2.4.0+dfsg-1_arm64.buildinfo 13483378a96301246c298437f47fac8383a5fbcac9788e02ba31039c0cf127d5 3068140 pbbamtools-dbgsym_2.4.0+dfsg-1_arm64.deb d9489cf72a2700f5c70338dc967504a43017f4ba911fe31cdbb60df7e427d681 119700 pbbamtools_2.4.0+dfsg-1_arm64.deb Files: bd3f6cd6c7c89bc77c41155bd3753cbe 88072 libdevel optional libpbbam-dev_2.4.0+dfsg-1_arm64.deb 6c5a01fa948a11a4efc65c02890560f1 17831192 debug optional libpbbam2.4.0-dbgsym_2.4.0+dfsg-1_arm64.deb 5574616f1df08890388d25737798c8c3 712680 libs optional libpbbam2.4.0_2.4.0+dfsg-1_arm64.deb 93e75d2ea1bfc2318a4ed84824ed9121 9591 science optional pbbam_2.4.0+dfsg-1_arm64.buildinfo db8ccec109233e37e62d489bfe42eee7 3068140 debug optional pbbamtools-dbgsym_2.4.0+dfsg-1_arm64.deb a35bf638d6f2f6eec976ff47655a5e68 119700 science optional pbbamtools_2.4.0+dfsg-1_arm64.deb Sat Mar 1 01:46:36 UTC 2025 I: diffoscope 289 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_7-59158.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.9o4blbWp/pbbam_2.4.0+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.9o4blbWp/pbbam_2.4.0+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.9o4blbWp/pbbam_2.4.0+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.9o4blbWp/b1/pbbam_2.4.0+dfsg-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.9o4blbWp/b2/pbbam_2.4.0+dfsg-1_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 Service runtime: 219ms CPU time consumed: 220ms Sat Mar 1 01:46:37 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists. Sat Mar 1 01:46:37 UTC 2025 I: pbbam from trixie built successfully and reproducibly on arm64. Sat Mar 1 01:46:39 UTC 2025 I: Submitting .buildinfo files to external archives: Sat Mar 1 01:46:39 UTC 2025 I: Submitting 12K b1/pbbam_2.4.0+dfsg-1_arm64.buildinfo.asc Sat Mar 1 01:46:39 UTC 2025 I: Submitting 12K b2/pbbam_2.4.0+dfsg-1_arm64.buildinfo.asc Sat Mar 1 01:46:40 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Mar 1 01:46:40 UTC 2025 I: Done submitting .buildinfo files. Sat Mar 1 01:46:40 UTC 2025 I: Removing signed pbbam_2.4.0+dfsg-1_arm64.buildinfo.asc files: removed './b1/pbbam_2.4.0+dfsg-1_arm64.buildinfo.asc' removed './b2/pbbam_2.4.0+dfsg-1_arm64.buildinfo.asc'