I: pbuilder: network access will be disabled during build I: Current time: Fri Jun 6 22:23:59 +14 2025 I: pbuilder-time-stamp: 1749198239 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 gpgv: Signature made Wed Nov 8 18:23:00 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./pbbam_2.4.0+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting pbbam in pbbam-2.4.0+dfsg dpkg-source: info: unpacking pbbam_2.4.0+dfsg.orig.tar.xz dpkg-source: info: unpacking pbbam_2.4.0+dfsg-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/2449465/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 6 08:24 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2449465/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2449465/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=ae596f662fa54648a96cbcbcd067fe7f LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2449465 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.L00M3GwF/pbuilderrc_1S2G --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.L00M3GwF/b2 --logfile b2/build.log pbbam_2.4.0+dfsg-1.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 5 14:06 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2449465/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: amd64 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 ... 19695 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} 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} libarchive-zip-perl{a} libarchive13t64{a} libboost-dev{a} libboost1.83-dev{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libgtest-dev{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libpbcopper-dev{a} libpbcopper2.3.0{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libssl-dev{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} meson{a} netbase{a} ninja-build{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-cram{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-setuptools{a} python3.11{a} python3.11-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: ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 97 newly installed, 0 to remove and 0 not upgraded. Need to get 64.3 MB of archives. After unpacking 372 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.2-2 [346 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 39 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.7.1-5 [441 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 librhash0 amd64 1.4.3-3+b1 [132 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-1.1 [147 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.29.2-2 [2167 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.29.2-2 [10.7 MB] Get: 54 http://deb.debian.org/debian unstable/main amd64 d-shlibs all 0.106 [10.9 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 62 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 dh-exec amd64 0.29 [25.4 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 googletest all 1.14.0-1 [512 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-2.1+b1 [10.6 MB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 72 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.7.1-5 [433 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.7.1-5 [538 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.20-1 [54.5 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libgtest-dev amd64 1.14.0-1+b1 [250 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.1+really5.4.5-1 [293 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.19+ds-1.1+b1 [1667 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.4+20240414-1 [104 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libpbcopper2.3.0 amd64 2.3.0+dfsg-2 [740 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libpbcopper-dev amd64 2.3.0+dfsg-2 [1071 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-1+b2 [36.4 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.2.1-3 [2699 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 ninja-build amd64 1.11.1-2 [142 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 meson all 1.4.0-2 [603 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-1+b2 [14.0 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 python3-cram all 0.7-5 [17.6 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.19.2-1+b1 [645 kB] Fetched 64.3 MB in 1s (53.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19695 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... 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 ... 20011 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... 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Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Jun 6 08:25:12 UTC 2025. Universal Time is now: Fri Jun 6 08:25:12 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:amd64 (1.8.1-1+b2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libncurses6:amd64 (6.4+20240414-1) ... Setting up libproc2-0:amd64 (2:4.0.4-4) ... Setting up libssl-dev:amd64 (3.2.1-3) ... Setting up autopoint (0.21-14) ... Setting up libjsoncpp25:amd64 (1.9.5-6+b2) ... Setting up d-shlibs (0.106) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:amd64 (5.6.1+really5.4.5-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2449465/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/2449465/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/pbbam-2.4.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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 amd64 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-x86_64-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/x86_64-linux-gnu -Dpython.bytecompile=-1 The Meson build system Version: 1.4.0 Source dir: /build/reproducible-path/pbbam-2.4.0+dfsg Build dir: /build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu Build type: native build Project name: PacBioBAM Project version: 2.4.0 C compiler for the host machine: cc (gcc 13.2.0 "cc (Debian 13.2.0-24) 13.2.0") C linker for the host machine: cc ld.bfd 2.42 C++ compiler for the host machine: c++ (gcc 13.2.0 "c++ (Debian 13.2.0-24) 13.2.0") C++ linker for the host machine: c++ ld.bfd 2.42 Host machine cpu family: x86_64 Host machine cpu: x86_64 Compiler for C++ supports arguments -Wduplicated-cond: YES Compiler for C++ supports arguments -Wduplicated-branches: YES Compiler for C++ supports arguments -Wlogical-op: YES Compiler for C++ supports arguments -Wrestrict: YES Compiler for C++ supports arguments -Wnull-dereference: YES Compiler for C++ supports arguments -Wuseless-cast: YES Compiler for C++ supports arguments -Wdouble-promotion: YES Compiler for C++ supports arguments -Wshadow: YES Compiler for C++ supports arguments -Wformat=1: YES Run-time dependency threads found: YES Found pkg-config: 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 Run-time dependency htslib found: YES 1.19 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 1.14.0 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/x86_64-linux-gnu localstatedir : /var prefix : /usr sysconfdir : /etc wrap_mode : nodownload python.bytecompile: -1 Found ninja-1.11.1 at /usr/bin/ninja dh_auto_build -O--buildsystem=meson cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j42 -v [1/226] /usr/bin/meson --internal vcstagger ../src/LibraryGitHash.h.in src/LibraryGitHash.h 2.4.0 /build/reproducible-path/pbbam-2.4.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' git describe --always '--dirty=*' [2/226] /usr/bin/meson --internal vcstagger ../src/PbbamGitHash.cpp.in src/PbbamGitHash.cpp 2.4.0 /build/reproducible-path/pbbam-2.4.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' git describe --always '--dirty=*' [3/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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-ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_FastaSequence.cpp.o -MF tests/pbbam_test.p/src_test_FastaSequence.cpp.o.d -o tests/pbbam_test.p/src_test_FastaSequence.cpp.o -c ../tests/src/test_FastaSequence.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 -fcf-protection -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_FastqSequence.cpp.o -MF tests/pbbam_test.p/src_test_FastqSequence.cpp.o.d -o tests/pbbam_test.p/src_test_FastqSequence.cpp.o -c ../tests/src/test_FastqSequence.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 -fcf-protection -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_FastaCache.cpp.o -MF 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-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 -fcf-protection -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 [10/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_FaiZmwChunker.cpp.o -MF tests/pbbam_test.p/src_test_FaiZmwChunker.cpp.o.d -o tests/pbbam_test.p/src_test_FaiZmwChunker.cpp.o -c ../tests/src/test_FaiZmwChunker.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 -fcf-protection -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_BgzipFastaWriter.cpp.o -MF tests/pbbam_test.p/src_test_BgzipFastaWriter.cpp.o.d -o tests/pbbam_test.p/src_test_BgzipFastaWriter.cpp.o -c ../tests/src/test_BgzipFastaWriter.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 -fcf-protection -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 [13/226] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_DataSetGenomicIntervals.cpp.o -MF tests/pbbam_test.p/src_test_DataSetGenomicIntervals.cpp.o.d -o tests/pbbam_test.p/src_test_DataSetGenomicIntervals.cpp.o -c ../tests/src/test_DataSetGenomicIntervals.cpp [14/226] 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 -fcf-protection -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 [15/226] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond 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-Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/BgzipFastaWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/BgzipFastaWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/BgzipFastaWriter.cpp.o -c ../src/BgzipFastaWriter.cpp [49/226] 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 -fcf-protection -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/FaiIndex.cpp.o -MF src/libpbbam.so.2.4.0.p/FaiIndex.cpp.o.d -o src/libpbbam.so.2.4.0.p/FaiIndex.cpp.o -c ../src/FaiIndex.cpp [50/226] 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 -fcf-protection -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/BamRecordTags.cpp.o -MF src/libpbbam.so.2.4.0.p/BamRecordTags.cpp.o.d -o src/libpbbam.so.2.4.0.p/BamRecordTags.cpp.o -c ../src/BamRecordTags.cpp [51/226] 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 -fcf-protection -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/FileProducer.cpp.o -MF src/libpbbam.so.2.4.0.p/FileProducer.cpp.o.d -o src/libpbbam.so.2.4.0.p/FileProducer.cpp.o -c ../src/FileProducer.cpp [52/226] 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 -fcf-protection -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/DataSetXsd.cpp.o -MF src/libpbbam.so.2.4.0.p/DataSetXsd.cpp.o.d -o src/libpbbam.so.2.4.0.p/DataSetXsd.cpp.o -c ../src/DataSetXsd.cpp [53/226] 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 -fcf-protection -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/BgzipFastqWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/BgzipFastqWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/BgzipFastqWriter.cpp.o -c ../src/BgzipFastqWriter.cpp [54/226] 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 -fcf-protection -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/BamFileMerger.cpp.o -MF src/libpbbam.so.2.4.0.p/BamFileMerger.cpp.o.d -o src/libpbbam.so.2.4.0.p/BamFileMerger.cpp.o -c ../src/BamFileMerger.cpp [55/226] 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 -fcf-protection -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/FastaSequence.cpp.o -MF src/libpbbam.so.2.4.0.p/FastaSequence.cpp.o.d -o src/libpbbam.so.2.4.0.p/FastaSequence.cpp.o -c ../src/FastaSequence.cpp [56/226] 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 -fcf-protection -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 [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 -fcf-protection -Wdate-time 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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 [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 -fcf-protection -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 [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 -fcf-protection -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 [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 -fcf-protection -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 -fcf-protection -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 [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 -fcf-protection -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 [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 -fcf-protection -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 [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 -fcf-protection -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/DataSet.cpp.o -MF src/libpbbam.so.2.4.0.p/DataSet.cpp.o.d -o src/libpbbam.so.2.4.0.p/DataSet.cpp.o -c ../src/DataSet.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 -fcf-protection -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 [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 -fcf-protection -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 [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 -fcf-protection -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 [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 -fcf-protection -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++/13/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++/13/bits/basic_string.h:1236:7: note: declared here 1236 | operator[] (size_type __pos) const _GLIBCXX_NOEXCEPT | ^~~~~~~~ [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 -fcf-protection -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 [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 -fcf-protection -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 [119/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [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 -fcf-protection -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 [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 -fcf-protection -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 [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 -fcf-protection -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++/13/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++/13/bits/stl_tree.h:1800:25, 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++/13/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++/13/bits/stl_tree.h:446:11: warning: array subscript 25 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 446 | : _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++/13/bits/stl_tree.h:1800:25, 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++/13/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++/13/bits/stl_tree.h:446:35: warning: array subscript 27 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 446 | : _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++/13/bits/stl_tree.h:1801:20, 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++/13/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++/13/bits/stl_tree.h:208:27: warning: array subscript 4 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 208 | _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++/13/bits/stl_tree.h:1801:20, 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++/13/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++/13/bits/stl_tree.h:209:27: warning: array subscript 4 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 209 | _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++/13/bits/stl_tree.h:1801:20, 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++/13/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++/13/bits/stl_tree.h:209:25: warning: array subscript 4 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 209 | _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++/13/bits/stl_tree.h:1801:20, 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++/13/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++/13/bits/stl_tree.h:210:26: warning: array subscript 4 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 210 | _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++/13/bits/stl_tree.h:1801:20, 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++/13/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++/13/bits/stl_tree.h:211:21: warning: array subscript 4 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 211 | _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++/13/bits/stl_tree.h:1804:38, 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++/13/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++/13/bits/stl_tree.h:893:25: warning: array subscript 26 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 893 | _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++/13/bits/stl_tree.h:1804:38, 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++/13/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++/13/bits/stl_tree.h:894:26: warning: array subscript 27 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 894 | _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++/13/bits/stl_tree.h:1804:38, 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++/13/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++/13/bits/stl_tree.h:895:33: warning: array subscript 3 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 895 | _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++/13/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++/13/bits/stl_tree.h:1804:23: warning: array subscript 25 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 1804 | _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); | ^ [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 -fcf-protection -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 [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 -fcf-protection -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 [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 -fcf-protection -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 [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 -fcf-protection -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 [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 -fcf-protection -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 [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 -fcf-protection -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 [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 -fcf-protection -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 [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 -fcf-protection -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 [131/226] 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 -fcf-protection -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/BamRecord.cpp.o -MF src/libpbbam.so.2.4.0.p/BamRecord.cpp.o.d -o src/libpbbam.so.2.4.0.p/BamRecord.cpp.o -c ../src/BamRecord.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 -fcf-protection -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 [133/226] 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 -fcf-protection -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 [134/226] 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 -fcf-protection -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 [135/226] 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 -fcf-protection -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 [136/226] 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 -fcf-protection -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 [137/226] 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 -fcf-protection -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 [138/226] 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 -fcf-protection -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_BamRecordMapping.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordMapping.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordMapping.cpp.o -c ../tests/src/test_BamRecordMapping.cpp [139/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_Compare.cpp.o -MF tests/pbbam_test.p/src_test_Compare.cpp.o.d -o tests/pbbam_test.p/src_test_Compare.cpp.o -c ../tests/src/test_Compare.cpp [140/226] 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 -fcf-protection -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 [141/226] 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 -fcf-protection -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 [142/226] 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 -fcf-protection -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 [143/226] 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 -fcf-protection -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 [144/226] 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 -fcf-protection -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 [145/226] 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 -fcf-protection -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 [146/226] 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 -fcf-protection -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 [147/226] 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 -fcf-protection -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_Pulse2BaseCache.cpp.o -MF tests/pbbam_test.p/src_test_Pulse2BaseCache.cpp.o.d -o tests/pbbam_test.p/src_test_Pulse2BaseCache.cpp.o -c ../tests/src/test_Pulse2BaseCache.cpp [148/226] 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 -fcf-protection -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 [149/226] 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 -fcf-protection -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 [150/226] 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 -fcf-protection -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 [151/226] 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 -fcf-protection -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 [152/226] 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 -fcf-protection -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_SequenceUtils.cpp.o -MF tests/pbbam_test.p/src_test_SequenceUtils.cpp.o.d -o tests/pbbam_test.p/src_test_SequenceUtils.cpp.o -c ../tests/src/test_SequenceUtils.cpp [153/226] /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-x86_64-linux-gnu/tests Generating test data in /build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu/tests - Creating file: truncated.bam...done. - Creating file: chunking_emptyfilters.subreadset.xml...done. - Creating file: chunking_missingfilters.subreadset.xml...done. - Creating file: normal.fa...done. - Creating file: normal.fq...done. - Creating symlink: aligned.bam...done. - Creating symlink: aligned.bam.bai...done. - Creating symlink: aligned.bam.pbi...done. - Creating symlink: aligned2.bam...done. - Creating symlink: aligned2.bam.bai...done. - Creating symlink: aligned2.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam.pbi...done. - Creating symlink: missing_pbi.bam...done. [154/226] 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 -fcf-protection -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 [155/226] 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 -fcf-protection -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_StringUtils.cpp.o -MF tests/pbbam_test.p/src_test_StringUtils.cpp.o.d -o tests/pbbam_test.p/src_test_StringUtils.cpp.o -c ../tests/src/test_StringUtils.cpp [156/226] 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 -fcf-protection -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 [157/226] 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 -fcf-protection -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 [158/226] 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 -fcf-protection -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 [159/226] 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 -fcf-protection -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 [160/226] 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 -fcf-protection -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 [161/226] 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 -fcf-protection -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 [162/226] 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 -fcf-protection -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_LongCigar.cpp.o -MF tests/pbbam_test.p/src_test_LongCigar.cpp.o.d -o tests/pbbam_test.p/src_test_LongCigar.cpp.o -c ../tests/src/test_LongCigar.cpp [163/226] 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 -fcf-protection -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 [164/226] 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 -fcf-protection -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 [165/226] 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 -fcf-protection -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 [166/226] 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 -fcf-protection -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 [167/226] 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 -fcf-protection -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_IndexedFastqReader.cpp.o -MF tests/pbbam_test.p/src_test_IndexedFastqReader.cpp.o.d -o tests/pbbam_test.p/src_test_IndexedFastqReader.cpp.o -c ../tests/src/test_IndexedFastqReader.cpp [168/226] 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 -fcf-protection -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 [169/226] 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 -fcf-protection -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 [170/226] 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 -fcf-protection -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 [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 -fcf-protection -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_IndexedFastaReader.cpp.o -MF tests/pbbam_test.p/src_test_IndexedFastaReader.cpp.o.d -o tests/pbbam_test.p/src_test_IndexedFastaReader.cpp.o -c ../tests/src/test_IndexedFastaReader.cpp [172/226] 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 -fcf-protection -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 [173/226] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libhts.so -pthread /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group [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 -fcf-protection -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_ReadGroupInfo.cpp.o -MF tests/pbbam_test.p/src_test_ReadGroupInfo.cpp.o.d -o tests/pbbam_test.p/src_test_ReadGroupInfo.cpp.o -c ../tests/src/test_ReadGroupInfo.cpp [175/226] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/pugixml_pugixml.cpp.o -MF src/libpbbam.so.2.4.0.p/pugixml_pugixml.cpp.o.d -o src/libpbbam.so.2.4.0.p/pugixml_pugixml.cpp.o -c ../src/pugixml/pugixml.cpp [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 -fcf-protection -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 [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 -fcf-protection -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 [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 -fcf-protection -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 [179/226] 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 -fcf-protection -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 [180/226] 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 -fcf-protection -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 [181/226] 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 -fcf-protection -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 [182/226] 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 -fcf-protection -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 [183/226] 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 -fcf-protection -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 [184/226] 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 -fcf-protection -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 [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 -fcf-protection -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 [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 -fcf-protection -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 [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 -fcf-protection -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++/13/ios:45, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/bits/basic_string.h:765:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/bits/basic_string.h:765:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/13/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>::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++/13/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++/13/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++/13/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++/13/bits/basic_string.h:765:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/bits/basic_string.h:765:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/13/streambuf:492:30: warning: potential null pointer dereference [-Wnull-dereference] 492 | gptr() const { return _M_in_cur; } | ^~~~~~~~~ [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 -fcf-protection -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 [189/226] c++ -o src/libpbbam.so.2.4.0 src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamGitHash.cpp.o src/libpbbam.so.2.4.0.p/AlignmentPrinter.cpp.o src/libpbbam.so.2.4.0.p/BaiIndexCache.cpp.o src/libpbbam.so.2.4.0.p/BaiIndexedBamReader.cpp.o src/libpbbam.so.2.4.0.p/BamFile.cpp.o src/libpbbam.so.2.4.0.p/BamFileMerger.cpp.o src/libpbbam.so.2.4.0.p/BamHeader.cpp.o src/libpbbam.so.2.4.0.p/BamReader.cpp.o src/libpbbam.so.2.4.0.p/BamRecord.cpp.o src/libpbbam.so.2.4.0.p/BamRecordImpl.cpp.o src/libpbbam.so.2.4.0.p/BamRecordTags.cpp.o src/libpbbam.so.2.4.0.p/BamRecordView.cpp.o src/libpbbam.so.2.4.0.p/BamTagCodec.cpp.o src/libpbbam.so.2.4.0.p/BamWriter.cpp.o src/libpbbam.so.2.4.0.p/BgzipFastaWriter.cpp.o src/libpbbam.so.2.4.0.p/BgzipFastqWriter.cpp.o src/libpbbam.so.2.4.0.p/BgzipWriter.cpp.o src/libpbbam.so.2.4.0.p/ChemistryTable.cpp.o src/libpbbam.so.2.4.0.p/CollectionMetadata.cpp.o src/libpbbam.so.2.4.0.p/Compare.cpp.o src/libpbbam.so.2.4.0.p/CompositeBamReader.cpp.o src/libpbbam.so.2.4.0.p/CompositeFastaReader.cpp.o src/libpbbam.so.2.4.0.p/Config.cpp.o src/libpbbam.so.2.4.0.p/DataSet.cpp.o src/libpbbam.so.2.4.0.p/DataSetBaseTypes.cpp.o src/libpbbam.so.2.4.0.p/DataSetElement.cpp.o src/libpbbam.so.2.4.0.p/DataSetIO.cpp.o src/libpbbam.so.2.4.0.p/DataSetTypes.cpp.o src/libpbbam.so.2.4.0.p/DataSetXsd.cpp.o src/libpbbam.so.2.4.0.p/EntireFileQuery.cpp.o src/libpbbam.so.2.4.0.p/ErrnoReason.cpp.o src/libpbbam.so.2.4.0.p/FaiIndex.cpp.o src/libpbbam.so.2.4.0.p/FaiZmwChunker.cpp.o src/libpbbam.so.2.4.0.p/FastaCache.cpp.o src/libpbbam.so.2.4.0.p/FastaReader.cpp.o src/libpbbam.so.2.4.0.p/FastaSequence.cpp.o src/libpbbam.so.2.4.0.p/FastaSequenceQuery.cpp.o src/libpbbam.so.2.4.0.p/FastaWriter.cpp.o src/libpbbam.so.2.4.0.p/FastqReader.cpp.o src/libpbbam.so.2.4.0.p/FastqSequence.cpp.o src/libpbbam.so.2.4.0.p/FastqWriter.cpp.o src/libpbbam.so.2.4.0.p/FileProducer.cpp.o src/libpbbam.so.2.4.0.p/FileUtils.cpp.o src/libpbbam.so.2.4.0.p/FofnReader.cpp.o src/libpbbam.so.2.4.0.p/FormatUtils.cpp.o src/libpbbam.so.2.4.0.p/GenomicIntervalQuery.cpp.o src/libpbbam.so.2.4.0.p/IFastaWriter.cpp.o src/libpbbam.so.2.4.0.p/IFastqWriter.cpp.o src/libpbbam.so.2.4.0.p/IndexedBamWriter.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastaReader.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastqBgzfReader.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastqReader.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastqTextReader.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastqReaderImpl.cpp.o src/libpbbam.so.2.4.0.p/IRecordWriter.cpp.o src/libpbbam.so.2.4.0.p/KSeqReader.cpp.o src/libpbbam.so.2.4.0.p/LibraryInfo.cpp.o src/libpbbam.so.2.4.0.p/MD5.cpp.o src/libpbbam.so.2.4.0.p/MemoryUtils.cpp.o src/libpbbam.so.2.4.0.p/PbiBuilder.cpp.o src/libpbbam.so.2.4.0.p/PbiBuilderBase.cpp.o src/libpbbam.so.2.4.0.p/PbiFile.cpp.o src/libpbbam.so.2.4.0.p/PbiFilter.cpp.o src/libpbbam.so.2.4.0.p/PbiFilterQuery.cpp.o src/libpbbam.so.2.4.0.p/PbiFilterTypes.cpp.o src/libpbbam.so.2.4.0.p/PbiIndexedBamReader.cpp.o src/libpbbam.so.2.4.0.p/PbiIndexIO.cpp.o src/libpbbam.so.2.4.0.p/PbiRawData.cpp.o src/libpbbam.so.2.4.0.p/ProgramInfo.cpp.o src/libpbbam.so.2.4.0.p/ReadGroupInfo.cpp.o src/libpbbam.so.2.4.0.p/RecordType.cpp.o src/libpbbam.so.2.4.0.p/RunMetadata.cpp.o src/libpbbam.so.2.4.0.p/RunMetadataParser.cpp.o src/libpbbam.so.2.4.0.p/SamReader.cpp.o src/libpbbam.so.2.4.0.p/SamTagCodec.cpp.o src/libpbbam.so.2.4.0.p/SamWriter.cpp.o src/libpbbam.so.2.4.0.p/SequenceInfo.cpp.o src/libpbbam.so.2.4.0.p/StringUtilities.cpp.o src/libpbbam.so.2.4.0.p/Tag.cpp.o src/libpbbam.so.2.4.0.p/TagCollection.cpp.o src/libpbbam.so.2.4.0.p/TextFileReader.cpp.o src/libpbbam.so.2.4.0.p/TextFileWriter.cpp.o src/libpbbam.so.2.4.0.p/TimeUtils.cpp.o src/libpbbam.so.2.4.0.p/Validator.cpp.o src/libpbbam.so.2.4.0.p/ValidationErrors.cpp.o src/libpbbam.so.2.4.0.p/ValidationException.cpp.o src/libpbbam.so.2.4.0.p/Version.cpp.o src/libpbbam.so.2.4.0.p/VirtualZmwBamRecord.cpp.o src/libpbbam.so.2.4.0.p/VirtualZmwCompositeReader.cpp.o src/libpbbam.so.2.4.0.p/VirtualZmwReader.cpp.o src/libpbbam.so.2.4.0.p/VirtualRegion.cpp.o src/libpbbam.so.2.4.0.p/VirtualRegionTypeMap.cpp.o src/libpbbam.so.2.4.0.p/XmlReader.cpp.o src/libpbbam.so.2.4.0.p/XmlWriter.cpp.o src/libpbbam.so.2.4.0.p/WhitelistedZmwReadStitcher.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastaReader.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastqReader.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxBgzfReader.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxReaderImpl.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxTextReader.cpp.o src/libpbbam.so.2.4.0.p/ZmwGroupQuery.cpp.o src/libpbbam.so.2.4.0.p/ZmwReadStitcher.cpp.o src/libpbbam.so.2.4.0.p/ZmwQuery.cpp.o src/libpbbam.so.2.4.0.p/ZmwTypeMap.cpp.o src/libpbbam.so.2.4.0.p/bed_BedReader.cpp.o src/libpbbam.so.2.4.0.p/bed_BedWriter.cpp.o src/libpbbam.so.2.4.0.p/csv_CsvReader.cpp.o src/libpbbam.so.2.4.0.p/csv_CsvWriter.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfFile.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfFormat.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfHeader.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfHeaderTypes.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfQuery.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfReader.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfSort.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfVariant.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfWriter.cpp.o src/libpbbam.so.2.4.0.p/pugixml_pugixml.cpp.o src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamVersion.cpp.o -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,-soname,libpbbam.so.2.4.0 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wl,--start-group /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group [190/226] /usr/bin/meson --internal symbolextractor /build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-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 [191/226] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group [192/226] c++ -o tests/zero_byte_check/zero_byte_check tests/zero_byte_check/zero_byte_check.p/main.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group [193/226] 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 -fcf-protection -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 [194/226] 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 -fcf-protection -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 [195/226] 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 -fcf-protection -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 [196/226] 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 -fcf-protection -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 [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 -fcf-protection -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 [198/226] 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 -fcf-protection -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 [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 -fcf-protection -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 [200/226] 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 -fcf-protection -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 [201/226] 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 -fcf-protection -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 [202/226] 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 -fcf-protection -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 [203/226] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 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tests/pbbam_test.p/src_test_BamRecord.cpp.o -c ../tests/src/test_BamRecord.cpp ../tests/src/test_BamRecord.cpp: In member function ‘virtual void BAM_BamRecord_can_be_constructed_from_bamrecordimpl_Test::TestBody()’: ../tests/src/test_BamRecord.cpp:771:29: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 771 | BamRecord bam3(std::move(BamRecordTests::CreateBamImpl())); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/src/test_BamRecord.cpp:771:29: note: remove ‘std::move’ call ../tests/src/test_BamRecord.cpp:797:21: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 797 | bam4 = std::move(BamRecordTests::CreateBamImpl()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/src/test_BamRecord.cpp:797:21: note: remove ‘std::move’ call [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 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/usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group [208/226] 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 -fcf-protection -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 [209/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra 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-o tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -c ../tools/pbbamify/src/QueryLookup.cpp [212/226] 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 -fcf-protection -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 [213/226] 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 -fcf-protection -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 [214/226] 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 -fcf-protection -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 [215/226] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group [216/226] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast 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../tests/src/test_PbiFilterQuery.cpp [218/226] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [219/226] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group [220/226] 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 -fcf-protection -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 [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 -fcf-protection -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 In file included from ../tests/src/test_Tags.cpp:14: In function ‘testing::AssertionResult testing::internal::CmpHelperEQ(const char*, const char*, const T1&, const T2&) [with T1 = unsigned int; T2 = unsigned int]’, inlined from ‘static testing::AssertionResult testing::internal::EqHelper::Compare(const char*, const char*, const T1&, const T2&) [with T1 = unsigned int; T2 = unsigned int; typename std::enable_if<((! std::is_integral<_Tp>::value) || (! std::is_pointer<_Dp>::value))>::type* = 0]’ at /usr/include/gtest/gtest.h:1398:64, inlined from ‘virtual void BAM_Tag_can_describe_uint32_tag_Test::TestBody()’ at ../tests/src/test_Tags.cpp:391:5: /usr/include/gtest/gtest.h:1379:3: warning: ‘v2’ may be used uninitialized [-Wmaybe-uninitialized] 1379 | if (lhs == rhs) { | ^~ ../tests/src/test_Tags.cpp: In member function ‘virtual void BAM_Tag_can_describe_uint32_tag_Test::TestBody()’: ../tests/src/test_Tags.cpp:375:14: note: ‘v2’ was declared here 375 | uint32_t v2; | ^~ In function ‘testing::AssertionResult testing::internal::CmpHelperEQ(const char*, const char*, const T1&, const T2&) [with T1 = short unsigned int; T2 = short unsigned int]’, inlined from ‘static testing::AssertionResult testing::internal::EqHelper::Compare(const char*, const char*, const T1&, const T2&) [with T1 = short unsigned int; T2 = short unsigned int; typename std::enable_if<((! std::is_integral<_Tp>::value) || (! std::is_pointer<_Dp>::value))>::type* = 0]’ at /usr/include/gtest/gtest.h:1398:64, inlined from ‘virtual void BAM_Tag_can_describe_uint16_tag_Test::TestBody()’ at ../tests/src/test_Tags.cpp:343:5: /usr/include/gtest/gtest.h:1379:3: warning: ‘v2’ may be used uninitialized [-Wmaybe-uninitialized] 1379 | if (lhs == rhs) { | ^~ ../tests/src/test_Tags.cpp: In member function ‘virtual void BAM_Tag_can_describe_uint16_tag_Test::TestBody()’: ../tests/src/test_Tags.cpp:327:14: note: ‘v2’ was declared here 327 | uint16_t v2; | ^~ [222/226] 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 -fcf-protection -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 [223/226] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group [224/226] 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 -fcf-protection -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 [225/226] 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 -fcf-protection -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 [226/226] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/x86_64-linux-gnu/libgtest_main.a /usr/lib/x86_64-linux-gnu/libgtest.a /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group 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-x86_64-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/x86_64-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:/i/capture/the/path" 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-x86_64-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: 1.4.0 Source dir: /build/reproducible-path/pbbam-2.4.0+dfsg Build dir: /build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu Build type: native build Project name: PacBioBAM Project version: 2.4.0 C compiler for the host machine: cc (gcc 13.2.0 "cc (Debian 13.2.0-24) 13.2.0") C linker for the host machine: cc ld.bfd 2.42 C++ compiler for the host machine: c++ (gcc 13.2.0 "c++ (Debian 13.2.0-24) 13.2.0") C++ linker for the host machine: c++ ld.bfd 2.42 Host machine cpu family: x86_64 Host machine cpu: x86_64 Compiler for C++ supports arguments -Wduplicated-cond: YES (cached) Compiler for C++ supports arguments -Wduplicated-branches: YES (cached) Compiler for C++ supports arguments -Wlogical-op: YES (cached) Compiler for C++ supports arguments -Wrestrict: YES (cached) Compiler for C++ supports arguments -Wnull-dereference: YES (cached) Compiler for C++ supports arguments -Wuseless-cast: YES (cached) Compiler for C++ supports arguments -Wdouble-promotion: YES (cached) Compiler for C++ supports arguments -Wshadow: YES (cached) Compiler for C++ supports arguments -Wformat=1: YES (cached) Dependency threads found: YES unknown (cached) Dependency boost found: YES 1.83.0 (cached) Dependency zlib found: YES 1.3 (cached) Dependency htslib found: YES 1.19 (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 1.14.0 (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/x86_64-linux-gnu localstatedir : /var prefix : /usr sysconfdir : /etc wrap_mode : nodownload python.bytecompile: -1 Found ninja-1.11.1 at /usr/bin/ninja [1/15] Generating tests/pbbam_generate_data with a custom command [2/15] Generating src/PbbamGitHash.cpp with a custom command [3/14] Generating src/LibraryGitHash.h with a custom command [3/4] Installing files. Installing src/libpbbam.so.2.4.0 to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/lib/x86_64-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-x86_64-linux-gnu/meson-private/pbbam.pc to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/lib/x86_64-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/x86_64-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/x86_64-linux-gnu/pkgconfig \ debian/tmp/usr/lib/*/*.so Library package automatic movement utility --> libhts-dev package exists. --> libpbcopper-dev package exists. --> zlib1g-dev package exists. set -e install -d -m 755 debian/libpbbam-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libpbbam2.4.0/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libpbbam.so debian/libpbbam-dev/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libpbbam.so.2.4.0 debian/libpbbam2.4.0/usr/lib/x86_64-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/x86_64-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libpbbam-dev/usr/lib/x86_64-linux-gnu/pkgconfig find debian -name "lib*.la" -delete make[1]: Leaving directory '/build/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 dh_installdeb -O--buildsystem=meson dh_gencontrol -O--buildsystem=meson dh_md5sums -O--buildsystem=meson dh_builddeb -O--buildsystem=meson dpkg-deb: building package 'pbbamtools-dbgsym' in '../pbbamtools-dbgsym_2.4.0+dfsg-1_amd64.deb'. dpkg-deb: building package 'pbbamtools' in '../pbbamtools_2.4.0+dfsg-1_amd64.deb'. dpkg-deb: building package 'libpbbam2.4.0' in '../libpbbam2.4.0_2.4.0+dfsg-1_amd64.deb'. dpkg-deb: building package 'libpbbam2.4.0-dbgsym' in '../libpbbam2.4.0-dbgsym_2.4.0+dfsg-1_amd64.deb'. dpkg-deb: building package 'libpbbam-dev' in '../libpbbam-dev_2.4.0+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../pbbam_2.4.0+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../pbbam_2.4.0+dfsg-1_amd64.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: user script /srv/workspace/pbuilder/2449465/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2449465/tmp/hooks/B01_cleanup finished 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/2449465 and its subdirectories I: Current time: Fri Jun 6 22:27:12 +14 2025 I: pbuilder-time-stamp: 1749198432