Tue Apr 18 19:45:49 UTC 2023 I: starting to build pbbam/bookworm/amd64 on jenkins on '2023-04-18 19:45' Tue Apr 18 19:45:49 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_18/21809/console.log Tue Apr 18 19:45:49 UTC 2023 I: Downloading source for bookworm/pbbam=2.1.0+dfsg-2 --2023-04-18 19:45:50-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/pbbam/pbbam_2.1.0%2bdfsg-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2321 (2.3K) [text/prs.lines.tag] Saving to: ‘pbbam_2.1.0+dfsg-2.dsc’ 0K .. 100% 92.6M=0s 2023-04-18 19:45:50 (92.6 MB/s) - ‘pbbam_2.1.0+dfsg-2.dsc’ saved [2321/2321] Tue Apr 18 19:45:50 UTC 2023 I: pbbam_2.1.0+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: pbbam Binary: pbbamtools, libpbbam2.1.0, libpbbam-dev Architecture: any Version: 2.1.0+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://pbbam.readthedocs.org/en/latest/index.html Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/pbbam Vcs-Git: https://salsa.debian.org/med-team/pbbam.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@ Build-Depends: debhelper-compat (= 13), dh-exec, d-shlibs, meson, pkg-config, cmake, libboost-dev, zlib1g-dev, libssl-dev, libhts-dev, libpbcopper-dev (>= 1.8.0), python3-cram, libgtest-dev , samtools Package-List: libpbbam-dev deb libdevel optional arch=any libpbbam2.1.0 deb libs optional arch=any pbbamtools deb science optional arch=any Checksums-Sha1: ff295f4eb0f874f3e8166df0e86d75460a8391eb 7823140 pbbam_2.1.0+dfsg.orig.tar.xz ee3779ba4c671fdcaad91dfba9a06534e041d71b 8528 pbbam_2.1.0+dfsg-2.debian.tar.xz Checksums-Sha256: 86532b306ea9d34549ca2fd71ceab24b5f9352d74d32acb867a1116029602604 7823140 pbbam_2.1.0+dfsg.orig.tar.xz d15a35a63d30e6b59631b51800a8c8181e3024f0f285ec12f5136d491193c952 8528 pbbam_2.1.0+dfsg-2.debian.tar.xz Files: 5a5314ba5114fb1ec18d98bbc5513cfc 7823140 pbbam_2.1.0+dfsg.orig.tar.xz 1e8d6a4237860d0ae8c0abc59d25316c 8528 pbbam_2.1.0+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmM+oygRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEbEA//em0pX4VSI8U8mDfLcMBn+GJNLfkLLPs9 Gg2rPUu+ZSVTYCxQnb7vgHIRDXDW2Ux/zQNH2aA/04bs7IkOQeQbt2nOQ4VNDw8h x3V83sGcRwOTN8fQBio+56TRydrJ3EdXL4v3gUtM7zGLPiBvuAXV8V+af5Ud6sfa cCgqTC5XVIV5qSD0kQ1S4IacvxnfJVao485A0l1hNcx+hkUjlfaDzD/kYDISijMg ygvXISkf2IP9PkjhZN5nRSg31y0XRyWKg4T4sjyVOBgmi5Kc1d5aUR7YuCuNe0fJ L7/kaDTck7QDgSVpns6isfrdkZUzYR3IGj4+zAFMmW50S3VL+nrRg3/DwpVa7W7N xZsKU6WnErmKtICkyAsXaWi1895hhUiRCxLNPnyW0ZWgZXoy+c3XZeMJQKVjyOhJ zg+HYK5bwPm4lPcEozVTLY3xLFdCXGPCflOclzKcX5/I/Yt3NesE37QNCtxA8wzD MFMOuLWnWtmyOXIZet9qVyeMH1er9tvGXO7h9WE0auaOOHk9zL2PGLVVqbc+Ts4/ qJqPqTa3wDd8jENeFjGZqaZlkXk4hww65K6VRTNO7kMocCjz2/6LvN2/Y0Cnb+AA RynQoUhx/yGXPVUc29b+Stdm8nD7jFV4P2soU7TNcqQo+25hYc4c7YGnf2G1dPhP A4NgPZaz13Y= =GlF+ -----END PGP SIGNATURE----- Tue Apr 18 19:45:50 UTC 2023 I: Checking whether the package is not for us Tue Apr 18 19:45:50 UTC 2023 I: Starting 1st build on remote node ionos5-amd64.debian.net. Tue Apr 18 19:45:50 UTC 2023 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Tue Apr 18 19:49:59 UTC 2023 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon May 20 14:08:53 -12 2024 I: pbuilder-time-stamp: 1716257333 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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_2.1.0+dfsg-2.dsc] I: copying [./pbbam_2.1.0+dfsg.orig.tar.xz] I: copying [./pbbam_2.1.0+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Oct 5 21:43:04 2022 -12 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_2.1.0+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting pbbam in pbbam-2.1.0+dfsg dpkg-source: info: unpacking pbbam_2.1.0+dfsg.orig.tar.xz dpkg-source: info: unpacking pbbam_2.1.0+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_python3-cram.patch dpkg-source: info: applying python3.patch dpkg-source: info: applying results_with_latest_samtools.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1281860/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='9327fdc42c7a409ba33eb40237a24b2a' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1281860' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.MnqrMOK6/pbuilderrc_5j9R --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MnqrMOK6/b1 --logfile b1/build.log pbbam_2.1.0+dfsg-2.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos5-amd64 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Feb 12 2023 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 2023 more -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Feb 12 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/1281860/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 (>= 1.8.0), 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 ... 19596 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 (>= 1.8.0); 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} libarchive13{a} libboost-dev{a} libboost1.74-dev{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgtest-dev{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libjsoncpp25{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpbcopper-dev{a} libpbcopper2.0.0{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libssl-dev{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} m4{a} man-db{a} media-types{a} meson{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} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 89 newly installed, 0 to remove and 0 not upgraded. Need to get 58.9 MB of archives. After unpacking 334 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libarchive13 amd64 3.6.2-1 [343 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-8 [386 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libjsoncpp25 amd64 1.9.5-4 [78.6 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 librhash0 amd64 1.4.3-3 [134 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libuv1 amd64 1.44.2-1 [140 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 cmake-data all 3.25.1-1 [2026 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 cmake amd64 3.25.1-1 [8692 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 d-shlibs all 0.104 [18.6 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 dh-exec amd64 0.27 [27.8 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 googletest all 1.12.1-0.2 [506 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-20 [9510 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-8 [380 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libcurl4-gnutls-dev amd64 7.88.1-8 [481 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libdeflate-dev amd64 1.14-1 [53.3 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libgtest-dev amd64 1.12.1-0.2 [240 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 liblzma-dev amd64 5.4.1-0.2 [260 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libhts-dev amd64 1.16+ds-3 [1601 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-2 [103 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libpbcopper2.0.0 amd64 2.0.0+dfsg-2 [606 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libpbcopper-dev amd64 2.0.0+dfsg-2 [920 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libpkgconf3 amd64 1.8.1-1 [36.1 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libssl-dev amd64 3.0.8-1 [2427 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 ninja-build amd64 1.11.1-1 [136 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-2 [76.2 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-2 [131 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 meson all 1.0.1-5 [548 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 python3-cram all 0.7-5 [17.6 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 samtools amd64 1.16.1-1 [607 kB] Fetched 58.9 MB in 1s (76.4 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 ... 19596 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... 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 ... 19912 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20346 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../01-libproc2-0_2%3a4.0.2-3_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.2-3_amd64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../05-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../08-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../11-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../18-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../19-libxml2_2.9.14+dfsg-1.1+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.1+b3) ... Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../20-libarchive13_3.6.2-1_amd64.deb ... Unpacking libarchive13:amd64 (3.6.2-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../21-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../22-libsasl2-modules-db_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../23-libsasl2-2_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../24-libldap-2.5-0_2.5.13+dfsg-5_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../25-libnghttp2-14_1.52.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.52.0-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../26-libpsl5_0.21.2-1_amd64.deb ... Unpacking libpsl5:amd64 (0.21.2-1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../27-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../28-libssh2-1_1.10.0-3+b1_amd64.deb ... Unpacking libssh2-1:amd64 (1.10.0-3+b1) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../29-libcurl4_7.88.1-8_amd64.deb ... Unpacking libcurl4:amd64 (7.88.1-8) ... Selecting previously unselected package libjsoncpp25:amd64. Preparing to unpack .../30-libjsoncpp25_1.9.5-4_amd64.deb ... Unpacking libjsoncpp25:amd64 (1.9.5-4) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../31-librhash0_1.4.3-3_amd64.deb ... Unpacking librhash0:amd64 (1.4.3-3) ... Selecting previously unselected package libuv1:amd64. Preparing to unpack .../32-libuv1_1.44.2-1_amd64.deb ... Unpacking libuv1:amd64 (1.44.2-1) ... Selecting previously unselected package cmake-data. Preparing to unpack .../33-cmake-data_3.25.1-1_all.deb ... Unpacking cmake-data (3.25.1-1) ... Selecting previously unselected package cmake. Preparing to unpack .../34-cmake_3.25.1-1_amd64.deb ... Unpacking cmake (3.25.1-1) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../35-d-shlibs_0.104_all.deb ... Unpacking d-shlibs (0.104) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../36-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../37-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../38-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../39-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../40-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../41-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../42-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../43-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../44-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package gettext. Preparing to unpack .../45-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../46-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../47-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../48-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package dh-exec. Preparing to unpack .../49-dh-exec_0.27_amd64.deb ... Unpacking dh-exec (0.27) ... Selecting previously unselected package googletest. Preparing to unpack .../50-googletest_1.12.1-0.2_all.deb ... Unpacking googletest (1.12.1-0.2) ... Selecting previously unselected package libboost1.74-dev:amd64. Preparing to unpack .../51-libboost1.74-dev_1.74.0+ds1-20_amd64.deb ... Unpacking libboost1.74-dev:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-dev:amd64. Preparing to unpack .../52-libboost-dev_1.74.0.3_amd64.deb ... Unpacking libboost-dev:amd64 (1.74.0.3) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../53-libcurl3-gnutls_7.88.1-8_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.88.1-8) ... Selecting previously unselected package libcurl4-gnutls-dev:amd64. Preparing to unpack .../54-libcurl4-gnutls-dev_7.88.1-8_amd64.deb ... Unpacking libcurl4-gnutls-dev:amd64 (7.88.1-8) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../55-libdeflate0_1.14-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.14-1) ... Selecting previously unselected package libdeflate-dev:amd64. Preparing to unpack .../56-libdeflate-dev_1.14-1_amd64.deb ... Unpacking libdeflate-dev:amd64 (1.14-1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/pbbam-2.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pbbam_2.1.0+dfsg-2_source.changes dpkg-buildpackage: info: source package pbbam dpkg-buildpackage: info: source version 2.1.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=meson debian/rules override_dh_auto_clean make[1]: Entering directory '/build/pbbam-2.1.0+dfsg' dh_auto_clean find -name "*.deb.t" -delete rm -f -r /build/pbbam-2.1.0+dfsg/gendata make[1]: Leaving directory '/build/pbbam-2.1.0+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 && LC_ALL=C.UTF-8 meson setup .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-linux-gnu The Meson build system Version: 1.0.1 Source dir: /build/pbbam-2.1.0+dfsg Build dir: /build/pbbam-2.1.0+dfsg/obj-x86_64-linux-gnu Build type: native build Project name: PacBioBAM Project version: 2.1.0 C++ compiler for the host machine: c++ (gcc 12.2.0 "c++ (Debian 12.2.0-14) 12.2.0") C++ linker for the host machine: c++ ld.bfd 2.40 Host machine cpu family: x86_64 Host machine cpu: x86_64 Compiler for C++ supports arguments -Wduplicated-cond: YES Compiler for C++ supports arguments -Wduplicated-branches: YES Compiler for C++ supports arguments -Wlogical-op: YES Compiler for C++ supports arguments -Wrestrict: YES Compiler for C++ supports arguments -Wnull-dereference: YES Compiler for C++ supports arguments -Wuseless-cast: YES Compiler for C++ supports arguments -Wdouble-promotion: YES Compiler for C++ supports arguments -Wshadow: YES Compiler for C++ supports arguments -Wformat=1: YES Run-time dependency threads found: YES Found pkg-config: /usr/bin/pkg-config (1.8.1) Run-time dependency Boost found: YES 1.74.0 (/usr/include) Run-time dependency zlib found: YES 1.2.13 Run-time dependency htslib found: YES 1.16 Run-time dependency pbcopper found: YES 2.0.0 Configuring PbbamVersion.cpp using configuration Configuring LibraryVersion.h using configuration Program tools/check-formatting found: YES (/build/pbbam-2.1.0+dfsg/tools/check-formatting) Program python3 found: YES (/usr/bin/python3) Program cram3 found: YES (/usr/bin/cram3) Run-time dependency GTest found: YES 1.12.1 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 2.1.0 User defined options buildtype : plain libdir : lib/x86_64-linux-gnu localstatedir: /var prefix : /usr sysconfdir : /etc wrap_mode : nodownload 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 -j16 -v [1/224] /usr/bin/meson --internal vcstagger ../src/LibraryGitHash.h.in src/LibraryGitHash.h 2.1.0 /build/pbbam-2.1.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' git describe --always '--dirty=*' [2/224] /usr/bin/meson --internal vcstagger ../src/PbbamGitHash.cpp.in src/PbbamGitHash.cpp 2.1.0 /build/pbbam-2.1.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' git describe --always '--dirty=*' [3/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict 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-Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/CompositeBamReader.cpp.o -MF src/libpbbam.so.2.1.0.p/CompositeBamReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/CompositeBamReader.cpp.o -c ../src/CompositeBamReader.cpp [39/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/FaiZmwChunker.cpp.o -MF src/libpbbam.so.2.1.0.p/FaiZmwChunker.cpp.o.d -o src/libpbbam.so.2.1.0.p/FaiZmwChunker.cpp.o -c ../src/FaiZmwChunker.cpp [40/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/CollectionMetadata.cpp.o -MF src/libpbbam.so.2.1.0.p/CollectionMetadata.cpp.o.d -o src/libpbbam.so.2.1.0.p/CollectionMetadata.cpp.o -c ../src/CollectionMetadata.cpp [41/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/EntireFileQuery.cpp.o -MF src/libpbbam.so.2.1.0.p/EntireFileQuery.cpp.o.d -o src/libpbbam.so.2.1.0.p/EntireFileQuery.cpp.o -c ../src/EntireFileQuery.cpp [42/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/FastaSequence.cpp.o -MF src/libpbbam.so.2.1.0.p/FastaSequence.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastaSequence.cpp.o -c ../src/FastaSequence.cpp [43/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/DataSetBaseTypes.cpp.o -MF src/libpbbam.so.2.1.0.p/DataSetBaseTypes.cpp.o.d -o src/libpbbam.so.2.1.0.p/DataSetBaseTypes.cpp.o -c ../src/DataSetBaseTypes.cpp [44/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/FastqSequence.cpp.o -MF src/libpbbam.so.2.1.0.p/FastqSequence.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastqSequence.cpp.o -c ../src/FastqSequence.cpp [45/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_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 [46/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/FileProducer.cpp.o -MF src/libpbbam.so.2.1.0.p/FileProducer.cpp.o.d -o src/libpbbam.so.2.1.0.p/FileProducer.cpp.o -c ../src/FileProducer.cpp In file included from /usr/include/c++/12/string:40, from ../src/FileProducer.h:6, from ../src/FileProducer.cpp:3: In static member function ‘static constexpr std::char_traits::char_type* std::char_traits::copy(char_type*, const char_type*, std::size_t)’, inlined from ‘static constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:423:21, inlined from ‘static constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:418:7, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.tcc:532:22, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::assign(const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:1647:19, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:815:28, inlined from ‘PacBio::BAM::FileProducer::FileProducer(std::string, std::string)’ at ../src/FileProducer.cpp:29:25: /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets -4611686018427387902 and [-4611686018427387903, 4611686018427387904] may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ [47/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/DataSet.cpp.o -MF src/libpbbam.so.2.1.0.p/DataSet.cpp.o.d -o src/libpbbam.so.2.1.0.p/DataSet.cpp.o -c ../src/DataSet.cpp [48/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/FastaReader.cpp.o -MF src/libpbbam.so.2.1.0.p/FastaReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastaReader.cpp.o -c ../src/FastaReader.cpp [49/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/FastaCache.cpp.o -MF src/libpbbam.so.2.1.0.p/FastaCache.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastaCache.cpp.o -c ../src/FastaCache.cpp [50/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/FastaWriter.cpp.o -MF src/libpbbam.so.2.1.0.p/FastaWriter.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastaWriter.cpp.o -c ../src/FastaWriter.cpp [51/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/FastaSequenceQuery.cpp.o -MF src/libpbbam.so.2.1.0.p/FastaSequenceQuery.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastaSequenceQuery.cpp.o -c ../src/FastaSequenceQuery.cpp [52/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/BamRecord.cpp.o -MF src/libpbbam.so.2.1.0.p/BamRecord.cpp.o.d -o src/libpbbam.so.2.1.0.p/BamRecord.cpp.o -c ../src/BamRecord.cpp [53/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/FofnReader.cpp.o -MF src/libpbbam.so.2.1.0.p/FofnReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/FofnReader.cpp.o -c ../src/FofnReader.cpp [54/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/FormatUtils.cpp.o -MF src/libpbbam.so.2.1.0.p/FormatUtils.cpp.o.d -o src/libpbbam.so.2.1.0.p/FormatUtils.cpp.o -c ../src/FormatUtils.cpp [55/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/FileUtils.cpp.o -MF src/libpbbam.so.2.1.0.p/FileUtils.cpp.o.d -o src/libpbbam.so.2.1.0.p/FileUtils.cpp.o -c ../src/FileUtils.cpp In file included from /usr/include/c++/12/memory:76, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function.hpp:30, from /usr/include/boost/algorithm/string/detail/find_iterator.hpp:18, from /usr/include/boost/algorithm/string/find_iterator.hpp:24, from /usr/include/boost/algorithm/string/iter_find.hpp:27, from /usr/include/boost/algorithm/string/split.hpp:16, from /usr/include/boost/algorithm/string.hpp:23, from ../src/FileUtils.cpp:7: In member function ‘void std::default_delete<_Tp>::operator()(_Tp*) const [with _Tp = char]’, inlined from ‘std::unique_ptr<_Tp, _Dp>::~unique_ptr() [with _Tp = char; _Dp = std::default_delete]’ at /usr/include/c++/12/bits/unique_ptr.h:396:17, inlined from ‘static std::string PacBio::BAM::FileUtils::CurrentWorkingDirectory()’ at ../src/FileUtils.cpp:173:5: /usr/include/c++/12/bits/unique_ptr.h:95:9: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 95 | delete __ptr; | ^~~~~~~~~~~~ ../src/FileUtils.cpp: In static member function ‘static std::string PacBio::BAM::FileUtils::CurrentWorkingDirectory()’: ../src/FileUtils.cpp:163:62: note: returned from ‘void* operator new [](std::size_t)’ 163 | std::unique_ptr cwd(new char[chunkSize * chunks]); | ^ In member function ‘void std::default_delete<_Tp>::operator()(_Tp*) const [with _Tp = char]’, inlined from ‘std::unique_ptr<_Tp, _Dp>::~unique_ptr() [with _Tp = char; _Dp = std::default_delete]’ at /usr/include/c++/12/bits/unique_ptr.h:396:17, inlined from ‘static std::string PacBio::BAM::FileUtils::CurrentWorkingDirectory()’ at ../src/FileUtils.cpp:173:5: /usr/include/c++/12/bits/unique_ptr.h:95:9: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 95 | delete __ptr; | ^~~~~~~~~~~~ ../src/FileUtils.cpp: In static member function ‘static std::string PacBio::BAM::FileUtils::CurrentWorkingDirectory()’: ../src/FileUtils.cpp:163:62: note: returned from ‘void* operator new [](std::size_t)’ 163 | std::unique_ptr cwd(new char[chunkSize * chunks]); | ^ In member function ‘void std::default_delete<_Tp>::operator()(_Tp*) const [with _Tp = char]’, inlined from ‘std::unique_ptr<_Tp, _Dp>::~unique_ptr() [with _Tp = char; _Dp = std::default_delete]’ at /usr/include/c++/12/bits/unique_ptr.h:396:17, inlined from ‘static std::string PacBio::BAM::FileUtils::CurrentWorkingDirectory()’ at ../src/FileUtils.cpp:173:5: /usr/include/c++/12/bits/unique_ptr.h:95:9: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 95 | delete __ptr; | ^~~~~~~~~~~~ ../src/FileUtils.cpp: In static member function ‘static std::string PacBio::BAM::FileUtils::CurrentWorkingDirectory()’: ../src/FileUtils.cpp:163:62: note: returned from ‘void* operator new [](std::size_t)’ 163 | std::unique_ptr cwd(new char[chunkSize * chunks]); | ^ [56/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/FastqReader.cpp.o -MF src/libpbbam.so.2.1.0.p/FastqReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastqReader.cpp.o -c ../src/FastqReader.cpp [57/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/IndexedFastqBgzfReader.cpp.o -MF src/libpbbam.so.2.1.0.p/IndexedFastqBgzfReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/IndexedFastqBgzfReader.cpp.o -c ../src/IndexedFastqBgzfReader.cpp [58/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/FastqWriter.cpp.o -MF src/libpbbam.so.2.1.0.p/FastqWriter.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastqWriter.cpp.o -c ../src/FastqWriter.cpp [59/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/IndexedFastqReaderImpl.cpp.o -MF src/libpbbam.so.2.1.0.p/IndexedFastqReaderImpl.cpp.o.d -o src/libpbbam.so.2.1.0.p/IndexedFastqReaderImpl.cpp.o -c ../src/IndexedFastqReaderImpl.cpp [60/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/KSeqReader.cpp.o -MF src/libpbbam.so.2.1.0.p/KSeqReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/KSeqReader.cpp.o -c ../src/KSeqReader.cpp [61/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/IndexedFastqTextReader.cpp.o -MF src/libpbbam.so.2.1.0.p/IndexedFastqTextReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/IndexedFastqTextReader.cpp.o -c ../src/IndexedFastqTextReader.cpp [62/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/MD5.cpp.o -MF src/libpbbam.so.2.1.0.p/MD5.cpp.o.d -o src/libpbbam.so.2.1.0.p/MD5.cpp.o -c ../src/MD5.cpp [63/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/LibraryInfo.cpp.o -MF src/libpbbam.so.2.1.0.p/LibraryInfo.cpp.o.d -o src/libpbbam.so.2.1.0.p/LibraryInfo.cpp.o -c ../src/LibraryInfo.cpp [64/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/IFastaWriter.cpp.o -MF src/libpbbam.so.2.1.0.p/IFastaWriter.cpp.o.d -o src/libpbbam.so.2.1.0.p/IFastaWriter.cpp.o -c ../src/IFastaWriter.cpp [65/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/IFastqWriter.cpp.o -MF src/libpbbam.so.2.1.0.p/IFastqWriter.cpp.o.d -o src/libpbbam.so.2.1.0.p/IFastqWriter.cpp.o -c ../src/IFastqWriter.cpp [66/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/DataSetTypes.cpp.o -MF src/libpbbam.so.2.1.0.p/DataSetTypes.cpp.o.d -o src/libpbbam.so.2.1.0.p/DataSetTypes.cpp.o -c ../src/DataSetTypes.cpp In file included from /usr/include/c++/12/map:60, 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++/12/bits/stl_tree.h:1799:25, 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++/12/bits/stl_map.h:329:7, 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++/12/bits/stl_tree.h:444:11: warning: array subscript 25 is outside array bounds of ‘void [184]’ [-Warray-bounds] 444 | : _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++/12/bits/stl_tree.h:1799:25, 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++/12/bits/stl_map.h:329:7, 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++/12/bits/stl_tree.h:444:35: warning: array subscript 27 is outside array bounds of ‘void [184]’ [-Warray-bounds] 444 | : _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++/12/bits/stl_tree.h:1800:20, 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++/12/bits/stl_map.h:329:7, 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++/12/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++/12/bits/stl_tree.h:1800:20, 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++/12/bits/stl_map.h:329:7, 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++/12/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++/12/bits/stl_tree.h:1800:20, 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++/12/bits/stl_map.h:329:7, 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++/12/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++/12/bits/stl_tree.h:1800:20, 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++/12/bits/stl_map.h:329:7, 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++/12/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++/12/bits/stl_tree.h:1800:20, 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++/12/bits/stl_map.h:329:7, 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++/12/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++/12/bits/stl_tree.h:1803:38, 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++/12/bits/stl_map.h:329:7, 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++/12/bits/stl_tree.h:891:25: warning: array subscript 26 is outside array bounds of ‘void [184]’ [-Warray-bounds] 891 | _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++/12/bits/stl_tree.h:1803:38, 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++/12/bits/stl_map.h:329:7, 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++/12/bits/stl_tree.h:892:26: warning: array subscript 27 is outside array bounds of ‘void [184]’ [-Warray-bounds] 892 | _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++/12/bits/stl_tree.h:1803:38, 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++/12/bits/stl_map.h:329:7, 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++/12/bits/stl_tree.h:893:33: warning: array subscript 3 is outside array bounds of ‘void [184]’ [-Warray-bounds] 893 | _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++/12/bits/stl_map.h:329:7, 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++/12/bits/stl_tree.h:1803:23: warning: array subscript 25 is outside array bounds of ‘void [184]’ [-Warray-bounds] 1803 | _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); | ^ [67/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/GenomicIntervalQuery.cpp.o -MF src/libpbbam.so.2.1.0.p/GenomicIntervalQuery.cpp.o.d -o src/libpbbam.so.2.1.0.p/GenomicIntervalQuery.cpp.o -c ../src/GenomicIntervalQuery.cpp [68/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/IndexedFastaReader.cpp.o -MF src/libpbbam.so.2.1.0.p/IndexedFastaReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/IndexedFastaReader.cpp.o -c ../src/IndexedFastaReader.cpp [69/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/IRecordWriter.cpp.o -MF src/libpbbam.so.2.1.0.p/IRecordWriter.cpp.o.d -o src/libpbbam.so.2.1.0.p/IRecordWriter.cpp.o -c ../src/IRecordWriter.cpp [70/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/IndexedBamWriter.cpp.o -MF src/libpbbam.so.2.1.0.p/IndexedBamWriter.cpp.o.d -o src/libpbbam.so.2.1.0.p/IndexedBamWriter.cpp.o -c ../src/IndexedBamWriter.cpp [71/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/IndexedFastqReader.cpp.o -MF src/libpbbam.so.2.1.0.p/IndexedFastqReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/IndexedFastqReader.cpp.o -c ../src/IndexedFastqReader.cpp [72/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/MemoryUtils.cpp.o -MF src/libpbbam.so.2.1.0.p/MemoryUtils.cpp.o.d -o src/libpbbam.so.2.1.0.p/MemoryUtils.cpp.o -c ../src/MemoryUtils.cpp [73/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/RecordType.cpp.o -MF src/libpbbam.so.2.1.0.p/RecordType.cpp.o.d -o src/libpbbam.so.2.1.0.p/RecordType.cpp.o -c ../src/RecordType.cpp [74/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/PbiBuilder.cpp.o -MF src/libpbbam.so.2.1.0.p/PbiBuilder.cpp.o.d -o src/libpbbam.so.2.1.0.p/PbiBuilder.cpp.o -c ../src/PbiBuilder.cpp [75/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/PbiFile.cpp.o -MF src/libpbbam.so.2.1.0.p/PbiFile.cpp.o.d -o src/libpbbam.so.2.1.0.p/PbiFile.cpp.o -c ../src/PbiFile.cpp [76/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamRecord.cpp.o -MF tests/pbbam_test.p/src_test_BamRecord.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecord.cpp.o -c ../tests/src/test_BamRecord.cpp [77/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/RunMetadata.cpp.o -MF src/libpbbam.so.2.1.0.p/RunMetadata.cpp.o.d -o src/libpbbam.so.2.1.0.p/RunMetadata.cpp.o -c 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-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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/vcf_VcfQuery.cpp.o -MF src/libpbbam.so.2.1.0.p/vcf_VcfQuery.cpp.o.d -o src/libpbbam.so.2.1.0.p/vcf_VcfQuery.cpp.o -c ../src/vcf/VcfQuery.cpp [131/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread 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src/libpbbam.so.2.1.0.p/BaiIndexedBamReader.cpp.o src/libpbbam.so.2.1.0.p/BamFile.cpp.o src/libpbbam.so.2.1.0.p/BamFileMerger.cpp.o src/libpbbam.so.2.1.0.p/BamHeader.cpp.o src/libpbbam.so.2.1.0.p/BamReader.cpp.o src/libpbbam.so.2.1.0.p/BamRecord.cpp.o src/libpbbam.so.2.1.0.p/BamRecordImpl.cpp.o src/libpbbam.so.2.1.0.p/BamRecordTags.cpp.o src/libpbbam.so.2.1.0.p/BamRecordView.cpp.o src/libpbbam.so.2.1.0.p/BamTagCodec.cpp.o src/libpbbam.so.2.1.0.p/BamWriter.cpp.o src/libpbbam.so.2.1.0.p/BgzipFastaWriter.cpp.o src/libpbbam.so.2.1.0.p/BgzipFastqWriter.cpp.o src/libpbbam.so.2.1.0.p/BgzipWriter.cpp.o src/libpbbam.so.2.1.0.p/ChemistryTable.cpp.o src/libpbbam.so.2.1.0.p/CollectionMetadata.cpp.o src/libpbbam.so.2.1.0.p/Compare.cpp.o src/libpbbam.so.2.1.0.p/CompositeBamReader.cpp.o src/libpbbam.so.2.1.0.p/CompositeFastaReader.cpp.o src/libpbbam.so.2.1.0.p/Config.cpp.o src/libpbbam.so.2.1.0.p/DataSet.cpp.o src/libpbbam.so.2.1.0.p/DataSetBaseTypes.cpp.o src/libpbbam.so.2.1.0.p/DataSetElement.cpp.o src/libpbbam.so.2.1.0.p/DataSetIO.cpp.o src/libpbbam.so.2.1.0.p/DataSetTypes.cpp.o src/libpbbam.so.2.1.0.p/DataSetXsd.cpp.o src/libpbbam.so.2.1.0.p/EntireFileQuery.cpp.o src/libpbbam.so.2.1.0.p/ErrnoReason.cpp.o src/libpbbam.so.2.1.0.p/FaiIndex.cpp.o src/libpbbam.so.2.1.0.p/FaiZmwChunker.cpp.o src/libpbbam.so.2.1.0.p/FastaCache.cpp.o src/libpbbam.so.2.1.0.p/FastaReader.cpp.o src/libpbbam.so.2.1.0.p/FastaSequence.cpp.o src/libpbbam.so.2.1.0.p/FastaSequenceQuery.cpp.o src/libpbbam.so.2.1.0.p/FastaWriter.cpp.o src/libpbbam.so.2.1.0.p/FastqReader.cpp.o src/libpbbam.so.2.1.0.p/FastqSequence.cpp.o src/libpbbam.so.2.1.0.p/FastqWriter.cpp.o src/libpbbam.so.2.1.0.p/FileProducer.cpp.o src/libpbbam.so.2.1.0.p/FileUtils.cpp.o src/libpbbam.so.2.1.0.p/FofnReader.cpp.o src/libpbbam.so.2.1.0.p/FormatUtils.cpp.o src/libpbbam.so.2.1.0.p/GenomicIntervalQuery.cpp.o src/libpbbam.so.2.1.0.p/IFastaWriter.cpp.o src/libpbbam.so.2.1.0.p/IFastqWriter.cpp.o src/libpbbam.so.2.1.0.p/IndexedBamWriter.cpp.o src/libpbbam.so.2.1.0.p/IndexedFastaReader.cpp.o src/libpbbam.so.2.1.0.p/IndexedFastqBgzfReader.cpp.o src/libpbbam.so.2.1.0.p/IndexedFastqReader.cpp.o src/libpbbam.so.2.1.0.p/IndexedFastqTextReader.cpp.o src/libpbbam.so.2.1.0.p/IndexedFastqReaderImpl.cpp.o src/libpbbam.so.2.1.0.p/IRecordWriter.cpp.o src/libpbbam.so.2.1.0.p/KSeqReader.cpp.o src/libpbbam.so.2.1.0.p/LibraryInfo.cpp.o src/libpbbam.so.2.1.0.p/MD5.cpp.o src/libpbbam.so.2.1.0.p/MemoryUtils.cpp.o src/libpbbam.so.2.1.0.p/PbiBuilder.cpp.o src/libpbbam.so.2.1.0.p/PbiBuilderBase.cpp.o src/libpbbam.so.2.1.0.p/PbiFile.cpp.o src/libpbbam.so.2.1.0.p/PbiFilter.cpp.o src/libpbbam.so.2.1.0.p/PbiFilterQuery.cpp.o src/libpbbam.so.2.1.0.p/PbiFilterTypes.cpp.o src/libpbbam.so.2.1.0.p/PbiIndexedBamReader.cpp.o src/libpbbam.so.2.1.0.p/PbiIndexIO.cpp.o src/libpbbam.so.2.1.0.p/PbiRawData.cpp.o src/libpbbam.so.2.1.0.p/ProgramInfo.cpp.o src/libpbbam.so.2.1.0.p/ReadGroupInfo.cpp.o src/libpbbam.so.2.1.0.p/RecordType.cpp.o src/libpbbam.so.2.1.0.p/RunMetadata.cpp.o src/libpbbam.so.2.1.0.p/RunMetadataParser.cpp.o src/libpbbam.so.2.1.0.p/SamReader.cpp.o src/libpbbam.so.2.1.0.p/SamTagCodec.cpp.o src/libpbbam.so.2.1.0.p/SamWriter.cpp.o src/libpbbam.so.2.1.0.p/SequenceInfo.cpp.o src/libpbbam.so.2.1.0.p/StringUtilities.cpp.o src/libpbbam.so.2.1.0.p/Tag.cpp.o src/libpbbam.so.2.1.0.p/TagCollection.cpp.o src/libpbbam.so.2.1.0.p/TextFileReader.cpp.o src/libpbbam.so.2.1.0.p/TextFileWriter.cpp.o src/libpbbam.so.2.1.0.p/TimeUtils.cpp.o src/libpbbam.so.2.1.0.p/Validator.cpp.o src/libpbbam.so.2.1.0.p/ValidationErrors.cpp.o src/libpbbam.so.2.1.0.p/ValidationException.cpp.o src/libpbbam.so.2.1.0.p/Version.cpp.o src/libpbbam.so.2.1.0.p/VirtualZmwBamRecord.cpp.o src/libpbbam.so.2.1.0.p/VirtualZmwCompositeReader.cpp.o src/libpbbam.so.2.1.0.p/VirtualZmwReader.cpp.o src/libpbbam.so.2.1.0.p/VirtualRegion.cpp.o src/libpbbam.so.2.1.0.p/VirtualRegionTypeMap.cpp.o src/libpbbam.so.2.1.0.p/XmlReader.cpp.o src/libpbbam.so.2.1.0.p/XmlWriter.cpp.o src/libpbbam.so.2.1.0.p/WhitelistedZmwReadStitcher.cpp.o src/libpbbam.so.2.1.0.p/ZmwChunkedFastaReader.cpp.o src/libpbbam.so.2.1.0.p/ZmwChunkedFastqReader.cpp.o src/libpbbam.so.2.1.0.p/ZmwChunkedFastxBgzfReader.cpp.o src/libpbbam.so.2.1.0.p/ZmwChunkedFastxReaderImpl.cpp.o src/libpbbam.so.2.1.0.p/ZmwChunkedFastxTextReader.cpp.o src/libpbbam.so.2.1.0.p/ZmwGroupQuery.cpp.o src/libpbbam.so.2.1.0.p/ZmwReadStitcher.cpp.o src/libpbbam.so.2.1.0.p/ZmwQuery.cpp.o src/libpbbam.so.2.1.0.p/ZmwTypeMap.cpp.o src/libpbbam.so.2.1.0.p/bed_BedReader.cpp.o src/libpbbam.so.2.1.0.p/bed_BedWriter.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfFile.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfFormat.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfHeader.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfHeaderTypes.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfQuery.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfReader.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfSort.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfVariant.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfWriter.cpp.o src/libpbbam.so.2.1.0.p/pugixml_pugixml.cpp.o src/libpbbam.so.2.1.0.p/meson-generated_.._PbbamVersion.cpp.o -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,--start-group -Wl,-soname,libpbbam.so.2.1.0 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group [145/224] /usr/bin/meson --internal symbolextractor /build/pbbam-2.1.0+dfsg/obj-x86_64-linux-gnu src/libpbbam.so.2.1.0 src/libpbbam.so.2.1.0 src/libpbbam.so.2.1.0.p/libpbbam.so.2.1.0.symbols [146/224] 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/pbbam-2.1.0+dfsg=. 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-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 [162/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_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 [163/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_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 [164/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_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 [165/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_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 [166/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_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 [167/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_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 [168/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_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++/12/ios:43, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, 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>::sgetc() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/12/streambuf:346:49, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>::int_type std::istreambuf_iterator<_CharT, _Traits>::_M_get() const [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/12/bits/streambuf_iterator.h:206:69, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>::char_type std::istreambuf_iterator<_CharT, _Traits>::operator*() const [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/12/bits/streambuf_iterator.h:151:23, 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++/12/bits/basic_string.tcc:177:21, 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++/12/bits/basic_string.h:756:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/12/streambuf:493:30: warning: potential null pointer dereference [-Wnull-dereference] 493 | 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>::sgetc() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/12/streambuf:346:33, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>::int_type std::istreambuf_iterator<_CharT, _Traits>::_M_get() const [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/12/bits/streambuf_iterator.h:206:69, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>::char_type std::istreambuf_iterator<_CharT, _Traits>::operator*() const [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/12/bits/streambuf_iterator.h:151:23, 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++/12/bits/basic_string.tcc:177:21, 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++/12/bits/basic_string.h:756:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/12/streambuf:490:30: warning: potential null pointer dereference [-Wnull-dereference] 490 | 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++/12/streambuf:324:49, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>& std::istreambuf_iterator<_CharT, _Traits>::operator++() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/12/bits/streambuf_iterator.h:172:17, 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++/12/bits/basic_string.tcc:178:6, 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++/12/bits/basic_string.h:756:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/12/streambuf:493:30: warning: potential null pointer dereference [-Wnull-dereference] 493 | 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++/12/streambuf:324:33, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>& std::istreambuf_iterator<_CharT, _Traits>::operator++() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/12/bits/streambuf_iterator.h:172:17, 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++/12/bits/basic_string.tcc:178:6, 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++/12/bits/basic_string.h:756:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/12/streambuf:490:30: warning: potential null pointer dereference [-Wnull-dereference] 490 | 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++/12/streambuf:324:49, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>& std::istreambuf_iterator<_CharT, _Traits>::operator++() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/12/bits/streambuf_iterator.h:172:17, 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++/12/bits/basic_string.tcc:178:6, 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++/12/bits/basic_string.h:756:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/12/streambuf:493:30: warning: potential null pointer dereference [-Wnull-dereference] 493 | 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++/12/streambuf:324:33, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>& std::istreambuf_iterator<_CharT, _Traits>::operator++() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/12/bits/streambuf_iterator.h:172:17, 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++/12/bits/basic_string.tcc:178:6, 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++/12/bits/basic_string.h:756:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/12/streambuf:490:30: warning: potential null pointer dereference [-Wnull-dereference] 490 | 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++/12/streambuf:324:49, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>& std::istreambuf_iterator<_CharT, _Traits>::operator++() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/12/bits/streambuf_iterator.h:172:17, 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++/12/bits/basic_string.tcc:205:6, 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++/12/bits/basic_string.h:756:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/12/streambuf:493:30: warning: potential null pointer dereference [-Wnull-dereference] 493 | 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++/12/streambuf:324:33, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>& std::istreambuf_iterator<_CharT, _Traits>::operator++() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/12/bits/streambuf_iterator.h:172:17, 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++/12/bits/basic_string.tcc:205:6, 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++/12/bits/basic_string.h:756:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/12/streambuf:490:30: warning: potential null pointer dereference [-Wnull-dereference] 490 | gptr() const { return _M_in_cur; } | ^~~~~~~~~ [169/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_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 [170/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_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 [171/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_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 [172/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_PacBioIndex.cpp.o -MF tests/pbbam_test.p/src_test_PacBioIndex.cpp.o.d -o tests/pbbam_test.p/src_test_PacBioIndex.cpp.o -c ../tests/src/test_PacBioIndex.cpp [173/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_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 [174/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_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 [175/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_ReadGroupHashing.cpp.o -MF tests/pbbam_test.p/src_test_ReadGroupHashing.cpp.o.d -o tests/pbbam_test.p/src_test_ReadGroupHashing.cpp.o -c ../tests/src/test_ReadGroupHashing.cpp [176/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_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 [177/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_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 [178/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_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 [179/224] /usr/bin/python3 ../tests/scripts/generate_data.py /build/pbbam-2.1.0+dfsg/tests/data /build/pbbam-2.1.0+dfsg/obj-x86_64-linux-gnu/tests Generating test data in /build/pbbam-2.1.0+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. [180/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_VcfSort.cpp.o -MF tests/pbbam_test.p/src_test_VcfSort.cpp.o.d -o tests/pbbam_test.p/src_test_VcfSort.cpp.o -c ../tests/src/test_VcfSort.cpp [181/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_SegmentReads.cpp.o -MF tests/pbbam_test.p/src_test_SegmentReads.cpp.o.d -o tests/pbbam_test.p/src_test_SegmentReads.cpp.o -c ../tests/src/test_SegmentReads.cpp [182/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_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 [183/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_Version.cpp.o -MF tests/pbbam_test.p/src_test_Version.cpp.o.d -o tests/pbbam_test.p/src_test_Version.cpp.o -c ../tests/src/test_Version.cpp [184/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_PbiFilterQuery.cpp.o -MF tests/pbbam_test.p/src_test_PbiFilterQuery.cpp.o.d -o tests/pbbam_test.p/src_test_PbiFilterQuery.cpp.o -c ../tests/src/test_PbiFilterQuery.cpp [185/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_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 [186/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_VcfQuery.cpp.o -MF tests/pbbam_test.p/src_test_VcfQuery.cpp.o.d -o tests/pbbam_test.p/src_test_VcfQuery.cpp.o -c ../tests/src/test_VcfQuery.cpp [187/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_VcfWriter.cpp.o -MF tests/pbbam_test.p/src_test_VcfWriter.cpp.o.d -o tests/pbbam_test.p/src_test_VcfWriter.cpp.o -c ../tests/src/test_VcfWriter.cpp [188/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_Validator.cpp.o -MF tests/pbbam_test.p/src_test_Validator.cpp.o.d -o tests/pbbam_test.p/src_test_Validator.cpp.o -c ../tests/src/test_Validator.cpp [189/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/bam2sam.p/bam2sam_src_main.cpp.o -MF tools/bam2sam.p/bam2sam_src_main.cpp.o.d -o tools/bam2sam.p/bam2sam_src_main.cpp.o -c ../tools/bam2sam/src/main.cpp [190/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o -MF tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o.d -o tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o -c ../tools/bam2sam/src/Bam2SamWorkflow.cpp [191/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindex.p/pbindex_src_main.cpp.o -MF tools/pbindex.p/pbindex_src_main.cpp.o.d -o tools/pbindex.p/pbindex_src_main.cpp.o -c ../tools/pbindex/src/main.cpp [192/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/zero_byte_check/zero_byte_check.p/main.cpp.o -MF tests/zero_byte_check/zero_byte_check.p/main.cpp.o.d -o tests/zero_byte_check/zero_byte_check.p/main.cpp.o -c ../tests/zero_byte_check/main.cpp [193/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindex.p/pbindex_src_PbIndexSettings.cpp.o -MF tools/pbindex.p/pbindex_src_PbIndexSettings.cpp.o.d -o tools/pbindex.p/pbindex_src_PbIndexSettings.cpp.o -c ../tools/pbindex/src/PbIndexSettings.cpp [194/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o -MF tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o.d -o tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o -c ../tools/bam2sam/src/Bam2SamSettings.cpp In file included from /usr/include/c++/12/string:40, from ../tools/bam2sam/src/Bam2SamSettings.h:4, from ../tools/bam2sam/src/Bam2SamSettings.cpp:1: In static member function ‘static constexpr std::char_traits::char_type* std::char_traits::copy(char_type*, const char_type*, std::size_t)’, inlined from ‘static constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:423:21, inlined from ‘static constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:418:7, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.tcc:532:22, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::assign(const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:1647:19, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:815:28, inlined from ‘PacBio::Bam2Sam::Settings::Settings(const PacBio::CLI_v2::Results&)’ at ../tools/bam2sam/src/Bam2SamSettings.cpp:67:25: /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets -4611686018427387902 and [-4611686018427387903, 4611686018427387904] may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ [195/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o -MF tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o.d -o tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o -c ../tools/pbindex/src/PbIndexWorkflow.cpp [196/224] c++ -o tools/bam2sam tools/bam2sam.p/bam2sam_src_main.cpp.o tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libhts.so -pthread /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group [197/224] c++ -o tests/zero_byte_check/zero_byte_check tests/zero_byte_check/zero_byte_check.p/main.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../../src' -Wl,-rpath-link,/build/pbbam-2.1.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.1.0 /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 [198/224] c++ -o tools/pbindex tools/pbindex.p/pbindex_src_main.cpp.o tools/pbindex.p/pbindex_src_PbIndexSettings.cpp.o tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-2.1.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.1.0 /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 [199/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/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 [200/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_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 [201/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/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 [202/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/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 In file included from /usr/include/c++/12/string:40, from ../tools/pbindexdump/src/PbIndexDumpSettings.h:4, from ../tools/pbindexdump/src/PbIndexDumpSettings.cpp:1: In static member function ‘static constexpr std::char_traits::char_type* std::char_traits::copy(char_type*, const char_type*, std::size_t)’, inlined from ‘static constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:423:21, inlined from ‘static constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:418:7, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.tcc:532:22, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::assign(const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:1647:19, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:815:28, inlined from ‘PacBio::PbIndexDump::Settings::Settings(const PacBio::CLI_v2::Results&)’ at ../tools/pbindexdump/src/PbIndexDumpSettings.cpp:91:21: /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets -4611686018427387902 and [-4611686018427387903, 4611686018427387904] may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ [203/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/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 [204/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_WhitelistedZmwReadStitcher.cpp.o -MF tests/pbbam_test.p/src_test_WhitelistedZmwReadStitcher.cpp.o.d -o tests/pbbam_test.p/src_test_WhitelistedZmwReadStitcher.cpp.o -c ../tests/src/test_WhitelistedZmwReadStitcher.cpp [205/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/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 [206/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/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 In file included from /usr/include/c++/12/string:40, from ../tools/pbmerge/src/PbMergeSettings.h:4, from ../tools/pbmerge/src/PbMergeSettings.cpp:1: In static member function ‘static constexpr std::char_traits::char_type* std::char_traits::copy(char_type*, const char_type*, std::size_t)’, inlined from ‘static constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:423:21, inlined from ‘static constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:418:7, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.tcc:532:22, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::assign(const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:1647:19, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:815:28, inlined from ‘PacBio::PbMerge::Settings::Settings(const PacBio::CLI_v2::Results&)’ at ../tools/pbmerge/src/PbMergeSettings.cpp:76:22: /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets [2, 9223372036854775807] and 1 may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ [207/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_ZmwQuery.cpp.o -MF tests/pbbam_test.p/src_test_ZmwQuery.cpp.o.d -o tests/pbbam_test.p/src_test_ZmwQuery.cpp.o -c ../tests/src/test_ZmwQuery.cpp [208/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_PbBamifySettings.cpp.o -MF tools/pbbamify.p/pbbamify_src_PbBamifySettings.cpp.o.d -o tools/pbbamify.p/pbbamify_src_PbBamifySettings.cpp.o -c ../tools/pbbamify/src/PbBamifySettings.cpp [209/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_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 /usr/include/c++/12/istream:39, from /usr/include/c++/12/sstream:38, from ../tests/src/test_Tags.cpp:8: In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(short unsigned int) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘static void testing::internal::internal_stream_operator_without_lexical_name_lookup::StreamPrinter::PrintValue(const T&, std::ostream*) [with T = short unsigned int; = void; = std::basic_ostream&]’ at /usr/include/gtest/gtest-printers.h:216:9, inlined from ‘void testing::internal::PrintWithFallback(const T&, std::ostream*) [with T = short unsigned int]’ at /usr/include/gtest/gtest-printers.h:311:22, inlined from ‘void testing::internal::PrintTo(const T&, std::ostream*) [with T = short unsigned int]’ at /usr/include/gtest/gtest-printers.h:440:30, inlined from ‘static void testing::internal::UniversalPrinter::Print(const T&, std::ostream*) [with T = short unsigned int]’ at /usr/include/gtest/gtest-printers.h:702:12, inlined from ‘void testing::internal::UniversalPrint(const T&, std::ostream*) [with T = short unsigned int]’ at /usr/include/gtest/gtest-printers.h:999:30, inlined from ‘static void testing::internal::UniversalTersePrinter::Print(const T&, std::ostream*) [with T = short unsigned int]’ at /usr/include/gtest/gtest-printers.h:884:19, inlined from ‘std::string testing::PrintToString(const T&) [with T = short unsigned int]’ at /usr/include/gtest/gtest-printers.h:1037:44, inlined from ‘static std::string testing::internal::FormatForComparison::Format(const ToPrint&) [with ToPrint = short unsigned int; OtherOperand = short unsigned int]’ at /usr/include/gtest/gtest-printers.h:333:42, inlined from ‘std::string testing::internal::FormatForComparisonFailureMessage(const T1&, const T2&) [with T1 = short unsigned int; T2 = short unsigned int]’ at /usr/include/gtest/gtest-printers.h:414:51, inlined from ‘testing::AssertionResult testing::internal::CmpHelperEQFailure(const char*, const char*, const T1&, const T2&) [with T1 = short unsigned int; T2 = short unsigned int]’ at /usr/include/gtest/gtest.h:1343:70, inlined from ‘testing::AssertionResult testing::internal::CmpHelperEQ(const char*, const char*, const T1&, const T2&) [with T1 = short unsigned int; T2 = short unsigned int]’ at /usr/include/gtest/gtest.h:1362:69, 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:1377:64, inlined from ‘virtual void BAM_Tag_can_describe_uint16_tag_Test::TestBody()’ at ../tests/src/test_Tags.cpp:343:5: /usr/include/c++/12/ostream:185:25: warning: ‘v2’ may be used uninitialized [-Wmaybe-uninitialized] 185 | return _M_insert(static_cast(__n)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../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; | ^~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(unsigned int) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘static void testing::internal::internal_stream_operator_without_lexical_name_lookup::StreamPrinter::PrintValue(const T&, std::ostream*) [with T = unsigned int; = void; = std::basic_ostream&]’ at /usr/include/gtest/gtest-printers.h:216:9, inlined from ‘void testing::internal::PrintWithFallback(const T&, std::ostream*) [with T = unsigned int]’ at /usr/include/gtest/gtest-printers.h:311:22, inlined from ‘void testing::internal::PrintTo(const T&, std::ostream*) [with T = unsigned int]’ at /usr/include/gtest/gtest-printers.h:440:30, inlined from ‘static void testing::internal::UniversalPrinter::Print(const T&, std::ostream*) [with T = unsigned int]’ at /usr/include/gtest/gtest-printers.h:702:12, inlined from ‘void testing::internal::UniversalPrint(const T&, std::ostream*) [with T = unsigned int]’ at /usr/include/gtest/gtest-printers.h:999:30, inlined from ‘static void testing::internal::UniversalTersePrinter::Print(const T&, std::ostream*) [with T = unsigned int]’ at /usr/include/gtest/gtest-printers.h:884:19, inlined from ‘std::string testing::PrintToString(const T&) [with T = unsigned int]’ at /usr/include/gtest/gtest-printers.h:1037:44, inlined from ‘static std::string testing::internal::FormatForComparison::Format(const ToPrint&) [with ToPrint = unsigned int; OtherOperand = unsigned int]’ at /usr/include/gtest/gtest-printers.h:333:42, inlined from ‘std::string testing::internal::FormatForComparisonFailureMessage(const T1&, const T2&) [with T1 = unsigned int; T2 = unsigned int]’ at /usr/include/gtest/gtest-printers.h:414:51, inlined from ‘testing::AssertionResult testing::internal::CmpHelperEQFailure(const char*, const char*, const T1&, const T2&) [with T1 = unsigned int; T2 = unsigned int]’ at /usr/include/gtest/gtest.h:1343:70, inlined from ‘testing::AssertionResult testing::internal::CmpHelperEQ(const char*, const char*, const T1&, const T2&) [with T1 = unsigned int; T2 = unsigned int]’ at /usr/include/gtest/gtest.h:1362:69, 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:1377:64, inlined from ‘virtual void BAM_Tag_can_describe_uint32_tag_Test::TestBody()’ at ../tests/src/test_Tags.cpp:391:5: /usr/include/c++/12/ostream:196:25: warning: ‘v2’ may be used uninitialized [-Wmaybe-uninitialized] 196 | return _M_insert(static_cast(__n)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../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 member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(float) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘static void testing::internal::internal_stream_operator_without_lexical_name_lookup::StreamPrinter::PrintValue(const T&, std::ostream*) [with T = float; = void; = std::basic_ostream&]’ at /usr/include/gtest/gtest-printers.h:216:9, inlined from ‘void testing::internal::PrintWithFallback(const T&, std::ostream*) [with T = float]’ at /usr/include/gtest/gtest-printers.h:311:22, inlined from ‘void testing::internal::PrintTo(const T&, std::ostream*) [with T = float]’ at /usr/include/gtest/gtest-printers.h:440:30, inlined from ‘static void testing::internal::UniversalPrinter::Print(const T&, std::ostream*) [with T = float]’ at /usr/include/gtest/gtest-printers.h:702:12, inlined from ‘void testing::internal::UniversalPrint(const T&, std::ostream*) [with T = float]’ at /usr/include/gtest/gtest-printers.h:999:30, inlined from ‘static void testing::internal::UniversalTersePrinter::Print(const T&, std::ostream*) [with T = float]’ at /usr/include/gtest/gtest-printers.h:884:19, inlined from ‘std::string testing::PrintToString(const T&) [with T = float]’ at /usr/include/gtest/gtest-printers.h:1037:44, inlined from ‘static std::string testing::internal::FormatForComparison::Format(const ToPrint&) [with ToPrint = float; OtherOperand = float]’ at /usr/include/gtest/gtest-printers.h:333:42, inlined from ‘std::string testing::internal::FormatForComparisonFailureMessage(const T1&, const T2&) [with T1 = float; T2 = float]’ at /usr/include/gtest/gtest-printers.h:414:51, inlined from ‘testing::AssertionResult testing::internal::CmpHelperEQFailure(const char*, const char*, const T1&, const T2&) [with T1 = float; T2 = float]’ at /usr/include/gtest/gtest.h:1343:70, inlined from ‘testing::AssertionResult testing::internal::CmpHelperEQ(const char*, const char*, const T1&, const T2&) [with T1 = float; T2 = float]’ at /usr/include/gtest/gtest.h:1362:69, inlined from ‘static testing::AssertionResult testing::internal::EqHelper::Compare(const char*, const char*, const T1&, const T2&) [with T1 = float; T2 = float; typename std::enable_if<((! std::is_integral<_Tp>::value) || (! std::is_pointer<_Dp>::value))>::type* = 0]’ at /usr/include/gtest/gtest.h:1377:64, inlined from ‘virtual void BAM_Tag_can_describe_float_tag_Test::TestBody()’ at ../tests/src/test_Tags.cpp:412:5: /usr/include/c++/12/ostream:228:25: warning: ‘v2’ may be used uninitialized [-Wmaybe-uninitialized] 228 | return _M_insert(static_cast(__f)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/src/test_Tags.cpp: In member function ‘virtual void BAM_Tag_can_describe_float_tag_Test::TestBody()’: ../tests/src/test_Tags.cpp:399:11: note: ‘v2’ was declared here 399 | float v2; | ^~ [210/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_main.cpp.o -MF tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_main.cpp.o.d -o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_main.cpp.o -c ../tools/ccs-kinetics-bystrandify/src/main.cpp [211/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_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 [212/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_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 [213/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_main.cpp.o -MF tools/pbbamify.p/pbbamify_src_main.cpp.o.d -o tools/pbbamify.p/pbbamify_src_main.cpp.o -c ../tools/pbbamify/src/main.cpp [214/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -MF tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o.d -o tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -c ../tools/pbmerge/src/PbMergeWorkflow.cpp [215/224] c++ -o tools/pbmerge tools/pbmerge.p/pbmerge_src_main.cpp.o tools/pbmerge.p/pbmerge_src_PbMergeSettings.cpp.o tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-2.1.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.1.0 /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 [216/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/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 [217/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-2.1.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.1.0 /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 [218/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -MF tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o.d -o tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -c ../tools/pbbamify/src/QueryLookup.cpp [219/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o -MF tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o.d -o tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o -c ../tests/src/test_ZmwReadStitcher.cpp [220/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o -MF tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o.d -o tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o -c ../tools/pbbamify/src/PbBamifyWorkflow.cpp [221/224] c++ -o tools/pbbamify tools/pbbamify.p/pbbamify_src_main.cpp.o tools/pbbamify.p/pbbamify_src_PbBamifySettings.cpp.o tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-2.1.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.1.0 /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 [222/224] 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_DataSetCore.cpp.o tests/pbbam_test.p/src_test_DataSetGenomicIntervals.cpp.o tests/pbbam_test.p/src_test_DataSetIO.cpp.o tests/pbbam_test.p/src_test_DataSetQuery.cpp.o tests/pbbam_test.p/src_test_DataSetXsd.cpp.o tests/pbbam_test.p/src_test_EndToEnd.cpp.o tests/pbbam_test.p/src_test_EntireFileQuery.cpp.o tests/pbbam_test.p/src_test_FaiIndex.cpp.o tests/pbbam_test.p/src_test_FaiZmwChunker.cpp.o tests/pbbam_test.p/src_test_FastaCache.cpp.o tests/pbbam_test.p/src_test_FastaReader.cpp.o tests/pbbam_test.p/src_test_FastaSequence.cpp.o tests/pbbam_test.p/src_test_FastaSequenceQuery.cpp.o tests/pbbam_test.p/src_test_FastaWriter.cpp.o tests/pbbam_test.p/src_test_FastqReader.cpp.o tests/pbbam_test.p/src_test_FastqSequence.cpp.o tests/pbbam_test.p/src_test_FastqWriter.cpp.o tests/pbbam_test.p/src_test_FileUtils.cpp.o tests/pbbam_test.p/src_test_GenomicIntervalQuery.cpp.o tests/pbbam_test.p/src_test_IndexedBamWriter.cpp.o tests/pbbam_test.p/src_test_IndexedFastaReader.cpp.o tests/pbbam_test.p/src_test_IndexedFastqReader.cpp.o tests/pbbam_test.p/src_test_LongCigar.cpp.o tests/pbbam_test.p/src_test_PacBioIndex.cpp.o tests/pbbam_test.p/src_test_PbiFilter.cpp.o tests/pbbam_test.p/src_test_PbiFilterQuery.cpp.o tests/pbbam_test.p/src_test_QualityValues.cpp.o tests/pbbam_test.p/src_test_Pulse2BaseCache.cpp.o tests/pbbam_test.p/src_test_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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-2.1.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.1.0 /usr/lib/x86_64-linux-gnu/libgtest_main.a /usr/lib/x86_64-linux-gnu/libgtest.a -lpthread /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group [223/224] c++ -Itools/ccs-kinetics-bystrandify.p -Itools -I../tools -Iinclude -I../include -I../tools/ccs-kinetics-bystrandify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -MF tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o.d -o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -c ../tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp [224/224] c++ -o tools/ccs-kinetics-bystrandify tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_main.cpp.o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifySettings.cpp.o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-2.1.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.1.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group debian/rules override_dh_auto_test make[1]: Entering directory '/build/pbbam-2.1.0+dfsg' sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-2.1.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.1.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-2.1.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbbamify.t.in > tests/src/cram/pbbamify.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-2.1.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.1.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-2.1.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbindexdump_cpp.t.in > tests/src/cram/pbindexdump_cpp.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-2.1.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.1.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-2.1.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbindexdump_json.t.in > tests/src/cram/pbindexdump_json.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-2.1.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.1.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-2.1.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_aligned_ordering.t.in > tests/src/cram/pbmerge_aligned_ordering.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-2.1.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.1.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-2.1.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_dataset.t.in > tests/src/cram/pbmerge_dataset.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-2.1.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.1.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-2.1.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_fofn.t.in > tests/src/cram/pbmerge_fofn.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-2.1.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.1.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-2.1.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_mixed_ordering.t.in > tests/src/cram/pbmerge_mixed_ordering.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-2.1.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.1.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-2.1.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_pacbio_ordering.t.in > tests/src/cram/pbmerge_pacbio_ordering.deb.t dh_auto_configure -O--buildsystem=meson cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 meson setup .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-linux-gnu Directory already configured. Just run your build command (e.g. ninja) and Meson will regenerate as necessary. If ninja fails, run "ninja reconfigure" or "meson 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. To change option values, run "meson configure" instead. mkdir -p /build/pbbam-2.1.0+dfsg/gendata python3 tests/scripts/generate_data.py /build/pbbam-2.1.0+dfsg/tests/data /build/pbbam-2.1.0+dfsg/gendata Generating test data in /build/pbbam-2.1.0+dfsg/gendata - Creating file: truncated.bam...done. - Creating file: chunking_emptyfilters.subreadset.xml...done. - Creating file: chunking_missingfilters.subreadset.xml...done. - Creating file: normal.fa...done. - Creating file: normal.fq...done. - Creating symlink: aligned.bam...done. - Creating symlink: aligned.bam.bai...done. - Creating symlink: aligned.bam.pbi...done. - Creating symlink: aligned2.bam...done. - Creating symlink: aligned2.bam.bai...done. - Creating symlink: aligned2.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam.pbi...done. - Creating symlink: missing_pbi.bam...done. # Fix broken PATH synthetic_movie_all_path=`find $PWD -name synthetic_movie_all.subreadset.xml` ; \ sed -i -e "s?.GENERATEDDATADIR/synthetic_movie_all.subreadset.xml?${synthetic_movie_all_path}?" tests/src/cram/pbbamify* BINDIR=`dirname $(find $PWD -name pbmerge -type f -executable)`; \ LIBDIR=`find $PWD -name lib -type d`; \ PATH="$BINDIR:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" LD_LIBRARY_PATH="$LIBDIR:" \ cram3 -v --preserve-env tests/src/cram/pbbamify.deb.t tests/src/cram/pbindexdump_cpp.deb.t tests/src/cram/pbindexdump_json.deb.t tests/src/cram/pbmerge_aligned_ordering.deb.t tests/src/cram/pbmerge_dataset.deb.t tests/src/cram/pbmerge_fofn.deb.t tests/src/cram/pbmerge_mixed_ordering.deb.t tests/src/cram/pbmerge_pacbio_ordering.deb.t tests/src/cram/pbbamify.deb.t: passed tests/src/cram/pbindexdump_cpp.deb.t: passed tests/src/cram/pbindexdump_json.deb.t: passed tests/src/cram/pbmerge_aligned_ordering.deb.t: passed tests/src/cram/pbmerge_dataset.deb.t: passed tests/src/cram/pbmerge_fofn.deb.t: passed tests/src/cram/pbmerge_mixed_ordering.deb.t: passed tests/src/cram/pbmerge_pacbio_ordering.deb.t: passed # Ran 8 tests, 0 skipped, 0 failed. make[1]: Leaving directory '/build/pbbam-2.1.0+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/pbbam-2.1.0\+dfsg/debian/tmp LC_ALL=C.UTF-8 ninja install [0/1] Regenerating build files. Cleaning... 0 files. The Meson build system Version: 1.0.1 Source dir: /build/pbbam-2.1.0+dfsg Build dir: /build/pbbam-2.1.0+dfsg/obj-x86_64-linux-gnu Build type: native build Project name: PacBioBAM Project version: 2.1.0 C++ compiler for the host machine: c++ (gcc 12.2.0 "c++ (Debian 12.2.0-14) 12.2.0") C++ linker for the host machine: c++ ld.bfd 2.40 Host machine cpu family: x86_64 Host machine cpu: x86_64 Compiler for C++ supports arguments -Wduplicated-cond: YES (cached) Compiler for C++ supports arguments -Wduplicated-branches: YES (cached) Compiler for C++ supports arguments -Wlogical-op: YES (cached) Compiler for C++ supports arguments -Wrestrict: YES (cached) Compiler for C++ supports arguments -Wnull-dereference: YES (cached) Compiler for C++ supports arguments -Wuseless-cast: YES (cached) Compiler for C++ supports arguments -Wdouble-promotion: YES (cached) Compiler for C++ supports arguments -Wshadow: YES (cached) Compiler for C++ supports arguments -Wformat=1: YES (cached) Dependency threads found: YES unknown (cached) Dependency boost found: YES 1.74.0 (cached) Dependency zlib found: YES 1.2.13 (cached) Dependency htslib found: YES 1.16 (cached) Dependency pbcopper found: YES 2.0.0 (cached) Configuring PbbamVersion.cpp using configuration Configuring LibraryVersion.h using configuration Program tools/check-formatting found: YES (/build/pbbam-2.1.0+dfsg/tools/check-formatting) Program python3 found: YES (/usr/bin/python3) Program cram3 found: YES (/usr/bin/cram3) Dependency gtest found: YES 1.12.1 (cached) Configuring group.fofn using configuration Configuring PbbamTestData.h using configuration Configuring synthetic_movie_all.subreadset.xml using configuration Configuring Bam2SamVersion.h using configuration Configuring bam2sam.t using configuration Configuring PbIndexVersion.h using configuration Configuring PbIndexDumpVersion.h using configuration Configuring pbindexdump_json.t using configuration Configuring pbindexdump_cpp.t using configuration Configuring PbMergeVersion.h using configuration Configuring pbmerge_pacbio_ordering.t using configuration Configuring pbmerge_aligned_ordering.t using configuration Configuring pbmerge_mixed_ordering.t using configuration Configuring pbmerge_dataset.t using configuration Configuring pbmerge_fofn.t using configuration Configuring PbBamifyVersion.h using configuration Program samtools found: YES (/usr/bin/samtools) Configuring pbbamify.t using configuration Configuring CcsKineticsBystrandifyVersion.h using configuration Build targets in project: 12 PacBioBAM 2.1.0 User defined options buildtype : plain libdir : lib/x86_64-linux-gnu localstatedir: /var prefix : /usr sysconfdir : /etc wrap_mode : nodownload Found ninja-1.11.1 at /usr/bin/ninja [1/15] Generating tests/pbbam_generate_data with a custom command [2/15] Generating src/LibraryGitHash.h with a custom command [3/14] Generating src/PbbamGitHash.cpp with a custom command [3/4] Installing files. Installing src/libpbbam.so.2.1.0 to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu Installing tools/bam2sam to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/bin Installing tools/pbindex to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/bin Installing tools/pbindexdump to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/bin Installing tools/pbmerge to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/bin Installing tools/pbbamify to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/bin Installing tools/ccs-kinetics-bystrandify to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/bin Installing /build/pbbam-2.1.0+dfsg/include/pbbam/Accuracy.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/AlignmentPrinter.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/BaiIndexCache.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/BaiIndexedBamReader.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/BamFile.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/BamFileMerger.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/BamHeader.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/BamReader.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/BamRecord.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/BamRecordImpl.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/BamRecordTag.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/BamRecordView.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/BamTagCodec.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/BamWriter.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/BgzipFastaWriter.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/BgzipFastqWriter.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/BgzipWriter.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/Cigar.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/CigarOperation.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/ClipType.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/CollectionMetadata.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/Compare.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/CompositeBamReader.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/CompositeFastaReader.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/Config.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/DataSet.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/DataSetTypes.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/DataSetXsd.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/Deleters.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/EntireFileQuery.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/FaiIndex.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/FastaCache.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/FastaReader.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/FastaSequence.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/FastaSequenceQuery.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/FastaWriter.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/FastqReader.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/FastqSequence.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/FastqWriter.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/FormatUtils.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/FrameEncodingType.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/Frames.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/GenomicInterval.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/GenomicIntervalQuery.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/IFastaWriter.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/IFastqWriter.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/IndexedBamWriter.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/IndexedFastaReader.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/IndexedFastqReader.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/Interval.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/IRecordWriter.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/LibraryInfo.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/LocalContextFlags.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/MD5.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/MoveAppend.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/Orientation.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/PbbamVersion.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/PbiBasicTypes.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/PbiBuilder.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/PbiFile.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/PbiFilter.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/PbiFilterQuery.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/PbiFilterTypes.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/PbiIndexedBamReader.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/PbiRawData.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/Position.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/ProgramInfo.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/PulseBehavior.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/PulseExclusionReason.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/QualityValue.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/QualityValues.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/ReadGroupInfo.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/RecordType.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/RunMetadata.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/SamReader.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/SamTagCodec.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/SamWriter.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/SequenceInfo.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/SNR.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/Strand.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/StringUtilities.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/Tag.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/TagCollection.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/TextFileReader.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/TextFileWriter.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/Validator.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/ZmwGroupQuery.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/ZmwQuery.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/ZmwType.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/ZmwTypeMap.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/bed/BedReader.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/bed/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/bed/BedWriter.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/bed/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/exception/BundleChemistryMappingException.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/exception/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/exception/InvalidSequencingChemistryException.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/exception/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/exception/ValidationException.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/exception/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/internal/Compare.inl to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/internal/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/internal/CompositeBamReader.inl to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/internal/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/internal/DataSetBaseTypes.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/internal/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/internal/DataSetElement.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/internal/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/internal/DataSetElement.inl to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/internal/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/internal/PbiBasicTypes.inl to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/internal/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/internal/PbiFilter.inl to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/internal/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/internal/PbiFilterTypes.inl to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/internal/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/internal/QueryBase.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/internal/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/internal/QueryBase.inl to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/internal/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/vcf/VcfVariant.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/vcf/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/vcf/VcfFile.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/vcf/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/vcf/VcfFormat.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/vcf/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/vcf/VcfHeader.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/vcf/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/vcf/VcfHeaderTypes.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/vcf/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/vcf/VcfReader.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/vcf/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/vcf/VcfSort.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/vcf/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/vcf/VcfQuery.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/vcf/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/vcf/VcfWriter.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/vcf/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/virtual/VirtualPolymeraseBamRecord.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/virtual/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/virtual/VirtualPolymeraseCompositeReader.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/virtual/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/virtual/VirtualPolymeraseReader.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/virtual/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/virtual/VirtualRegion.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/virtual/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/virtual/VirtualRegionType.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/virtual/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/virtual/VirtualRegionTypeMap.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/virtual/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/virtual/VirtualZmwBamRecord.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/virtual/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/virtual/WhitelistedZmwReadStitcher.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/virtual/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/virtual/ZmwReadStitcher.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/virtual/ Installing /build/pbbam-2.1.0+dfsg/include/pbbam/virtual/ZmwWhitelistVirtualReader.h to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/include/pbbam/virtual/ Installing /build/pbbam-2.1.0+dfsg/obj-x86_64-linux-gnu/meson-private/pbbam.pc to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig Installing symlink pointing to libpbbam.so.2.1.0 to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libpbbam.so debian/rules override_dh_install make[1]: Entering directory '/build/pbbam-2.1.0+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/libpbbam2.1.0/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libpbbam.so debian/libpbbam-dev/usr/lib/x86_64-linux-gnu mv /build/pbbam-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libpbbam.so.2.1.0 debian/libpbbam2.1.0/usr/lib/x86_64-linux-gnu PKGDEV=libpbbam-dev PKGSHL=libpbbam2.1.0 install -d -m 755 debian/libpbbam-dev/usr/include mv debian/tmp/usr/include/pbbam debian/libpbbam-dev/usr/include install -d -m 755 debian/libpbbam-dev/usr/lib/x86_64-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libpbbam-dev/usr/lib/x86_64-linux-gnu/pkgconfig find debian -name "lib*.la" -delete make[1]: Leaving directory '/build/pbbam-2.1.0+dfsg' dh_installdocs -O--buildsystem=meson debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/pbbam-2.1.0+dfsg' dh_installchangelogs CHANGELOG.md make[1]: Leaving directory '/build/pbbam-2.1.0+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 dpkg-gencontrol: warning: package libpbbam-dev: substitution variable ${devlibs:Depends} unused, but is defined dh_md5sums -O--buildsystem=meson dh_builddeb -O--buildsystem=meson dpkg-deb: building package 'pbbamtools-dbgsym' in '../pbbamtools-dbgsym_2.1.0+dfsg-2_amd64.deb'. dpkg-deb: building package 'libpbbam2.1.0' in '../libpbbam2.1.0_2.1.0+dfsg-2_amd64.deb'. dpkg-deb: building package 'libpbbam2.1.0-dbgsym' in '../libpbbam2.1.0-dbgsym_2.1.0+dfsg-2_amd64.deb'. dpkg-deb: building package 'pbbamtools' in '../pbbamtools_2.1.0+dfsg-2_amd64.deb'. dpkg-deb: building package 'libpbbam-dev' in '../libpbbam-dev_2.1.0+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../pbbam_2.1.0+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../pbbam_2.1.0+dfsg-2_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: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1281860 and its subdirectories I: Current time: Mon May 20 14:13:01 -12 2024 I: pbuilder-time-stamp: 1716257581 Tue Apr 18 19:50:00 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Tue Apr 18 19:50:00 UTC 2023 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Tue Apr 18 20:05:58 UTC 2023 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Tue Apr 18 20:05:59 UTC 2023 I: pbbam_2.1.0+dfsg-2_amd64.changes: Format: 1.8 Date: Thu, 06 Oct 2022 11:27:28 +0200 Source: pbbam Binary: libpbbam-dev libpbbam2.1.0 libpbbam2.1.0-dbgsym pbbamtools pbbamtools-dbgsym Architecture: amd64 Version: 2.1.0+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libpbbam-dev - Pacific Biosciences binary alignment/map (BAM) library (headers) libpbbam2.1.0 - Pacific Biosciences binary alignment/map (BAM) library pbbamtools - processing Pacific Biosciences binary alignment/map files Changes: pbbam (2.1.0+dfsg-2) unstable; urgency=medium . * Fix watch file Checksums-Sha1: 8cef0038f9c36305a541477b548bae7d76ea116f 87600 libpbbam-dev_2.1.0+dfsg-2_amd64.deb df460a8f4c6fa78cd11eb330535ca935ce69798a 17390060 libpbbam2.1.0-dbgsym_2.1.0+dfsg-2_amd64.deb 3ae4473882aae5114638b4e1b613377365560f3d 760872 libpbbam2.1.0_2.1.0+dfsg-2_amd64.deb c99faa55af5d51c484169c34cbf9f5b4a82c46ff 8249 pbbam_2.1.0+dfsg-2_amd64.buildinfo 5a9289e79a0c4a96e3b3fb8b8ceee9fe3a4fef86 2758800 pbbamtools-dbgsym_2.1.0+dfsg-2_amd64.deb 64c07ee91417469f90e57f7c210224020157ddb5 125288 pbbamtools_2.1.0+dfsg-2_amd64.deb Checksums-Sha256: ce58a35a900d0cd8634e4c3ec22eb58604b116dd5afda85ece4da73681f021ad 87600 libpbbam-dev_2.1.0+dfsg-2_amd64.deb 629b0ccbc131fbaee66ce4edf28d29dd1db10b114a89933728fa55a2dc946908 17390060 libpbbam2.1.0-dbgsym_2.1.0+dfsg-2_amd64.deb b08efd053e0f7aa05a691cea2b359b3faa4f53b3810a8a080859f3994918c671 760872 libpbbam2.1.0_2.1.0+dfsg-2_amd64.deb 7a44eb88bcbe3747544c460e36b7e8732ceec465dc9a4144a4cd9c344d58a4b5 8249 pbbam_2.1.0+dfsg-2_amd64.buildinfo ee9d897b1749f219b8d62be71e4ce39535ff6f31a7a20079b540007e2b081862 2758800 pbbamtools-dbgsym_2.1.0+dfsg-2_amd64.deb 6ba0610001b8bf529c69540de7122ab436b96660c2e81bf18f5f227b5fc8039c 125288 pbbamtools_2.1.0+dfsg-2_amd64.deb Files: 1c98445f08855b9bc122a7c8dee7d961 87600 libdevel optional libpbbam-dev_2.1.0+dfsg-2_amd64.deb f87eb22ee0683a6076cb02d229a0155b 17390060 debug optional libpbbam2.1.0-dbgsym_2.1.0+dfsg-2_amd64.deb d4fc77ea33331a33bbd9eae1ebbc9a42 760872 libs optional libpbbam2.1.0_2.1.0+dfsg-2_amd64.deb ea7f410958fc185a59a46c19884b05a5 8249 science optional pbbam_2.1.0+dfsg-2_amd64.buildinfo 0e91a7a939ff69e9ca524ea01aba41e3 2758800 debug optional pbbamtools-dbgsym_2.1.0+dfsg-2_amd64.deb eac4b196fdcc7357e63b2202c0c2d052 125288 science optional pbbamtools_2.1.0+dfsg-2_amd64.deb Tue Apr 18 20:06:00 UTC 2023 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.MnqrMOK6/pbbam_2.1.0+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.MnqrMOK6/pbbam_2.1.0+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.MnqrMOK6/pbbam_2.1.0+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.MnqrMOK6/b1/pbbam_2.1.0+dfsg-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.MnqrMOK6/b2/pbbam_2.1.0+dfsg-2_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.678s) 0.678s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.293s) 0.292s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Tue Apr 18 20:06:02 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Tue Apr 18 20:06:02 UTC 2023 I: pbbam from bookworm built successfully and reproducibly on amd64. Tue Apr 18 20:06:04 UTC 2023 I: Submitting .buildinfo files to external archives: Tue Apr 18 20:06:04 UTC 2023 I: Submitting 12K b1/pbbam_2.1.0+dfsg-2_amd64.buildinfo.asc Tue Apr 18 20:06:05 UTC 2023 I: Submitting 12K b2/pbbam_2.1.0+dfsg-2_amd64.buildinfo.asc Tue Apr 18 20:06:07 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Apr 18 20:06:07 UTC 2023 I: Done submitting .buildinfo files. Tue Apr 18 20:06:07 UTC 2023 I: Removing signed pbbam_2.1.0+dfsg-2_amd64.buildinfo.asc files: removed './b1/pbbam_2.1.0+dfsg-2_amd64.buildinfo.asc' removed './b2/pbbam_2.1.0+dfsg-2_amd64.buildinfo.asc'