Wed Apr 17 07:38:29 UTC 2024 I: starting to build libseqlib/trixie/armhf on jenkins on '2024-04-17 07:38' Wed Apr 17 07:38:29 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_32/13450/console.log Wed Apr 17 07:38:29 UTC 2024 I: Downloading source for trixie/libseqlib=1.2.0+dfsg-11 --2024-04-17 07:38:29-- http://deb.debian.org/debian/pool/main/libs/libseqlib/libseqlib_1.2.0%2bdfsg-11.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2401 (2.3K) [text/prs.lines.tag] Saving to: ‘libseqlib_1.2.0+dfsg-11.dsc’ 0K .. 100% 297M=0s 2024-04-17 07:38:29 (297 MB/s) - ‘libseqlib_1.2.0+dfsg-11.dsc’ saved [2401/2401] Wed Apr 17 07:38:29 UTC 2024 I: libseqlib_1.2.0+dfsg-11.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libseqlib Binary: libseqlib2, libseqlib-dev Architecture: any Version: 1.2.0+dfsg-11 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/walaj/SeqLib Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/libseqlib Vcs-Git: https://salsa.debian.org/med-team/libseqlib.git Build-Depends: debhelper-compat (= 13), d-shlibs, pkg-config, pkg-kde-tools, libhts-dev, libcurl4-gnutls-dev | libcurl4-dev, zlib1g-dev, libfml-dev (>= 0.1+git20190320.b499514), libbwa-dev, libjsoncpp-dev, libssw-dev, libbz2-dev Package-List: libseqlib-dev deb libdevel optional arch=any libseqlib2 deb libs optional arch=any Checksums-Sha1: 584cb70cc2d11d595f26ec50763d11ca570395c5 148996 libseqlib_1.2.0+dfsg.orig.tar.xz 89ee20e44e0e76c6efce309a56e33556a76149bd 15456 libseqlib_1.2.0+dfsg-11.debian.tar.xz Checksums-Sha256: 408ee92e5041ff45d9d259d1507ef783e74c565d02e0c623ef0a67a7c387b953 148996 libseqlib_1.2.0+dfsg.orig.tar.xz 9e85fd66de1a1e1fcb576e045cfd1fefbeed75b222450032dfdc0b39a39ba2ea 15456 libseqlib_1.2.0+dfsg-11.debian.tar.xz Files: 8d8f26bf4fd751789bbc53bd7319355a 148996 libseqlib_1.2.0+dfsg.orig.tar.xz 6f36289dd0bbde1824dc445037845166 15456 libseqlib_1.2.0+dfsg-11.debian.tar.xz Dgit: 279a189ccc52e73b124a50bcfe14717ee68c64d8 debian archive/debian/1.2.0+dfsg-11 https://git.dgit.debian.org/libseqlib -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmV7fQAUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdowIxAAxOwXiOsLHzl8ozOX9E3nR4m7iV6w /+2iDm3S90Xj/MRyr6A6BoJ7ikHHkIgICBHYAdsQJ1pAjkuMLd5QnKhGPyOieZjA JqwybgsoFhg5onEV1YXIFePTvyB5LbSEAFWa4J97do06AJjdnwpCEiszxvcdMQrC 3b4URe/BBdsB/eMcY/7R5Vs5L9xH1ol/vF9e0sxj8pOxX91rOkdXd0B4KQ70QJuq x4yCjF3O8cNl3ntE6+hizMBcVLqwMgo5BlmdfmS+sBGuLOBVxVkz0AZzhjfa1Uol jgesCiUP1UR8JeCmd+p4Y+Vxr2zRJlz6MAiJOxT8UfPh98PVyGnmeCTd8OL39OA5 AcT/JTlMDxXA1rv0sAMQkcJBlMPNHr+8zZWPbH2/GndaQgwnY8iQhILPbW4H5+YQ dOlKVNHZNOcWpZZwedR7yPybOfXIKl7CKQdlQFc6Kp6gsnRmXE6V9OR0JvhkuJRa 03o7/25eByPNYpHar7x1H3PXd/ksUOp78xP8RZad7MisAVzS+wz2dsQDSmwvgayK MxSCn18sCu/3USnrsRvMHg2BQHD2oIDx4ApxliCmIWdEsfq8ixEjFawTj/U2evV5 34zqyBvZPS9gaVq4N5Zush80tKxOq8NaY4SYejlvPSCUTSqVoPgOoIV+aml+zXAD cmcRNsM7KLyr36M= =JgTs -----END PGP SIGNATURE----- Wed Apr 17 07:38:29 UTC 2024 I: Checking whether the package is not for us Wed Apr 17 07:38:29 UTC 2024 I: Starting 1st build on remote node virt64c-armhf-rb.debian.net. Wed Apr 17 07:38:29 UTC 2024 I: Preparing to do remote build '1' on virt64c-armhf-rb.debian.net. Wed Apr 17 07:41:26 UTC 2024 I: Deleting $TMPDIR on virt64c-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Apr 16 19:38:36 -12 2024 I: pbuilder-time-stamp: 1713339516 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [libseqlib_1.2.0+dfsg-11.dsc] I: copying [./libseqlib_1.2.0+dfsg.orig.tar.xz] I: copying [./libseqlib_1.2.0+dfsg-11.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Dec 14 22:09:04 2023 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libseqlib_1.2.0+dfsg-11.dsc: no acceptable signature found dpkg-source: info: extracting libseqlib in libseqlib-1.2.0+dfsg dpkg-source: info: unpacking libseqlib_1.2.0+dfsg.orig.tar.xz dpkg-source: info: unpacking libseqlib_1.2.0+dfsg-11.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs.patch dpkg-source: info: applying adapt_to_debian_fermi-lite.patch dpkg-source: info: applying fix_fermi-lite_usage.patch dpkg-source: info: applying fix_htslib_usage.patch dpkg-source: info: applying fml_include_path.patch dpkg-source: info: applying dynamic_lib.patch dpkg-source: info: applying use_debian_packaged_jsoncpp.patch dpkg-source: info: applying use_debian_packaged_ssw.patch dpkg-source: info: applying pkg-config.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/14750/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='6361a15cc89947ef95b48bed396d771e' 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='14750' 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.GMPVcTK8/pbuilderrc_AlNW --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.GMPVcTK8/b1 --logfile b1/build.log libseqlib_1.2.0+dfsg-11.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt64c 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 16 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/14750/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: armhf 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), d-shlibs, pkg-config, pkg-kde-tools, libhts-dev, libcurl4-gnutls-dev | libcurl4-dev, zlib1g-dev, libfml-dev (>= 0.1+git20190320.b499514), libbwa-dev, libjsoncpp-dev, libssw-dev, libbz2-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19635 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 d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on pkg-kde-tools; however: Package pkg-kde-tools is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-gnutls-dev | libcurl4-dev; however: Package libcurl4-gnutls-dev is not installed. Package libcurl4-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libfml-dev (>= 0.1+git20190320.b499514); however: Package libfml-dev is not installed. pbuilder-satisfydepends-dummy depends on libbwa-dev; however: Package libbwa-dev is not installed. pbuilder-satisfydepends-dummy depends on libjsoncpp-dev; however: Package libjsoncpp-dev is not installed. pbuilder-satisfydepends-dummy depends on libssw-dev; however: Package libssw-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev 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} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libbwa-dev{a} libbz2-dev{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfml-dev{a} libfml0{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libjsoncpp-dev{a} libjsoncpp25{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libssw-dev{a} libssw0{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} pkg-config{a} pkg-kde-tools{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libwww-perl lynx publicsuffix wget 0 packages upgraded, 74 newly installed, 0 to remove and 0 not upgraded. Need to get 29.6 MB of archives. After unpacking 103 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf libpython3.11-minimal armhf 3.11.8-1 [802 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.5.0-2+b2 [80.2 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf python3.11-minimal armhf 3.11.8-1 [1707 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf python3-minimal armhf 3.11.6-1 [26.2 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf tzdata all 2024a-1 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf readline-common all 8.2-3 [69.1 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libreadline8 armhf 8.2-3+b1 [144 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf libpython3.11-stdlib armhf 3.11.8-1 [1709 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf python3.11 armhf 3.11.8-1 [597 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf libpython3-stdlib armhf 3.11.6-1 [9224 B] Get: 13 http://deb.debian.org/debian trixie/main armhf python3 armhf 3.11.6-1 [26.2 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-2+b1 [314 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libmagic1 armhf 1:5.45-2+b1 [97.9 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-2+b1 [42.2 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-3 [1088 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.39.3-6 [81.2 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.0-3 [1367 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf d-shlibs all 0.106 [10.9 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 37 http://deb.debian.org/debian trixie/main armhf libelf1 armhf 0.190-1+b1 [171 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1 [101 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b2 [599 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b3 [284 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf libbwa-dev armhf 0.7.17-7+b3 [147 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf libbz2-dev armhf 1.0.8-5.1 [28.3 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-4+b1 [18.2 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-4+b1 [50.1 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5+b3 [158 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.59.0-1 [62.0 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf libssh2-1 armhf 1.11.0-4 [197 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf libcurl3-gnutls armhf 8.5.0-2 [378 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf libcurl4-gnutls-dev armhf 8.5.0-2 [490 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.20-1 [35.9 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf libdeflate-dev armhf 1.20-1 [44.0 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf libfml0 armhf 0.1+git20190320.b499514-1+b1 [70.8 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg-3+b1 [904 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf libfml-dev armhf 0.1+git20190320.b499514-1+b1 [82.4 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf libhtscodecs2 armhf 1.6.0-1+b1 [61.3 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf libhts3 armhf 1.19+ds-1 [394 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf liblzma-dev armhf 5.6.1+really5.4.5-1 [281 kB] Get: 65 http://deb.debian.org/debian trixie/main armhf libhts-dev armhf 1.19+ds-1 [1598 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf libjsoncpp25 armhf 1.9.5-6+b2 [69.9 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf libjsoncpp-dev armhf 1.9.5-6+b2 [24.8 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf libpkgconf3 armhf 1.8.1-1+b2 [31.9 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf libssw0 armhf 1.1-14 [20.8 kB] Get: 70 http://deb.debian.org/debian trixie/main armhf libssw-dev armhf 1.1-14 [24.0 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf pkgconf-bin armhf 1.8.1-1+b2 [28.9 kB] Get: 72 http://deb.debian.org/debian trixie/main armhf pkgconf armhf 1.8.1-1+b2 [26.2 kB] Get: 73 http://deb.debian.org/debian trixie/main armhf pkg-config armhf 1.8.1-1+b2 [14.0 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf pkg-kde-tools all 0.15.38 [97.8 kB] Fetched 29.6 MB in 1s (49.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. 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Setting up media-types (10.1.0) ... Setting up libpipeline1:armhf (1.5.7-2) ... Setting up libpsl5:armhf (0.21.2-1+b1) ... Setting up libicu72:armhf (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:armhf (1.1.0-2+b3) ... Setting up libnghttp2-14:armhf (1.59.0-1) ... Setting up libmagic1:armhf (1:5.45-2+b1) ... Setting up libdeflate0:armhf (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-2+b1) ... Setting up libfml0:armhf (0.1+git20190320.b499514-1+b1) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-4+b1) ... Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Apr 17 07:39:17 UTC 2024. Universal Time is now: Wed Apr 17 07:39:17 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:armhf (1.8.1-1+b2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up autopoint (0.21-14) ... Setting up libjsoncpp25:armhf (1.9.5-6+b2) ... Setting up d-shlibs (0.106) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-4+b1) ... Setting up autoconf (2.71-3) ... Setting up libbwa-dev (0.7.17-7+b3) ... Setting up liblzma-dev:armhf (5.6.1+really5.4.5-1) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg-3+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libssh2-1:armhf (1.11.0-4) ... Setting up netbase (6.4) ... Setting up libdeflate-dev:armhf (1.20-1) ... Setting up libelf1:armhf (0.190-1+b1) ... Setting up libssw0:armhf (1.1-14) ... Setting up readline-common (8.2-3) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b2) ... Setting up libbz2-dev:armhf (1.0.8-5.1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libjsoncpp-dev:armhf (1.9.5-6+b2) ... Setting up gettext (0.21-14+b1) ... Setting up libfml-dev:armhf (0.1+git20190320.b499514-1+b1) ... Setting up libssw-dev:armhf (1.1-14) ... Setting up libtool (2.4.7-7) ... Setting up libreadline8:armhf (8.2-3+b1) ... Setting up libldap-2.5-0:armhf (2.5.13+dfsg-5+b3) ... Setting up pkgconf:armhf (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up pkg-config:armhf (1.8.1-1+b2) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:armhf (3.11.8-1) ... Setting up libcurl3-gnutls:armhf (8.5.0-2) ... Setting up libcurl4-gnutls-dev:armhf (8.5.0-2) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3-stdlib:armhf (3.11.6-1) ... Setting up python3.11 (3.11.8-1) ... Setting up libhts3:armhf (1.19+ds-1) ... Setting up libhts-dev:armhf (1.19+ds-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.6-1) ... Setting up pkg-kde-tools (0.15.38) ... Processing triggers for libc-bin (2.37-15) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/libseqlib-1.2.0+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 > ../libseqlib_1.2.0+dfsg-11_source.changes dpkg-buildpackage: info: source package libseqlib dpkg-buildpackage: info: source version 1.2.0+dfsg-11 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --with pkgkde_symbolshelper dh_clean debian/rules binary dh binary --with pkgkde_symbolshelper dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.ac, libtoolize: and rerunning libtoolize and aclocal. libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am. libtoolize: 'AC_PROG_RANLIB' is rendered obsolete by 'LT_INIT' configure.ac:6: warning: The macro `AC_CONFIG_HEADER' is obsolete. configure.ac:6: You should run autoupdate. ./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from... configure.ac:6: the top level configure.ac:19: warning: The macro `AC_PROG_LIBTOOL' is obsolete. configure.ac:19: You should run autoupdate. aclocal.m4:122: AC_PROG_LIBTOOL is expanded from... configure.ac:19: the top level configure.ac:17: installing './compile' configure.ac:19: installing './config.guess' configure.ac:19: installing './config.sub' configure.ac:4: installing './install-sh' configure.ac:4: installing './missing' src/Makefile.am: installing './depcomp' dh_auto_configure ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for ranlib... ranlib checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... (cached) ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for zlib.h... yes checking for library containing gzopen... -lz checking for library containing lzma_code... -llzma checking for library containing BZ2_bzBuffToBuffDecompress... -lbz2 checking for library containing clock_gettime... none required checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for htslib... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/seqtools/Makefile config.status: creating libseqlib.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build make -j3 make[1]: Entering directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' make all-recursive make[2]: Entering directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' Making all in src make[3]: Entering directory '/build/reproducible-path/libseqlib-1.2.0+dfsg/src' /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-FastqReader.lo `test -f 'FastqReader.cpp' || echo './'`FastqReader.cpp /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BFC.lo `test -f 'BFC.cpp' || echo './'`BFC.cpp /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-ReadFilter.lo `test -f 'ReadFilter.cpp' || echo './'`ReadFilter.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c FastqReader.cpp -fPIC -DPIC -o .libs/libseqlib_la-FastqReader.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c ReadFilter.cpp -fPIC -DPIC -o .libs/libseqlib_la-ReadFilter.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BFC.cpp -fPIC -DPIC -o .libs/libseqlib_la-BFC.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c FastqReader.cpp -o libseqlib_la-FastqReader.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BFC.cpp -o libseqlib_la-BFC.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-SeqPlot.lo `test -f 'SeqPlot.cpp' || echo './'`SeqPlot.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c SeqPlot.cpp -fPIC -DPIC -o .libs/libseqlib_la-SeqPlot.o /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-GenomicRegion.lo `test -f 'GenomicRegion.cpp' || echo './'`GenomicRegion.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c GenomicRegion.cpp -fPIC -DPIC -o .libs/libseqlib_la-GenomicRegion.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c SeqPlot.cpp -o libseqlib_la-SeqPlot.o >/dev/null 2>&1 In file included from /usr/include/c++/13/vector:72, from ../SeqLib/ReadFilter.h:7, from ReadFilter.cpp:1: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const SeqLib::Filter::AbstractRule&}; _Tp = SeqLib::Filter::AbstractRule; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SeqLib::Filter::AbstractRule; _Alloc = std::allocator]', inlined from 'void SeqLib::Filter::ReadFilter::AddRule(const SeqLib::Filter::AbstractRule&)' at ReadFilter.cpp:139:31: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SeqLib::Filter::AbstractRule; _Alloc = std::allocator]', inlined from 'void SeqLib::Filter::ReadFilterCollection::CheckHasIncluder()' at ReadFilter.cpp:282:31: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-RefGenome.lo `test -f 'RefGenome.cpp' || echo './'`RefGenome.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c RefGenome.cpp -fPIC -DPIC -o .libs/libseqlib_la-RefGenome.o In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SeqLib::Filter::AbstractRule; _Alloc = std::allocator]', inlined from 'SeqLib::Filter::ReadFilterCollection::ReadFilterCollection(const std::string&, const SeqLib::BamHeader&)' at ReadFilter.cpp:252:33: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SeqLib::Filter::AbstractRule; _Alloc = std::allocator]', inlined from 'SeqLib::Filter::ReadFilterCollection::ReadFilterCollection(const std::string&, const SeqLib::BamHeader&)' at ReadFilter.cpp:259:31: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c RefGenome.cpp -o libseqlib_la-RefGenome.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BamWriter.lo `test -f 'BamWriter.cpp' || echo './'`BamWriter.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamWriter.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamWriter.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c ReadFilter.cpp -o libseqlib_la-ReadFilter.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamWriter.cpp -o libseqlib_la-BamWriter.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BamReader.lo `test -f 'BamReader.cpp' || echo './'`BamReader.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamReader.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamReader.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c GenomicRegion.cpp -o libseqlib_la-GenomicRegion.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamReader.cpp -o libseqlib_la-BamReader.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BWAWrapper.lo `test -f 'BWAWrapper.cpp' || echo './'`BWAWrapper.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BWAWrapper.cpp -fPIC -DPIC -o .libs/libseqlib_la-BWAWrapper.o /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BamRecord.lo `test -f 'BamRecord.cpp' || echo './'`BamRecord.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamRecord.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamRecord.o In file included from /usr/include/c++/13/vector:72, from ../SeqLib/BWAWrapper.h:5, from BWAWrapper.cpp:9: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mem_aln_t&}; _Tp = mem_aln_t; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from ../SeqLib/BWAWrapper.h:7: /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/13/bits/stl_algo.h:61: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mem_aln_t; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mem_aln_t; _Alloc = std::allocator]', inlined from 'void SeqLib::BWAWrapper::AlignSequence(const std::string&, const std::string&, SeqLib::BamRecordVector&, bool, double, int) const' at BWAWrapper.cpp:297:18: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const mem_aln_t&, const mem_aln_t&)]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, inlined from 'void SeqLib::BWAWrapper::AlignSequence(const std::string&, const std::string&, SeqLib::BamRecordVector&, bool, double, int) const' at BWAWrapper.cpp:301:14: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const mem_aln_t&, const mem_aln_t&)]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, inlined from 'void SeqLib::BWAWrapper::AlignSequence(const std::string&, const std::string&, SeqLib::BamRecordVector&, bool, double, int) const' at BWAWrapper.cpp:301:14: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BWAWrapper.cpp -o libseqlib_la-BWAWrapper.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-FermiAssembler.lo `test -f 'FermiAssembler.cpp' || echo './'`FermiAssembler.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c FermiAssembler.cpp -fPIC -DPIC -o .libs/libseqlib_la-FermiAssembler.o In file included from /usr/include/c++/13/vector:72, from ../SeqLib/BamRecord.h:6, from BamRecord.cpp:1: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'std::vector SeqLib::BamRecord::GetSmartDoubleTag(const std::string&) const' at BamRecord.cpp:578:15: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'std::vector SeqLib::BamRecord::GetSmartDoubleTag(const std::string&) const' at BamRecord.cpp:580:20: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamRecord.cpp -o libseqlib_la-BamRecord.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c FermiAssembler.cpp -o libseqlib_la-FermiAssembler.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BamHeader.lo `test -f 'BamHeader.cpp' || echo './'`BamHeader.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamHeader.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamHeader.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamHeader.cpp -o libseqlib_la-BamHeader.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -version-info 2:0 -lfml `/usr/bin/pkg-config --libs htslib` `/usr/bin/pkg-config --libs jsoncpp` -lssw -Wl,-z,relro -Wl,-z,now -o libseqlib.la -rpath /usr/lib/arm-linux-gnueabihf libseqlib_la-FastqReader.lo libseqlib_la-BFC.lo libseqlib_la-ReadFilter.lo libseqlib_la-SeqPlot.lo libseqlib_la-GenomicRegion.lo libseqlib_la-RefGenome.lo libseqlib_la-BamWriter.lo libseqlib_la-BamReader.lo libseqlib_la-BWAWrapper.lo libseqlib_la-BamRecord.lo libseqlib_la-FermiAssembler.lo libseqlib_la-BamHeader.lo -lbz2 -llzma -lz -pthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/13/crtbeginS.o .libs/libseqlib_la-FastqReader.o .libs/libseqlib_la-BFC.o .libs/libseqlib_la-ReadFilter.o .libs/libseqlib_la-SeqPlot.o .libs/libseqlib_la-GenomicRegion.o .libs/libseqlib_la-RefGenome.o .libs/libseqlib_la-BamWriter.o .libs/libseqlib_la-BamReader.o .libs/libseqlib_la-BWAWrapper.o .libs/libseqlib_la-BamRecord.o .libs/libseqlib_la-FermiAssembler.o .libs/libseqlib_la-BamHeader.o -lfml -lhts -ljsoncpp -lssw -lbz2 -llzma -lz -L/usr/lib/gcc/arm-linux-gnueabihf/13 -L/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/13/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/13/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/crtn.o -g -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -pthread -Wl,-soname -Wl,libseqlib.so.2 -o .libs/libseqlib.so.2.0.0 libtool: link: (cd ".libs" && rm -f "libseqlib.so.2" && ln -s "libseqlib.so.2.0.0" "libseqlib.so.2") libtool: link: (cd ".libs" && rm -f "libseqlib.so" && ln -s "libseqlib.so.2.0.0" "libseqlib.so") libtool: link: ar cr .libs/libseqlib.a libseqlib_la-FastqReader.o libseqlib_la-BFC.o libseqlib_la-ReadFilter.o libseqlib_la-SeqPlot.o libseqlib_la-GenomicRegion.o libseqlib_la-RefGenome.o libseqlib_la-BamWriter.o libseqlib_la-BamReader.o libseqlib_la-BWAWrapper.o libseqlib_la-BamRecord.o libseqlib_la-FermiAssembler.o libseqlib_la-BamHeader.o libtool: link: ranlib .libs/libseqlib.a libtool: link: ( cd ".libs" && rm -f "libseqlib.la" && ln -s "../libseqlib.la" "libseqlib.la" ) make[3]: Leaving directory '/build/reproducible-path/libseqlib-1.2.0+dfsg/src' make[3]: Entering directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' make[3]: Leaving directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' make[2]: Leaving directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' dh_auto_test make -j3 check "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' Making check in src make[2]: Entering directory '/build/reproducible-path/libseqlib-1.2.0+dfsg/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/libseqlib-1.2.0+dfsg/src' make[2]: Entering directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' make[2]: Leaving directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j1 install DESTDIR=/build/reproducible-path/libseqlib-1.2.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' echo "mkdir -p lib && cp src/libseqlib.a fermi-lite/libfml.a bwa/libbwa.a htslib/libhts.a lib" mkdir -p lib && cp src/libseqlib.a fermi-lite/libfml.a bwa/libbwa.a htslib/libhts.a lib make[1]: Leaving directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' dh_install # Trick to get also headers moved by d-shlibmove cp -a SeqLib debian # note: also GenomicRegionCollection.cpp is really needed by freebayes d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --movedev debian/SeqLib usr/include \ --override s/libfml0-dev/libfml-dev/ \ --override s/libssw0-dev/libssw-dev/ \ src/.libs/libseqlib.so Library package automatic movement utility --> libfml-dev package exists. --> libhts-dev package exists. --> libjsoncpp-dev package exists. --> libssw-dev package exists. --> zlib1g-dev package exists. set -e install -d -m 755 debian/libseqlib-dev/usr/lib/arm-linux-gnueabihf install -d -m 755 debian/libseqlib2/usr/lib/arm-linux-gnueabihf mv src/.libs/libseqlib.a debian/libseqlib-dev/usr/lib/arm-linux-gnueabihf mv src/.libs/libseqlib.so debian/libseqlib-dev/usr/lib/arm-linux-gnueabihf mv /build/reproducible-path/libseqlib-1.2.0+dfsg/src/.libs/libseqlib.so.2 debian/libseqlib2/usr/lib/arm-linux-gnueabihf mv /build/reproducible-path/libseqlib-1.2.0+dfsg/src/.libs/libseqlib.so.2.0.0 debian/libseqlib2/usr/lib/arm-linux-gnueabihf PKGDEV=libseqlib-dev PKGSHL=libseqlib2 install -d -m 755 debian/libseqlib-dev/usr/include mv debian/SeqLib debian/libseqlib-dev/usr/include mkdir -p /build/reproducible-path/libseqlib-1.2.0+dfsg/debian/libseqlib-dev/usr/lib/arm-linux-gnueabihf/pkgconfig mv libseqlib.pc /build/reproducible-path/libseqlib-1.2.0+dfsg/debian/libseqlib-dev/usr/lib/arm-linux-gnueabihf/pkgconfig make[1]: Leaving directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: symbol kseq_read used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol err_fclose used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol bns_destroy used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol bwt_bwtupdate_core used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol mem_reg2aln used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol bwt_dump_bwt used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol bwt_dump_sa used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol err_xopen_core used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol err_fflush used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol bwt_cal_sa used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: 12 other similar warnings have been skipped (use -v to see them all) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libseqlib2-dbgsym' in '../libseqlib2-dbgsym_1.2.0+dfsg-11_armhf.deb'. dpkg-deb: building package 'libseqlib2' in '../libseqlib2_1.2.0+dfsg-11_armhf.deb'. dpkg-deb: building package 'libseqlib-dev' in '../libseqlib-dev_1.2.0+dfsg-11_armhf.deb'. dpkg-genbuildinfo --build=binary -O../libseqlib_1.2.0+dfsg-11_armhf.buildinfo dpkg-genchanges --build=binary -O../libseqlib_1.2.0+dfsg-11_armhf.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/14750 and its subdirectories I: Current time: Tue Apr 16 19:41:08 -12 2024 I: pbuilder-time-stamp: 1713339668 Wed Apr 17 07:41:32 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt32c-armhf-rb.debian.net. Wed Apr 17 07:41:32 UTC 2024 I: Preparing to do remote build '2' on virt32c-armhf-rb.debian.net. Wed Apr 17 07:44:31 UTC 2024 I: Deleting $TMPDIR on virt32c-armhf-rb.debian.net. Wed Apr 17 07:44:33 UTC 2024 I: libseqlib_1.2.0+dfsg-11_armhf.changes: Format: 1.8 Date: Thu, 14 Dec 2023 23:01:06 +0100 Source: libseqlib Binary: libseqlib-dev libseqlib2 libseqlib2-dbgsym Architecture: armhf Version: 1.2.0+dfsg-11 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: libseqlib-dev - C++ htslib/bwa-mem/fermi interface for interrogating sequence dat libseqlib2 - C++ htslib/bwa-mem/fermi interface for interrogating sequence dat Closes: 1047821 Changes: libseqlib (1.2.0+dfsg-11) unstable; urgency=medium . * d/clean: new: cleanup leftovers. (Closes: #1047821) Checksums-Sha1: 6ca1cfedb7012495067308230771cea34c5b92de 210264 libseqlib-dev_1.2.0+dfsg-11_armhf.deb 9440315a789d5bf92ee089d789a3725fc656ed5c 2184256 libseqlib2-dbgsym_1.2.0+dfsg-11_armhf.deb 2e48376dc1f8f14f981be50ce076cfa7c9d04b57 138788 libseqlib2_1.2.0+dfsg-11_armhf.deb 16ee78947e03554a1b1180d3c2462a978bbe8fd7 7470 libseqlib_1.2.0+dfsg-11_armhf.buildinfo Checksums-Sha256: 5a421db789551714ec0c47c10662d0c169be91d028fb9c6adce1d49e692c9890 210264 libseqlib-dev_1.2.0+dfsg-11_armhf.deb 40f95e7a64f4c9ae52bd5893b3a691cc2173c67d3e5e20e7688eda504f35ad3b 2184256 libseqlib2-dbgsym_1.2.0+dfsg-11_armhf.deb 5917c7b601cb6f609faa4a56b4bcbb52c29cc45da557dba490a2349f4b05b5d7 138788 libseqlib2_1.2.0+dfsg-11_armhf.deb 7392e2aaae40c1509e1e2cccfecd03a8ec8eacadd681b21520e6d338c3c16d0e 7470 libseqlib_1.2.0+dfsg-11_armhf.buildinfo Files: f4fdb967192daf49735a9cc84f250e7c 210264 libdevel optional libseqlib-dev_1.2.0+dfsg-11_armhf.deb 3983296af577fbbcec290e0f9af620dd 2184256 debug optional libseqlib2-dbgsym_1.2.0+dfsg-11_armhf.deb cdb93c315f5b26230e71e5dae13a90a4 138788 libs optional libseqlib2_1.2.0+dfsg-11_armhf.deb cbda50618739b0a6945fda6d350f40a1 7470 science optional libseqlib_1.2.0+dfsg-11_armhf.buildinfo Wed Apr 17 07:44:35 UTC 2024 I: diffoscope 264 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_32-13450.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.GMPVcTK8/libseqlib_1.2.0+dfsg-11.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.GMPVcTK8/libseqlib_1.2.0+dfsg-11.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.GMPVcTK8/libseqlib_1.2.0+dfsg-11.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.GMPVcTK8/b1/libseqlib_1.2.0+dfsg-11_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.GMPVcTK8/b2/libseqlib_1.2.0+dfsg-11_armhf.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: 0.383s) 0.383s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.045s) 0.045s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 717ms CPU time consumed: 718ms Wed Apr 17 07:44:36 UTC 2024 I: diffoscope 264 found no differences in the changes files, and a .buildinfo file also exists. Wed Apr 17 07:44:36 UTC 2024 I: libseqlib from trixie built successfully and reproducibly on armhf. Wed Apr 17 07:44:38 UTC 2024 I: Submitting .buildinfo files to external archives: Wed Apr 17 07:44:38 UTC 2024 I: Submitting 12K b1/libseqlib_1.2.0+dfsg-11_armhf.buildinfo.asc Wed Apr 17 07:44:39 UTC 2024 I: Submitting 12K b2/libseqlib_1.2.0+dfsg-11_armhf.buildinfo.asc Wed Apr 17 07:44:41 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Apr 17 07:44:41 UTC 2024 I: Done submitting .buildinfo files. Wed Apr 17 07:44:41 UTC 2024 I: Removing signed libseqlib_1.2.0+dfsg-11_armhf.buildinfo.asc files: removed './b1/libseqlib_1.2.0+dfsg-11_armhf.buildinfo.asc' removed './b2/libseqlib_1.2.0+dfsg-11_armhf.buildinfo.asc'