Fri Apr 14 13:11:05 UTC 2023 I: starting to build libgkarrays/bookworm/amd64 on jenkins on '2023-04-14 13:10' Fri Apr 14 13:11:05 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_29/10041/console.log Fri Apr 14 13:11:05 UTC 2023 I: Downloading source for bookworm/libgkarrays=2.1.0+dfsg-4 --2023-04-14 13:11:05-- http://cdn-fastly.deb.debian.org/debian/pool/main/libg/libgkarrays/libgkarrays_2.1.0%2bdfsg-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2093 (2.0K) [text/prs.lines.tag] Saving to: ‘libgkarrays_2.1.0+dfsg-4.dsc’ 0K .. 100% 171M=0s 2023-04-14 13:11:05 (171 MB/s) - ‘libgkarrays_2.1.0+dfsg-4.dsc’ saved [2093/2093] Fri Apr 14 13:11:05 UTC 2023 I: libgkarrays_2.1.0+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libgkarrays Binary: libgkarrays1, libgkarrays-dev Architecture: any Version: 2.1.0+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://crac.gforge.inria.fr/gkarrays/ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/libgkarrays Vcs-Git: https://salsa.debian.org/med-team/libgkarrays.git Build-Depends: debhelper-compat (= 13), d-shlibs, zlib1g-dev Package-List: libgkarrays-dev deb libdevel optional arch=any libgkarrays1 deb libs optional arch=any Checksums-Sha1: fd7dafda51703ba61c8221ba158143c376bc1d86 97880 libgkarrays_2.1.0+dfsg.orig.tar.xz 63b9ce09e2eb0312bfd77bdd65c638431f280b68 10864 libgkarrays_2.1.0+dfsg-4.debian.tar.xz Checksums-Sha256: bb73beac8d9c3e6b4acfebba325904a98653357f8373ec60ed3614ff6f04bb84 97880 libgkarrays_2.1.0+dfsg.orig.tar.xz 98714dab107f399e6eba7346b24fc9e53b53df62acfdd9fe09d2a8e9feae8b6a 10864 libgkarrays_2.1.0+dfsg-4.debian.tar.xz Files: e810e849c1eb934e0a366d27d8043015 97880 libgkarrays_2.1.0+dfsg.orig.tar.xz 673814d6be34c44098468bfe724bf406 10864 libgkarrays_2.1.0+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl+2PvERHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHsnQ//aukPMjW26GtPszSe9gDB6uxawG6qG8n2 uo6+YU7PZbK/afVGtgzmI++U6NATxQZhzVl13NYW2UU4wpuNiHGx1UXNRTvnbPxB jj1olVjv9mB/h2kjOCqD05TiJgM39OhwzNV0wOjsy3OG7A8bHwVKkLBbkksLM40J I4o2YfH+jG1oapsMhaecbdJEg20G82fQGGpgKDcWW1gvzd+FYH7mpJuujz5CWSFO Ce0BEbmhhavUmlFxwFXDiEWxFySEim+g1Zoxud6vvmnW2/2EE9bcWRgFbG1LIYC6 Uj9DfWLIOJDUB8rdzsqeFOq+CIgDjoACbGVdKa1OOHdzB92fqQ3dPXCReWT4Wdf4 ZyfUbjjtZzjD3qS46qUmUFoDErVidES1qbcDgSUcc6QiW6fmsbXOESuZDYRueJlk S1s26SFNXPgzNgSbivcrXdgKTM2CioBifejiooi7LzbPtHiaGxxX64AEU3NtFYj9 5vBI0PZn4RsSTae9PO1MsFy9mUjuh/y+/n3TXcx7swBalfIhLp9lu8QBVs0YpBcO XdpCwvbtsqNG11M75TAAdIZX+VB/CR9YgH5fJWl7VMRj8vpP3W2/TzFTQaFfxtqd CsvE1ehFCfcYcJfeq7nctUFep88xwEvUPyPW5eNVv6zS5yeB0GBFdDm9kHXkCrb3 aERJp8AT2b0= =/sWu -----END PGP SIGNATURE----- Fri Apr 14 13:11:05 UTC 2023 I: Checking whether the package is not for us Fri Apr 14 13:11:05 UTC 2023 I: Starting 1st build on remote node ionos11-amd64.debian.net. Fri Apr 14 13:11:05 UTC 2023 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Fri Apr 14 13:12:52 UTC 2023 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Apr 14 01:11:07 -12 2023 I: pbuilder-time-stamp: 1681477867 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 [libgkarrays_2.1.0+dfsg-4.dsc] I: copying [./libgkarrays_2.1.0+dfsg.orig.tar.xz] I: copying [./libgkarrays_2.1.0+dfsg-4.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Nov 18 21:46:25 2020 -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 ./libgkarrays_2.1.0+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting libgkarrays in libgkarrays-2.1.0+dfsg dpkg-source: info: unpacking libgkarrays_2.1.0+dfsg.orig.tar.xz dpkg-source: info: unpacking libgkarrays_2.1.0+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying proper_soname.patch dpkg-source: info: applying fix_pkg-config.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2661004/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=15' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='c75953236e9047269e77273c75ebac11' 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='2661004' 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.Az4AYAPc/pbuilderrc_Zmqf --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.Az4AYAPc/b1 --logfile b1/build.log libgkarrays_2.1.0+dfsg-4.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Feb 12 08:05 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 01:20 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 22:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 02:43 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 01:33 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 22:02 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 22:02 more -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Feb 12 08:05 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 04:31 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 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 22:02 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar -rwxr-xr-x 1 root root 14520 Nov 2 04:31 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 20:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 22:02 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 22:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 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/2661004/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), d-shlibs, zlib1g-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 ... 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 d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-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} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 19.7 MB of archives. After unpacking 73.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 d-shlibs all 0.104 [18.6 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Fetched 19.7 MB in 0s (47.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-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 .../14-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../15-d-shlibs_0.104_all.deb ... Unpacking d-shlibs (0.104) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-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 .../20-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 .../21-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... 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Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-12) ... Setting up d-shlibs (0.104) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.1+b3) ... 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 gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-8) ... 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/libgkarrays-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 > ../libgkarrays_2.1.0+dfsg-4_source.changes dpkg-buildpackage: info: source package libgkarrays dpkg-buildpackage: info: source version 2.1.0+dfsg-4 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 dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf aclocal: warning: couldn't open directory 'config/m4': No such file or directory autoreconf: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: warning: couldn't open directory 'm4': No such file or directory libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:32: warning: The macro `AM_PROG_LIBTOOL' is obsolete. configure.in:32: You should run autoupdate. m4/libtool.m4:101: AM_PROG_LIBTOOL is expanded from... configure.in:32: the top level configure.in:74: warning: The macro `AC_HEADER_STDC' is obsolete. configure.in:74: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.in:74: the top level autoheader: warning: autoconf input should be named 'configure.ac', not 'configure.in' automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:32: installing './compile' configure.in:32: installing './config.guess' configure.in:32: installing './config.sub' configure.in:31: installing './install-sh' configure.in:31: installing './missing' automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' doc/Makefile.am:2: warning: suffix '.texinfo' for Texinfo files is discouraged; use '.texi' instead doc/Makefile.am:2: installing 'doc/texinfo.tex' libProgressBar/Makefile.am: installing './depcomp' libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'config/m4'. libtoolize: copying file 'config/m4/libtool.m4' libtoolize: copying file 'config/m4/ltoptions.m4' libtoolize: copying file 'config/m4/ltsugar.m4' libtoolize: copying file 'config/m4/ltversion.m4' libtoolize: copying file 'config/m4/lt~obsolete.m4' configure.ac:213: installing 'config/compile' configure.ac:231: installing 'config/config.guess' configure.ac:231: installing 'config/config.sub' configure.ac:206: installing 'config/install-sh' configure.ac:206: installing 'config/missing' doc/Makefile.am:107: installing 'config/texinfo.tex' src/Makefile.am:117: warning: source file '$(SUX_DIR)/rank9b.cpp' is in a subdirectory, src/Makefile.am:117: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least one source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, this automake: behavior may change in a future Automake major version, with object automake: files being placed in the same subdirectory as the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. src/Makefile.am: installing 'config/depcomp' tests/Makefile.am:125: warning: wildcard dataset/*.fa: non-POSIX variable name tests/Makefile.am:125: (probably a GNU make extension) parallel-tests: installing 'config/test-driver' dh_auto_configure ./configure --build=x86_64-linux-gnu --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/x86_64-linux-gnu --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... /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 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 gawk... (cached) mawk 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 how to run the C preprocessor... gcc -E checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for texi2dvi... no checking for pdftex... no checking for kpsewhich... no configure: WARNING: The 'texi2dvi' or 'pdftex' program could not be found. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases. configure: WARNING: The 'texi2dvi' or 'pdftex' is missing a correct latex installation. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases. checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /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 the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu 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... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /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 -m elf_x86_64) 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 -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) 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 -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for ld used by gcc... (cached) /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... (cached) yes checking for dpkg... /usr/bin/dpkg checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for sys/time.h... yes checking for inline... inline checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking for gettimeofday... yes checking for memset... yes checking for select... yes checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for size_t... yes checking for uint8_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for unsigned long long int... yes checking for gzread in -lz... yes checking for pthread_create in -lpthread... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating postinst chmod: cannot access 'prerm': No such file or directory config.status: creating prerm config.status: creating control config.status: creating libGkArrays.pc config.status: creating Makefile config.status: creating src/Makefile config.status: creating tests/Makefile config.status: creating src/sux/Makefile config.status: creating src/kseq/Makefile config.status: creating doc/Makefile config.status: creating doc/libGkArrays.3 config.status: creating doc/package.texi config.status: creating config/config.h config.status: executing depfiles commands config.status: executing libtool commands === configuring in src/libProgressBar-1.2.0 (/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0) configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr' '--build=x86_64-linux-gnu' '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' '--sysconfdir=/etc' '--localstatedir=/var' '--disable-silent-rules' '--libdir=${prefix}/lib/x86_64-linux-gnu' '--runstatedir=/run' '--disable-maintainer-mode' '--disable-dependency-tracking' 'build_alias=x86_64-linux-gnu' 'CXXFLAGS=-g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' 'LDFLAGS=-Wl,-z,relro -Wl,-z,now' 'CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2' 'CFLAGS=-g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' --cache-file=/dev/null --srcdir=. checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /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 build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc 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 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 a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /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 x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu 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... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /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 -m elf_x86_64) 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 whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) none checking for g++... g++ 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 dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) 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 -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for dpkg... /usr/bin/dpkg checking for rpmbuild... no checking for rpm... no checking for texi2dvi... no checking for pdftex... no checking for kpsewhich... no configure: WARNING: The 'texi2dvi' or 'pdftex' program could not be found. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases. configure: WARNING: The 'texi2dvi' or 'pdftex' is missing a correct latex installation. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases. checking for an ANSI C-conforming const... yes checking for inline... inline checking for sys/mkdev.h... no checking for sys/sysmacros.h... yes checking for size_t... yes checking for working alloca.h... yes checking for alloca... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for struct stat.st_blocks... yes checking whether ln -s works... yes checking for egrep... (cached) /bin/grep -E checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for sys/time.h... yes checking for time.h... yes checking for sys/sysmacros.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for memory.h... yes checking for fcntl.h... yes checking for alloca.h... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating postinst chmod: cannot access 'prerm': No such file or directory config.status: creating prerm config.status: creating libProgressBar.lsm config.status: creating libProgressBar.spec config.status: creating control config.status: creating libProgressBar.pc config.status: creating Makefile config.status: creating libProgressBar/Makefile config.status: creating doc/Makefile config.status: creating doc/libProgressBar.3 config.status: creating libProgressBar/config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build make -j15 make[1]: Entering directory '/build/libgkarrays-2.1.0+dfsg' Making all in src make[2]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src' Making all in kseq make[3]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/kseq' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/kseq' Making all in sux make[3]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/sux' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/sux' Making all in libProgressBar-1.2.0 make[3]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0' Making all in libProgressBar make[4]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' make all-am make[5]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O6 -Wall --pedantic --ansi -c -o testPB.o testPB.cpp /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O6 -Wall --pedantic --ansi -c -o progressBar.lo progressBar.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O6 -Wall --pedantic --ansi -c progressBar.cpp -fPIC -DPIC -o .libs/progressBar.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O6 -Wall --pedantic --ansi -c progressBar.cpp -o progressBar.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -O6 -Wall --pedantic --ansi -version-info 1:2:1 -Wl,-z,relro -Wl,-z,now -o libProgressBar.la -rpath /usr/lib/x86_64-linux-gnu progressBar.lo libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o .libs/progressBar.o -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o 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-I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c largebinvect.cxx -fPIC -DPIC -o .libs/largebinvect.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c solArray.cpp -fPIC -DPIC -o .libs/solArray.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkCFPSBuilder.cpp -fPIC -DPIC -o .libs/gkCFPSBuilder.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c bitvector.cxx -fPIC -DPIC -o .libs/bitvector.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c utils.cpp -fPIC -DPIC -o .libs/utils.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c sux/rank9b.cpp -fPIC -DPIC -o .libs/rank9b.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readsReader.cpp -fPIC -DPIC -o .libs/readsReader.o sux/rank9b.cpp: In member function 'uint64_t rank9b::rank(uint64_t)': sux/rank9b.cpp:144:100: warning: suggest parentheses around '-' inside '>>' [-Wparentheses] 144 | return counts[ block ] + ( counts[ block + 1 ] >> ( offset + ( offset >> sizeof offset * 8 - 4 & 0x8 ) ) * 9 & 0x1FF ) + count( bits[ word ] & ( ( 1ULL << k % 64 ) - 1 ) ); | ~~~~~~~~~~~~~~~~~~^~~ sux/rank9b.cpp: In member function 'uint64_t rank9b::select(uint64_t)': sux/rank9b.cpp:207:88: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses] 207 | const uint64_t rank_in_word = rank_in_block - ( subcounts >> ( offset_in_block - 1 & 7 ) * 9 & 0x1FF ); | ~~~~~~~~~~~~~~~~^~~ In file included from ./readsReader.h:109, from ./gkArrays.h:115, from buildTables.cpp:111: ./kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ ./kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' 227 | __KSEQ_READ | ^~~~~~~~~~~ ./readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' 111 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c bitvector.cxx -o bitvector.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c sux/rank9b.cpp -o rank9b.o >/dev/null 2>&1 In file included from readsReader.h:109, from gkArrays.h:115, from gkArraysBuilder.h:105, from gkArraysBuilder.cpp:103: kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' 227 | __KSEQ_READ | ^~~~~~~~~~~ readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' 111 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c largebinvect.cxx -o largebinvect.o >/dev/null 2>&1 In file included from readsReader.h:109, from gkArrays.h:115, from gkCFPSBuilder.cpp:110: kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' 227 | __KSEQ_READ | ^~~~~~~~~~~ readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' 111 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ gkSABuilder.cpp: In function 'int64_t gkarrays::partition(SolArray*, SolArray*, uintSA, uintSA, uintSA)': gkSABuilder.cpp:340:24: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 340 | while(i <= end && values->get(i) < pivotv||((pivotv==values->get(i)) &&(pivotp>sa->get(i)))); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./readsReader.h:109, from ./gkArrays.h:115, from ./gkSABuilder.h:108, from gkSABuilder.cpp:104: ./readsReader.h: At global scope: ./kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ ./kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' 227 | __KSEQ_READ | ^~~~~~~~~~~ ./readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' 111 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ In file included from ./readsReader.h:109, from ./gkArrays.h:115, from ./gkIFABuilder.h:107, from gkIFABuilder.cpp:105: ./kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ ./kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' 227 | __KSEQ_READ | ^~~~~~~~~~~ ./readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' 111 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c utils.cpp -o utils.o >/dev/null 2>&1 In file included from readsReader.h:109, from gkArrays.h:115, from gkArrays.cpp:113: kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' 227 | __KSEQ_READ | ^~~~~~~~~~~ readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' 111 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkArraysBuilder.cpp -o gkArraysBuilder.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c solArray.cpp -o solArray.o >/dev/null 2>&1 gkArrays.cpp: In member function 'char* gkarrays::gkArrays::getTagFactor(uint, uint, uint)': gkArrays.cpp:454:14: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' output may be truncated copying 4 bytes from a string of length 4 [-Wstringop-truncation] 454 | strncpy(&final_dna[previous_length], dna, 4); | ^ gkArrays.cpp:460:14: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' output may be truncated copying between 0 and 3 bytes from a string of length 4 [-Wstringop-truncation] 460 | strncpy(&final_dna[previous_length], dna, (p+fact_length+readPos)%4); | ^ gkArrays.cpp: In member function 'char* gkarrays::gkArrays::getTag(uint)': gkArrays.cpp:425:14: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' output may be truncated copying 4 bytes from a string of length 4 [-Wstringop-truncation] 425 | strncpy(&final_dna[previous_length], dna, 4); | ^ gkArrays.cpp:430:14: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' output may be truncated copying between 0 and 3 bytes from a string of length 4 [-Wstringop-truncation] 430 | strncpy(&final_dna[previous_length], dna, nextReadPos%4); | ^ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkCFPSBuilder.cpp -o gkCFPSBuilder.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readsReader.cpp -o readsReader.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkIFABuilder.cpp -o gkIFABuilder.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkArrays.cpp -o gkArrays.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkSABuilder.cpp -o gkSABuilder.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 2:0:1 -lpthread -L/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar -Wl,-z,relro -Wl,-z,now -o libGkArrays.la -rpath /usr/lib/x86_64-linux-gnu gkArrays.lo solArray.lo utils.lo gkArraysBuilder.lo gkSABuilder.lo gkCFPSBuilder.lo gkIFABuilder.lo readsReader.lo largebinvect.lo bitvector.lo rank9b.lo -lpthread -lz libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o .libs/gkArrays.o .libs/solArray.o .libs/utils.o .libs/gkArraysBuilder.o .libs/gkSABuilder.o .libs/gkCFPSBuilder.o .libs/gkIFABuilder.o .libs/readsReader.o .libs/largebinvect.o .libs/bitvector.o .libs/rank9b.o -Wl,-rpath -Wl,/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -L/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs /build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs/libProgressBar.so -lpthread -lz -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libGkArrays.so.1 -o .libs/libGkArrays.so.1.1.0 libtool: link: (cd ".libs" && rm -f "libGkArrays.so.1" && ln -s "libGkArrays.so.1.1.0" "libGkArrays.so.1") libtool: link: (cd ".libs" && rm -f "libGkArrays.so" && ln -s "libGkArrays.so.1.1.0" "libGkArrays.so") libtool: link: ar cr .libs/libGkArrays.a gkArrays.o solArray.o utils.o gkArraysBuilder.o gkSABuilder.o gkCFPSBuilder.o gkIFABuilder.o readsReader.o largebinvect.o bitvector.o rank9b.o libtool: link: ranlib .libs/libGkArrays.a libtool: link: ( cd ".libs" && rm -f "libGkArrays.la" && ln -s "../libGkArrays.la" "libGkArrays.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -lpthread -L/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar -Wl,-z,relro -Wl,-z,now -o buildTables buildTables.o libGkArrays.la -lpthread -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/buildTables buildTables.o /build/libgkarrays-2.1.0+dfsg/src/.libs/libGkArrays.so -L/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs /build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs/libProgressBar.so ./.libs/libGkArrays.so -lpthread -lz make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src' make[2]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src' Making all in tests make[2]: Entering directory '/build/libgkarrays-2.1.0+dfsg/tests' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/tests' make[2]: Entering directory '/build/libgkarrays-2.1.0+dfsg' cp "libGkArrays.pc" "libGkArrays-2.1.0.pc" make[2]: Leaving directory '/build/libgkarrays-2.1.0+dfsg' make[1]: Leaving directory '/build/libgkarrays-2.1.0+dfsg' dh_auto_test make -j15 check "TESTSUITEFLAGS=-j15 --verbose" VERBOSE=1 make[1]: Entering directory '/build/libgkarrays-2.1.0+dfsg' Making check in src make[2]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src' Making check in kseq make[3]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/kseq' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/kseq' Making check in sux make[3]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/sux' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/sux' Making check in libProgressBar-1.2.0 make[3]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0' Making check in libProgressBar make[4]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' make[4]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' make[4]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0' make[4]: Nothing to be done for 'check-am'. make[4]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0' make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0' make[3]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src' make[2]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src' Making check in tests make[2]: Entering directory '/build/libgkarrays-2.1.0+dfsg/tests' make variableAndFixedLength testPairedEnd testVariableFixed testConsistency make[3]: Entering directory '/build/libgkarrays-2.1.0+dfsg/tests' g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg/tests/../src -DDATADIR=\"./\" -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o variableAndFixedLength.o variableAndFixedLength.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg/tests/../src -DDATADIR=\"./\" -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o compareVariableFixed.o compareVariableFixed.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg/tests/../src -DDATADIR=\"./\" -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o testPairedEnd.o testPairedEnd.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg/tests/../src -DDATADIR=\"./\" -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o checkPairedEnd.o checkPairedEnd.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg/tests/../src -DDATADIR=\"./\" -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o testVariableFixed.o testVariableFixed.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg/tests/../src -DDATADIR=\"./\" -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o testConsistency.o testConsistency.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg/tests/../src -DDATADIR=\"./\" -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o checkConsistency.o checkConsistency.cpp In file included from /build/libgkarrays-2.1.0+dfsg/tests/../src/readsReader.h:109, from checkPairedEnd.cpp:104: /build/libgkarrays-2.1.0+dfsg/tests/../src/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ /build/libgkarrays-2.1.0+dfsg/tests/../src/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' 227 | __KSEQ_READ | ^~~~~~~~~~~ /build/libgkarrays-2.1.0+dfsg/tests/../src/readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' 111 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ In file included from /build/libgkarrays-2.1.0+dfsg/tests/../src/readsReader.h:109, from /build/libgkarrays-2.1.0+dfsg/tests/../src/gkArrays.h:115, from compareVariableFixed.cpp:109: /build/libgkarrays-2.1.0+dfsg/tests/../src/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ /build/libgkarrays-2.1.0+dfsg/tests/../src/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' 227 | __KSEQ_READ | ^~~~~~~~~~~ /build/libgkarrays-2.1.0+dfsg/tests/../src/readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' 111 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ In file included from /build/libgkarrays-2.1.0+dfsg/tests/../src/readsReader.h:109, from /build/libgkarrays-2.1.0+dfsg/tests/../src/gkArrays.h:115, from checkConsistency.cpp:104: /build/libgkarrays-2.1.0+dfsg/tests/../src/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ /build/libgkarrays-2.1.0+dfsg/tests/../src/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' 227 | __KSEQ_READ | ^~~~~~~~~~~ /build/libgkarrays-2.1.0+dfsg/tests/../src/readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' 111 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o testPairedEnd testPairedEnd.o checkPairedEnd.o -lpthread -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/testPairedEnd testPairedEnd.o checkPairedEnd.o /build/libgkarrays-2.1.0+dfsg/tests/../src/.libs/libGkArrays.so -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -lpthread -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o variableAndFixedLength variableAndFixedLength.o compareVariableFixed.o -lpthread -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o testVariableFixed testVariableFixed.o compareVariableFixed.o -lpthread -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/testVariableFixed testVariableFixed.o compareVariableFixed.o /build/libgkarrays-2.1.0+dfsg/tests/../src/.libs/libGkArrays.so -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -lpthread -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/variableAndFixedLength variableAndFixedLength.o compareVariableFixed.o /build/libgkarrays-2.1.0+dfsg/tests/../src/.libs/libGkArrays.so -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -lpthread -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o testConsistency testConsistency.o checkConsistency.o -lpthread -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/testConsistency testConsistency.o checkConsistency.o /build/libgkarrays-2.1.0+dfsg/tests/../src/.libs/libGkArrays.so -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -lpthread -lz make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/tests' make check-TESTS make[3]: Entering directory '/build/libgkarrays-2.1.0+dfsg/tests' make[4]: Entering directory '/build/libgkarrays-2.1.0+dfsg/tests' PASS: testPairedEnd PASS: testVariableFixed PASS: testConsistency ============================================================================ Testsuite summary for libGkArrays 2.1.0 ============================================================================ # TOTAL: 3 # PASS: 3 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/tests' make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/tests' make[2]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/tests' make[2]: Entering directory '/build/libgkarrays-2.1.0+dfsg' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/build/libgkarrays-2.1.0+dfsg' make[1]: Leaving directory '/build/libgkarrays-2.1.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j1 install DESTDIR=/build/libgkarrays-2.1.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/libgkarrays-2.1.0+dfsg' Making install in src make[2]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src' Making install in kseq make[3]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/kseq' make[4]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/kseq' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays-2.1.0/kseq' /usr/bin/install -c -m 644 kseq.h '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays-2.1.0/kseq' make[4]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/kseq' make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/kseq' Making install in sux make[3]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/sux' make[4]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/sux' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays-2.1.0/sux' /usr/bin/install -c -m 644 macros.h popcount.h rank9b.h '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays-2.1.0/sux' make[4]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/sux' make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/sux' Making install in libProgressBar-1.2.0 make[3]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0' Making install in libProgressBar make[4]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' make[5]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' /bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libProgressBar.la '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libProgressBar.so.0.1.2 /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libProgressBar.so.0.1.2 libtool: install: (cd /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libProgressBar.so.0.1.2 libProgressBar.so.0 || { rm -f libProgressBar.so.0 && ln -s libProgressBar.so.0.1.2 libProgressBar.so.0; }; }) libtool: install: (cd /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libProgressBar.so.0.1.2 libProgressBar.so || { rm -f libProgressBar.so && ln -s libProgressBar.so.0.1.2 libProgressBar.so; }; }) libtool: install: /usr/bin/install -c .libs/libProgressBar.lai /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libProgressBar.la libtool: install: /usr/bin/install -c .libs/libProgressBar.a /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libProgressBar.a libtool: install: chmod 644 /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libProgressBar.a libtool: install: ranlib /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libProgressBar.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libProgressBar-1.2.0/include' /usr/bin/install -c -m 644 config.h '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libProgressBar-1.2.0/include' /bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libProgressBar-1.2.0' /usr/bin/install -c -m 644 progressBar.h '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libProgressBar-1.2.0' make install-data-hook make[6]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' ln -s -f libProgressBar-1.2.0 /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libProgressBar make[6]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' make[5]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' make[4]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' make[4]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0' make[5]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0' make[5]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 libProgressBar-1.2.0.pc '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' make install-data-hook make[6]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0' ln -s -f libProgressBar-1.2.0.pc /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/libProgressBar.pc make[6]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0' make[5]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0' make[4]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0' make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0' make[3]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src' make[4]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src' /bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libGkArrays.la '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: warning: relinking 'libGkArrays.la' libtool: install: (cd /build/libgkarrays-2.1.0+dfsg/src; /bin/bash "/build/libgkarrays-2.1.0+dfsg/libtool" --tag CXX --mode=relink g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 2:0:1 -lpthread -L/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar -Wl,-z,relro -Wl,-z,now -o libGkArrays.la -rpath /usr/lib/x86_64-linux-gnu gkArrays.lo solArray.lo utils.lo gkArraysBuilder.lo gkSABuilder.lo gkCFPSBuilder.lo gkIFABuilder.lo readsReader.lo largebinvect.lo bitvector.lo rank9b.lo -lpthread -lz -inst-prefix-dir /build/libgkarrays-2.1.0+dfsg/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o .libs/gkArrays.o .libs/solArray.o .libs/utils.o .libs/gkArraysBuilder.o .libs/gkSABuilder.o .libs/gkCFPSBuilder.o .libs/gkIFABuilder.o .libs/readsReader.o .libs/largebinvect.o .libs/bitvector.o .libs/rank9b.o -L/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -L/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -lProgressBar -lpthread -lz -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libGkArrays.so.1 -o .libs/libGkArrays.so.1.1.0 libtool: install: /usr/bin/install -c .libs/libGkArrays.so.1.1.0T /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libGkArrays.so.1.1.0 libtool: install: (cd /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libGkArrays.so.1.1.0 libGkArrays.so.1 || { rm -f libGkArrays.so.1 && ln -s libGkArrays.so.1.1.0 libGkArrays.so.1; }; }) libtool: install: (cd /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libGkArrays.so.1.1.0 libGkArrays.so || { rm -f libGkArrays.so && ln -s libGkArrays.so.1.1.0 libGkArrays.so; }; }) libtool: install: /usr/bin/install -c .libs/libGkArrays.lai /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libGkArrays.la libtool: install: /usr/bin/install -c .libs/libGkArrays.a /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libGkArrays.a libtool: install: chmod 644 /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libGkArrays.a libtool: install: ranlib /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libGkArrays.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays-2.1.0' /usr/bin/install -c -m 644 gkArrays.h solArray.h gkArraysTypes.h gkArraysBuilder.h gkSABuilder.h gkCFPSBuilder.h gkIFABuilder.h readsReader.h bitvector.hxx largebinvect.hxx bitvector.cxx largebinvect.cxx binvect.hxx '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays-2.1.0' /bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libGkArrays-2.1.0/include' /usr/bin/install -c -m 644 /build/libgkarrays-2.1.0+dfsg/config/config.h '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libGkArrays-2.1.0/include' make install-data-hook make[5]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src' ln -s -f libGkArrays-2.1.0 /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/include/libGkArrays make[5]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src' make[4]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src' make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src' make[2]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src' Making install in tests make[2]: Entering directory '/build/libgkarrays-2.1.0+dfsg/tests' make[3]: Entering directory '/build/libgkarrays-2.1.0+dfsg/tests' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/tests' make[2]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/tests' make[2]: Entering directory '/build/libgkarrays-2.1.0+dfsg' make[3]: Entering directory '/build/libgkarrays-2.1.0+dfsg' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 libGkArrays-2.1.0.pc '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' make install-data-hook make[4]: Entering directory '/build/libgkarrays-2.1.0+dfsg' ln -s -f libGkArrays-2.1.0.pc /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/libGkArrays.pc make[4]: Leaving directory '/build/libgkarrays-2.1.0+dfsg' make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg' make[2]: Leaving directory '/build/libgkarrays-2.1.0+dfsg' make[1]: Leaving directory '/build/libgkarrays-2.1.0+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/libgkarrays-2.1.0+dfsg' dh_install d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --override s/libProgressBar0-dev// \ --movedev debian/tmp/usr/include usr \ --movedev debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig usr/lib/x86_64-linux-gnu \ debian/tmp/usr/lib/x86_64-linux-gnu/libGkArrays.so Library package automatic movement utility --> zlib1g-dev package exists. set -e install -d -m 755 debian/libgkarrays-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libgkarrays1/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libGkArrays.a debian/libgkarrays-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libGkArrays.so debian/libgkarrays-dev/usr/lib/x86_64-linux-gnu mv /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libGkArrays.so.1 debian/libgkarrays1/usr/lib/x86_64-linux-gnu mv /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libGkArrays.so.1.1.0 debian/libgkarrays1/usr/lib/x86_64-linux-gnu PKGDEV=libgkarrays-dev PKGSHL=libgkarrays1 install -d -m 755 debian/libgkarrays-dev/usr mv debian/tmp/usr/include debian/libgkarrays-dev/usr install -d -m 755 debian/libgkarrays-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig debian/libgkarrays-dev/usr/lib/x86_64-linux-gnu # now move libProgressBar manually dh_install -p libgkarrays1 usr/lib/x86_64-linux-gnu/libProgressBar.so.0* usr/lib/x86_64-linux-gnu chmod -x debian/*/usr/lib/x86_64-linux-gnu/libProgressBar.so.0.* dh_install -p libgkarrays-dev usr/lib/x86_64-linux-gnu/libProgressBar.so usr/lib/x86_64-linux-gnu dh_install -p libgkarrays-dev usr/lib/x86_64-linux-gnu/libProgressBar.a usr/lib/x86_64-linux-gnu dh_install -p libgkarrays-dev usr/lib/x86_64-linux-gnu/libGkArrays-2.1.0/include/* usr/include/libGkArrays-2.1.0 dh_install -p libgkarrays-dev usr/lib/x86_64-linux-gnu/libProgressBar-1.2.0/include/* usr/include/libProgressBar-1.2.0 find debian/tmp -name "lib*.la" -delete make[1]: Leaving directory '/build/libgkarrays-2.1.0+dfsg' dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dwz: debian/libgkarrays1/usr/lib/x86_64-linux-gnu/libProgressBar.so.0.1.2: .debug_info section not present dwz: Too few files for multifile optimization dh_dwz: warning: No dwz multifile created, but not explicitly requested either so ignoring it. dh_dwz: warning: Common issues include no debug information at all (missing -g) and dh_dwz: warning: compressed debug information (#931891). dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libgkarrays-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package libgkarrays-dev: substitution variable ${devlibs:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'libgkarrays1' in '../libgkarrays1_2.1.0+dfsg-4_amd64.deb'. dpkg-deb: building package 'libgkarrays1-dbgsym' in '../libgkarrays1-dbgsym_2.1.0+dfsg-4_amd64.deb'. dpkg-deb: building package 'libgkarrays-dev' in '../libgkarrays-dev_2.1.0+dfsg-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../libgkarrays_2.1.0+dfsg-4_amd64.buildinfo dpkg-genchanges --build=binary -O../libgkarrays_2.1.0+dfsg-4_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/2661004 and its subdirectories I: Current time: Fri Apr 14 01:12:52 -12 2023 I: pbuilder-time-stamp: 1681477972 Fri Apr 14 13:12:52 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Fri Apr 14 13:12:52 UTC 2023 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Fri Apr 14 13:14:03 UTC 2023 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Fri Apr 14 13:14:03 UTC 2023 I: libgkarrays_2.1.0+dfsg-4_amd64.changes: Format: 1.8 Date: Thu, 19 Nov 2020 10:41:29 +0100 Source: libgkarrays Binary: libgkarrays-dev libgkarrays1 libgkarrays1-dbgsym Architecture: amd64 Version: 2.1.0+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libgkarrays-dev - library to query large collection of NGS sequences (development) libgkarrays1 - library to query large collection of NGS sequences Closes: 975072 Changes: libgkarrays (2.1.0+dfsg-4) unstable; urgency=medium . * Fix installation of shared library Closes: #975072 Checksums-Sha1: eedbe4be47bb1e58318881be60884e9b7437397a 85628 libgkarrays-dev_2.1.0+dfsg-4_amd64.deb 8cde94d18d696e6c432f7aec064f0d77299418b5 198140 libgkarrays1-dbgsym_2.1.0+dfsg-4_amd64.deb 1560c2f84b15769818deb3a45548da0c202d1829 57196 libgkarrays1_2.1.0+dfsg-4_amd64.deb a46a1810ab3b1ecc1a84942ced057146bf501123 5957 libgkarrays_2.1.0+dfsg-4_amd64.buildinfo Checksums-Sha256: cd4debd286294b777c7a92d21be2d0caa80f5ad54d1506d182651087d3b1eb15 85628 libgkarrays-dev_2.1.0+dfsg-4_amd64.deb 64db1a4b64d7e4a5a86dbf6c35a12ca35f9bdef58374d15fea81895547993999 198140 libgkarrays1-dbgsym_2.1.0+dfsg-4_amd64.deb f2e846853561a30fbf2179e9f75c576cb4019c86a7a331d4b8eec75fdd4ece97 57196 libgkarrays1_2.1.0+dfsg-4_amd64.deb 10a60ededaaec01c9e1556b5429f7fe0c3562469b87bf30cb26155b6e61455b3 5957 libgkarrays_2.1.0+dfsg-4_amd64.buildinfo Files: 23dd9eea99a9652e435bc5382a2742e8 85628 libdevel optional libgkarrays-dev_2.1.0+dfsg-4_amd64.deb 2743d0c210e0af328419d7910fd7335b 198140 debug optional libgkarrays1-dbgsym_2.1.0+dfsg-4_amd64.deb 19bb5fe8d5714c9a69bb0271d5fc1842 57196 libs optional libgkarrays1_2.1.0+dfsg-4_amd64.deb 368ac407e33511adcd5bdc42476666cb 5957 science optional libgkarrays_2.1.0+dfsg-4_amd64.buildinfo Fri Apr 14 13:14:04 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.Az4AYAPc/libgkarrays_2.1.0+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Az4AYAPc/libgkarrays_2.1.0+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Az4AYAPc/libgkarrays_2.1.0+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Az4AYAPc/b1/libgkarrays_2.1.0+dfsg-4_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Az4AYAPc/b2/libgkarrays_2.1.0+dfsg-4_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: 0.351s) 0.351s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.022s) 0.021s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Fri Apr 14 13:14:05 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Fri Apr 14 13:14:05 UTC 2023 I: libgkarrays from bookworm built successfully and reproducibly on amd64. Fri Apr 14 13:14:07 UTC 2023 I: Submitting .buildinfo files to external archives: Fri Apr 14 13:14:07 UTC 2023 I: Submitting 8.0K b1/libgkarrays_2.1.0+dfsg-4_amd64.buildinfo.asc Fri Apr 14 13:14:07 UTC 2023 I: Submitting 8.0K b2/libgkarrays_2.1.0+dfsg-4_amd64.buildinfo.asc Fri Apr 14 13:14:08 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Apr 14 13:14:08 UTC 2023 I: Done submitting .buildinfo files. Fri Apr 14 13:14:08 UTC 2023 I: Removing signed libgkarrays_2.1.0+dfsg-4_amd64.buildinfo.asc files: removed './b1/libgkarrays_2.1.0+dfsg-4_amd64.buildinfo.asc' removed './b2/libgkarrays_2.1.0+dfsg-4_amd64.buildinfo.asc'