Thu Apr 4 13:26:05 UTC 2024 I: starting to build progressivemauve/trixie/i386 on jenkins on '2024-04-04 13:25' Thu Apr 4 13:26:05 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_5/14376/console.log Thu Apr 4 13:26:05 UTC 2024 I: Downloading source for trixie/progressivemauve=1.2.0+4713+dfsg-5 --2024-04-04 13:26:05-- http://deb.debian.org/debian/pool/main/p/progressivemauve/progressivemauve_1.2.0%2b4713%2bdfsg-5.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2306 (2.3K) [text/prs.lines.tag] Saving to: ‘progressivemauve_1.2.0+4713+dfsg-5.dsc’ 0K .. 100% 341M=0s 2024-04-04 13:26:05 (341 MB/s) - ‘progressivemauve_1.2.0+4713+dfsg-5.dsc’ saved [2306/2306] Thu Apr 4 13:26:05 UTC 2024 I: progressivemauve_1.2.0+4713+dfsg-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: progressivemauve Binary: progressivemauve Architecture: any Version: 1.2.0+4713+dfsg-5 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://darlinglab.org/mauve/user-guide/mauvealigner.html Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/progressivemauve Vcs-Git: https://salsa.debian.org/med-team/progressivemauve.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), pkgconf, libboost-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-iostreams-dev, libgenome-dev, libmuscle-dev, libmems-dev Package-List: progressivemauve deb science optional arch=any Checksums-Sha1: 3b09d613f64fa9237d8c0566c02823136a253208 96084 progressivemauve_1.2.0+4713+dfsg.orig.tar.xz 5e9df9e187c44ab12a59092bb61aae5751cba848 17944 progressivemauve_1.2.0+4713+dfsg-5.debian.tar.xz Checksums-Sha256: e5f43b4e5af5d6ddb6d4bac91a919d0d2706ff42f51a4209d2d15be8a12c3772 96084 progressivemauve_1.2.0+4713+dfsg.orig.tar.xz 2cf77a36474fb18bfb2e7d4ef9153cd0f4db9c3d9f38ca4790a1bdb636170b91 17944 progressivemauve_1.2.0+4713+dfsg-5.debian.tar.xz Files: b9f9a0377aeccaa353cc4a491452003a 96084 progressivemauve_1.2.0+4713+dfsg.orig.tar.xz 7aa58d54810bbc9e520ad251273a9fa6 17944 progressivemauve_1.2.0+4713+dfsg-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl/GozMRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtERgQ//RUDAb1wMwYkBg/gCWMmgHTm7x0uBKM58 YPsTbMNpvTknr4z5sLwUSHpZhFiJ6LdNjL7lzfY6xU2Z3F/bwbPKVgLkj/SPb7eY bLA2d/+QAwYdm22WVnvAlpDDerPVrLFFX3bOB6IMthdLlV+yfMEOUUKeyRGouJo3 vWWa5IT47M5PZW0TpeqUf3/mMg3LWH0k2hIAtR4e0bWVfBdbatSJZpPjAj+QKnj0 1qMwN9vy2EIihRSgC7viqUKcbzR8eRFUIyXZULYPRQm5aAYpdE4CU2WWVmkkhS2H AMXYEy5pimfS2NMllVE6GHaGnejgudVZYVxsix9a8yO+HGPTqJYFiZfU6INWzN74 CVITsB0HeiSVsiVb2LAJysr24/8D6uqwgEJPHAA6ICBQa2JYbRDJacKlzMzcJ3TM p9HdZjkDJ3qdZVEhEgHTTSe3BrBcybmeQfo1EIU3sdSCIrDuQnPfYBk8zSfsKqd1 ddMIJqlB2dtgKvc1vd5n1WibVPz92FpQ+W7CZ2izCUqcicghn2OKPFFN8IlyAhBu zyHwQDAoEIc1iLZeNTQwoztifjNDx8U/n+7nyPP+CrVIM3pKaLQU/Cn1U0fNfprv ur1G0HfknpRlJ+LoFYdDwwFeWfiX7p07Tuj7MTnkTI7E7thfzYOTjpLtiMrWxiOR ziwuQhTQYl4= =FUT7 -----END PGP SIGNATURE----- Thu Apr 4 13:26:05 UTC 2024 I: Checking whether the package is not for us Thu Apr 4 13:26:05 UTC 2024 I: Starting 1st build on remote node ionos12-i386.debian.net. Thu Apr 4 13:26:05 UTC 2024 I: Preparing to do remote build '1' on ionos12-i386.debian.net. Thu Apr 4 13:29:05 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Apr 4 01:26:07 -12 2024 I: pbuilder-time-stamp: 1712237167 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: using eatmydata during job I: Copying source file I: copying [progressivemauve_1.2.0+4713+dfsg-5.dsc] I: copying [./progressivemauve_1.2.0+4713+dfsg.orig.tar.xz] I: copying [./progressivemauve_1.2.0+4713+dfsg-5.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Dec 1 20:10:27 2020 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 ./progressivemauve_1.2.0+4713+dfsg-5.dsc: no acceptable signature found dpkg-source: info: extracting progressivemauve in progressivemauve-1.2.0+4713+dfsg dpkg-source: info: unpacking progressivemauve_1.2.0+4713+dfsg.orig.tar.xz dpkg-source: info: unpacking progressivemauve_1.2.0+4713+dfsg-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_build.patch dpkg-source: info: applying do_not_build_static_binaries.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying use-native-getopt.patch dpkg-source: info: applying adapt-to-unversioned-libs.patch dpkg-source: info: applying fix_FTBFS_boost1.67.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/49834/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='7b39e19dc3894c59af0e8946f1b975fc' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='49834' 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.Ha1vlnA3/pbuilderrc_2qrw --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.Ha1vlnA3/b1 --logfile b1/build.log progressivemauve_1.2.0+4713+dfsg-5.dsc' SUDO_GID='112' SUDO_UID='107' 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 ionos12-i386 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 4 11:26 /bin -> usr/bin I: user script /srv/workspace/pbuilder/49834/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: i386 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), pkgconf, libboost-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-iostreams-dev, libgenome-dev, libmuscle-dev, libmems-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 ... 19876 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 pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-system-dev; however: Package libboost-system-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-filesystem-dev; however: Package libboost-filesystem-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libgenome-dev; however: Package libgenome-dev is not installed. pbuilder-satisfydepends-dummy depends on libmuscle-dev; however: Package libmuscle-dev is not installed. pbuilder-satisfydepends-dummy depends on libmems-dev; however: Package libmems-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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-dev{a} libboost-filesystem-dev{a} libboost-filesystem1.83-dev{a} libboost-filesystem1.83.0{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-system-dev{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost1.83-dev{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgenome-dev{a} libgenome0{a} libicu-dev{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libmems-dev{a} libmems1{a} libmuscle-dev{a} libmuscle1{a} libpipeline1{a} libpkgconf3{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{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, 58 newly installed, 0 to remove and 0 not upgraded. Need to get 46.5 MB of archives. After unpacking 322 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-2+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libmagic1 i386 1:5.45-2+b1 [114 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-2+b1 [43.0 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-3 [1195 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.39.3-6 [93.3 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-1+b2 [39.6 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.0-3 [1413 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main i386 libelf1 i386 0.190-1+b1 [182 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1 [118 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b2 [727 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 icu-devtools i386 72.1-4+b1 [216 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libboost1.83-dev i386 1.83.0-2+b2 [10.6 MB] Get: 33 http://deb.debian.org/debian trixie/main i386 libboost-atomic1.83.0 i386 1.83.0-2+b2 [234 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 libboost-atomic1.83-dev i386 1.83.0-2+b2 [235 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libboost-dev i386 1.83.0.2+b2 [3840 B] Get: 36 http://deb.debian.org/debian trixie/main i386 libboost-filesystem1.83.0 i386 1.83.0-2+b2 [287 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libboost-system1.83.0 i386 1.83.0-2+b2 [230 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 libboost-system1.83-dev i386 1.83.0-2+b2 [231 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 libboost-filesystem1.83-dev i386 1.83.0-2+b2 [302 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 libboost-filesystem-dev i386 1.83.0.2+b2 [3640 B] Get: 41 http://deb.debian.org/debian trixie/main i386 libboost-regex1.83.0 i386 1.83.0-2+b2 [328 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 libicu-dev i386 72.1-4+b1 [10.6 MB] Get: 43 http://deb.debian.org/debian trixie/main i386 libboost-regex1.83-dev i386 1.83.0-2+b2 [347 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 libboost-iostreams1.83-dev i386 1.83.0-2+b2 [264 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 libboost-iostreams-dev i386 1.83.0.2+b2 [3588 B] Get: 46 http://deb.debian.org/debian trixie/main i386 libboost-program-options1.83.0 i386 1.83.0-2+b2 [358 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 libboost-program-options1.83-dev i386 1.83.0-2+b2 [388 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 libboost-program-options-dev i386 1.83.0.2+b2 [3616 B] Get: 49 http://deb.debian.org/debian trixie/main i386 libboost-system-dev i386 1.83.0.2+b2 [3740 B] Get: 50 http://deb.debian.org/debian trixie/main i386 libgenome0 i386 1.3.11+svn20110227.4616-6 [132 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 libgenome-dev i386 1.3.11+svn20110227.4616-6 [203 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 libmuscle1 i386 3.7+4565-7 [235 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 libmems1 i386 1.6.0+4725-9+b2 [690 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 libmuscle-dev i386 3.7+4565-7 [294 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 libmems-dev i386 1.6.0+4725-9+b2 [979 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 libpkgconf3 i386 1.8.1-1+b2 [38.5 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 pkgconf-bin i386 1.8.1-1+b2 [30.2 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 pkgconf i386 1.8.1-1+b2 [26.2 kB] Fetched 46.5 MB in 1s (35.9 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 ... 19876 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../02-libmagic1_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic1:i386 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-2+b1_i386.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_i386.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-3_i386.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.39.3-6_i386.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../08-libpipeline1_1.5.7-1+b2_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-1+b2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.0-3_i386.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... 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_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... 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Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/progressivemauve-1.2.0+4713+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 > ../progressivemauve_1.2.0+4713+dfsg-5_source.changes dpkg-buildpackage: info: source package progressivemauve dpkg-buildpackage: info: source version 1.2.0+4713+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf configure.ac:12: warning: 'AM_CONFIG_HEADER': this macro is obsolete. configure.ac:12: You should use the 'AC_CONFIG_HEADERS' macro instead. ./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from... aclocal.m4:745: AM_CONFIG_HEADER is expanded from... configure.ac:12: the top level configure.ac:27: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:27: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:27: the top level configure.ac:71: warning: The macro `AC_HEADER_TIME' is obsolete. configure.ac:71: You should run autoupdate. ./lib/autoconf/headers.m4:743: AC_HEADER_TIME is expanded from... configure.ac:71: the top level configure.ac:91: warning: AC_OUTPUT should be used without arguments. configure.ac:91: You should run autoupdate. configure.ac:21: installing 'config/compile' configure.ac:9: installing 'config/config.guess' configure.ac:9: installing 'config/config.sub' configure.ac:11: installing 'config/install-sh' configure.ac:11: installing 'config/missing' Makefile.am: installing './INSTALL' src/Makefile.am:12: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/Makefile.am: installing 'config/depcomp' src/Makefile.am:51: warning: variable 'EXTRA_mauveStatic_SOURCES' is defined but no program or src/Makefile.am:51: library has 'mauveStatic' as canonical name (possible typo) src/Makefile.am:49: warning: variable 'mauveStatic_SOURCES' is defined but no program or src/Makefile.am:49: library has 'mauveStatic' as canonical name (possible typo) src/Makefile.am:160: warning: variable 'progressiveMauveStatic_SOURCES' is defined but no program or src/Makefile.am:160: library has 'progressiveMauveStatic' as canonical name (possible typo) src/Makefile.am:50: warning: variable 'mauveStatic_LDADD' is defined but no program or src/Makefile.am:50: library has 'mauveStatic' as canonical name (possible typo) src/Makefile.am:161: warning: variable 'progressiveMauveStatic_LDADD' is defined but no program or src/Makefile.am:161: library has 'progressiveMauveStatic' as canonical name (possible typo) src/Makefile.am:52: warning: variable 'mauveStatic_DEPENDENCIES' is defined but no program or src/Makefile.am:52: library has 'mauveStatic' as canonical name (possible typo) dh_auto_configure ./configure --build=i686-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/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking target system type... i686-pc-linux-gnu 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 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 whether make supports the include directive... yes (GNU style) checking dependency style of gcc... 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 whether ln -s works... yes 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 sys/time.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for getopt_long... yes checking for getopt... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for DEPS... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for memset... yes checking for libintl.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for wchar.h... yes checking for GNU libc compatible malloc... yes checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for size_t... yes checking how to run the C preprocessor... gcc -E checking whether gcc needs -traditional... no 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/config.h config.status: executing depfiles commands dh_auto_build make -j11 make[1]: Entering directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg' Making all in src make[2]: Entering directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg/src' make all-am make[3]: Entering directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg/src' g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mauveAligner.o mauveAligner.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scoreAlignment.o scoreAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqueMerCount.o uniqueMerCount.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o toRawSequence.o toRawSequence.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mfa2xmfa.o mfa2xmfa.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o addUnalignedIntervals.o addUnalignedIntervals.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o toMultiFastA.o toMultiFastA.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o getAlignmentWindows.o getAlignmentWindows.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o uniquifyTrees.o uniquifyTrees.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o toGrimmFormat.o toGrimmFormat.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mauveToXMFA.o mauveToXMFA.cpp In file included from /usr/include/c++/13/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from toMultiFastA.cpp:2: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stripGapColumns.o stripGapColumns.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o progressiveMauve.o progressiveMauve.cpp In file included from /usr/include/c++/13/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from mauveAligner.cpp:30: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ In file included from /usr/include/c++/13/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from getAlignmentWindows.cpp:14: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ mauveAligner.cpp:413:62: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 413 | cerr << "mauveAligner " << " build date " << __DATE__ << " at " << __TIME__ << endl; | ^~~~~~~~ mauveAligner.cpp:413:84: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 413 | cerr << "mauveAligner " << " build date " << __DATE__ << " at " << __TIME__ << endl; | ^~~~~~~~ In file included from /usr/include/c++/13/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from addUnalignedIntervals.cpp:2: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UniqueMatchFinder.o UniqueMatchFinder.cpp In file included from /usr/include/c++/13/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from progressiveMauve.cpp:26: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ progressiveMauve.cpp:417:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 417 | cerr << "progressiveMauve " << " build date " << __DATE__ << " at " << __TIME__ << endl; | ^~~~~~~~ progressiveMauve.cpp:417:88: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 417 | cerr << "progressiveMauve " << " build date " << __DATE__ << " at " << __TIME__ << endl; | ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o extractBCITrees.o extractBCITrees.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o createBackboneMFA.o createBackboneMFA.cpp In file included from /usr/include/c++/13/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from createBackboneMFA.cpp:2: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o repeatoire.o repeatoire.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alignmentProjector.o alignmentProjector.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stripSubsetLCBs.o stripSubsetLCBs.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o projectAndStrip.o projectAndStrip.cpp In file included from /usr/include/c++/13/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from repeatoire.cpp:4: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o makeBadgerMatrix.o makeBadgerMatrix.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o randomGeneSample.o randomGeneSample.cpp In file included from /usr/include/c++/13/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from /usr/include/libMems/ProgressiveAligner.h:21, from alignmentProjector.cpp:18: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ In file included from /usr/include/c++/13/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from projectAndStrip.cpp:18: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ In file included from /usr/include/c++/13/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from randomGeneSample.cpp:18: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o getOrthologList.o getOrthologList.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bbFilter.o bbFilter.cpp In file included from /usr/include/c++/13/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from getOrthologList.cpp:18: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ In file included from /usr/include/c++/13/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from /usr/include/libMems/Backbone.h:24, from bbFilter.cpp:1: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bbAnalyze.o bbAnalyze.cpp In file included from /usr/include/c++/13/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from /usr/include/libMems/Backbone.h:24, from bbAnalyze.cpp:4: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o backbone_global_to_local.o backbone_global_to_local.cpp In file included from /usr/include/c++/13/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from /usr/include/libMems/Backbone.h:24, from backbone_global_to_local.cpp:2: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o xmfa2maf.o xmfa2maf.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o coordinateTranslate.o coordinateTranslate.cpp g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wl,-z,relro -Wl,-z,now -o mauveAligner mauveAligner.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE In file included from /usr/include/c++/13/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from /usr/include/libMems/ProgressiveAligner.h:21, from xmfa2maf.cpp:2: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o scoreAlignment scoreAlignment.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o uniqueMerCount uniqueMerCount.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o toRawSequence toRawSequence.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o mfa2xmfa mfa2xmfa.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o addUnalignedIntervals addUnalignedIntervals.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o toMultiFastA toMultiFastA.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o getAlignmentWindows getAlignmentWindows.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o uniquifyTrees uniquifyTrees.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o toGrimmFormat toGrimmFormat.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o mauveToXMFA mauveToXMFA.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o stripGapColumns stripGapColumns.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o progressiveMauve progressiveMauve.o UniqueMatchFinder.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o extractBCITrees extractBCITrees.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o createBackboneMFA createBackboneMFA.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o stripSubsetLCBs stripSubsetLCBs.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o makeBadgerMatrix makeBadgerMatrix.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o bbFilter bbFilter.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o projectAndStrip projectAndStrip.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o randomGeneSample randomGeneSample.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o alignmentProjector alignmentProjector.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o backbone_global_to_local backbone_global_to_local.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o getOrthologList getOrthologList.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o coordinateTranslate coordinateTranslate.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o xmfa2maf xmfa2maf.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o bbAnalyze bbAnalyze.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o repeatoire repeatoire.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE make[3]: Leaving directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg/src' make[2]: Leaving directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg/src' make[2]: Entering directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg' make[1]: Leaving directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg' dh_auto_test make -j11 check "TESTSUITEFLAGS=-j11 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg' Making check in src make[2]: Entering directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg/src' make[2]: Leaving directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg/src' make[2]: Entering directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg' make[1]: Leaving directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/progressivemauve/ make -j11 install DESTDIR=/build/reproducible-path/progressivemauve-1.2.0\+4713\+dfsg/debian/progressivemauve AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg' Making install in src make[2]: Entering directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg/src' make[3]: Entering directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg/src' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg/debian/progressivemauve/usr/bin' /usr/bin/install -c mauveAligner scoreAlignment uniqueMerCount toRawSequence mfa2xmfa addUnalignedIntervals toMultiFastA getAlignmentWindows uniquifyTrees toGrimmFormat mauveToXMFA stripGapColumns progressiveMauve extractBCITrees createBackboneMFA repeatoire alignmentProjector stripSubsetLCBs projectAndStrip makeBadgerMatrix randomGeneSample getOrthologList bbFilter bbAnalyze backbone_global_to_local xmfa2maf coordinateTranslate '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg/debian/progressivemauve/usr/bin' make[3]: Leaving directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg/src' make[2]: Leaving directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg/src' make[2]: Entering directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg' make[3]: Entering directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg' 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/reproducible-path/progressivemauve-1.2.0+4713+dfsg' make[2]: Leaving directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg' make[1]: Leaving directory '/build/reproducible-path/progressivemauve-1.2.0+4713+dfsg' dh_installdocs dh_installchangelogs dh_installman 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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'progressivemauve' in '../progressivemauve_1.2.0+4713+dfsg-5_i386.deb'. dpkg-deb: building package 'progressivemauve-dbgsym' in '../progressivemauve-dbgsym_1.2.0+4713+dfsg-5_i386.deb'. dpkg-genbuildinfo --build=binary -O../progressivemauve_1.2.0+4713+dfsg-5_i386.buildinfo dpkg-genchanges --build=binary -O../progressivemauve_1.2.0+4713+dfsg-5_i386.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/49834 and its subdirectories I: Current time: Thu Apr 4 01:29:04 -12 2024 I: pbuilder-time-stamp: 1712237344 Thu Apr 4 13:29:05 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos6-i386.debian.net. Thu Apr 4 13:29:05 UTC 2024 I: Preparing to do remote build '2' on ionos6-i386.debian.net. Thu Apr 4 13:32:43 UTC 2024 I: Deleting $TMPDIR on ionos6-i386.debian.net. Thu Apr 4 13:32:44 UTC 2024 I: progressivemauve_1.2.0+4713+dfsg-5_i386.changes: Format: 1.8 Date: Mon, 30 Nov 2020 17:33:02 +0100 Source: progressivemauve Binary: progressivemauve progressivemauve-dbgsym Architecture: i386 Version: 1.2.0+4713+dfsg-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: progressivemauve - multiple genome alignment algorithms Changes: progressivemauve (1.2.0+4713+dfsg-5) unstable; urgency=medium . * Standards-Version: 4.5.1 (routine-update) * debhelper-compat 13 (routine-update) * Remove trailing whitespace in debian/changelog (routine-update) * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Trim trailing whitespace. * Use secure URI in Homepage field. Checksums-Sha1: 5bd7b7461a1704f3f70d6bede72b17736f31a164 14392000 progressivemauve-dbgsym_1.2.0+4713+dfsg-5_i386.deb 974159b73a6ff787a85a5a44761a838e2d45753b 6664 progressivemauve_1.2.0+4713+dfsg-5_i386.buildinfo 061cf3992d5cd726d4a4f1b998ff27e473db5060 863192 progressivemauve_1.2.0+4713+dfsg-5_i386.deb Checksums-Sha256: b621d8e3eb220928b49bed498546e2341c63a24de25c66bbc2dfa89098aec486 14392000 progressivemauve-dbgsym_1.2.0+4713+dfsg-5_i386.deb 8bf176ad24ba4dc4dbb5c6c81e27cf844f0a065101c2d6fb3f9d77847919683a 6664 progressivemauve_1.2.0+4713+dfsg-5_i386.buildinfo a16078289e42e8651026f1b819bada92f3cf0200c8c0d83155f9117549ecd63d 863192 progressivemauve_1.2.0+4713+dfsg-5_i386.deb Files: ee4f5c72e4639d6eaecc8be014397e9b 14392000 debug optional progressivemauve-dbgsym_1.2.0+4713+dfsg-5_i386.deb 1d52415fccfe38ba96ebaa73c562c684 6664 science optional progressivemauve_1.2.0+4713+dfsg-5_i386.buildinfo 13a0f180b58b7d1b0f98508345ab33ea 863192 science optional progressivemauve_1.2.0+4713+dfsg-5_i386.deb Thu Apr 4 13:32:45 UTC 2024 I: diffoscope 262 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_5-14376.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Ha1vlnA3/progressivemauve_1.2.0+4713+dfsg-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Ha1vlnA3/progressivemauve_1.2.0+4713+dfsg-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Ha1vlnA3/progressivemauve_1.2.0+4713+dfsg-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Ha1vlnA3/b1/progressivemauve_1.2.0+4713+dfsg-5_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.Ha1vlnA3/b2/progressivemauve_1.2.0+4713+dfsg-5_i386.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: 0.483s) 0.483s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.176s) 0.176s 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: 784ms CPU time consumed: 784ms Thu Apr 4 13:32:46 UTC 2024 I: diffoscope 262 found no differences in the changes files, and a .buildinfo file also exists. Thu Apr 4 13:32:46 UTC 2024 I: progressivemauve from trixie built successfully and reproducibly on i386. Thu Apr 4 13:32:47 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Apr 4 13:32:47 UTC 2024 I: Submitting 8.0K b1/progressivemauve_1.2.0+4713+dfsg-5_i386.buildinfo.asc Thu Apr 4 13:32:48 UTC 2024 I: Submitting 8.0K b2/progressivemauve_1.2.0+4713+dfsg-5_i386.buildinfo.asc Thu Apr 4 13:32:49 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Apr 4 13:32:49 UTC 2024 I: Done submitting .buildinfo files. Thu Apr 4 13:32:49 UTC 2024 I: Removing signed progressivemauve_1.2.0+4713+dfsg-5_i386.buildinfo.asc files: removed './b1/progressivemauve_1.2.0+4713+dfsg-5_i386.buildinfo.asc' removed './b2/progressivemauve_1.2.0+4713+dfsg-5_i386.buildinfo.asc'