I: pbuilder: network access will be disabled during build I: Current time: Fri Jul 12 00:53:40 +14 2024 I: pbuilder-time-stamp: 1720695220 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: 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 Wed Dec 2 10:10:27 2020 +14 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/65045/tmp/hooks/D01_modify_environment starting debug: Running on ionos16-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jul 12 00:53 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/65045/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/65045/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=8993201a24014c99a527e05dca45b50f LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=65045 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.KMHjh72J/pbuilderrc_Qd4i --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.KMHjh72J/b2 --logfile b2/build.log --extrapackages usrmerge 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-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Apr 24 2023 bash -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 42920 Sep 21 2022 cat -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp -rwxr-xr-x 1 root root 136916 Jan 6 2023 dash -rwxr-xr-x 1 root root 137160 Sep 21 2022 date -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd -rwxr-xr-x 1 root root 108940 Sep 21 2022 df -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir -rwxr-xr-x 1 root root 87760 Mar 24 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname -rwxr-xr-x 1 root root 38760 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 84272 Mar 24 2023 findmnt -rwsr-xr-x 1 root root 30240 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 218680 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip -rwxr-xr-x 1 root root 21916 Dec 20 2022 hostname -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln -rwxr-xr-x 1 root root 55600 Mar 24 2023 login -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls -rwxr-xr-x 1 root root 214568 Mar 24 2023 lsblk -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 63016 Mar 24 2023 more -rwsr-xr-x 1 root root 58912 Mar 24 2023 mount -rwxr-xr-x 1 root root 13856 Mar 24 2023 mountpoint -rwxr-xr-x 1 root root 157932 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 22308 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 133224 Jan 6 2023 sed lrwxrwxrwx 1 root root 9 Jul 12 00:53 sh -> /bin/bash -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty -rwsr-xr-x 1 root root 83492 Mar 24 2023 su -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync -rwxr-xr-x 1 root root 598456 Apr 7 2023 tar -rwxr-xr-x 1 root root 13860 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch -rwxr-xr-x 1 root root 34664 Sep 21 2022 true -rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 30236 Mar 24 2023 umount -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir -rwxr-xr-x 1 root root 71216 Mar 24 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/65045/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 ... 19599 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-dev{a} libboost-filesystem-dev{a} libboost-filesystem1.74-dev{a} libboost-filesystem1.74.0{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-program-options-dev{a} libboost-program-options1.74-dev{a} libboost-program-options1.74.0{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-system-dev{a} libboost-system1.74-dev{a} libboost-system1.74.0{a} libboost1.74-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, 56 newly installed, 0 to remove and 0 not upgraded. Need to get 45.0 MB of archives. After unpacking 299 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB] Get: 4 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB] Get: 6 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 7 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB] Get: 8 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB] Get: 9 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB] Get: 10 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB] Get: 11 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB] Get: 12 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB] Get: 24 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB] Get: 25 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB] Get: 26 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.2 [720 kB] Get: 27 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB] Get: 28 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main i386 icu-devtools i386 72.1-3 [214 kB] Get: 32 http://deb.debian.org/debian bookworm/main i386 libboost1.74-dev i386 1.74.0+ds1-21 [9508 kB] Get: 33 http://deb.debian.org/debian bookworm/main i386 libboost-dev i386 1.74.0.3 [4548 B] Get: 34 http://deb.debian.org/debian bookworm/main i386 libboost-filesystem1.74.0 i386 1.74.0+ds1-21 [264 kB] Get: 35 http://deb.debian.org/debian bookworm/main i386 libboost-system1.74.0 i386 1.74.0+ds1-21 [218 kB] Get: 36 http://deb.debian.org/debian bookworm/main i386 libboost-system1.74-dev i386 1.74.0+ds1-21 [219 kB] Get: 37 http://deb.debian.org/debian bookworm/main i386 libboost-filesystem1.74-dev i386 1.74.0+ds1-21 [286 kB] Get: 38 http://deb.debian.org/debian bookworm/main i386 libboost-filesystem-dev i386 1.74.0.3 [4368 B] Get: 39 http://deb.debian.org/debian bookworm/main i386 libboost-regex1.74.0 i386 1.74.0+ds1-21 [509 kB] Get: 40 http://deb.debian.org/debian bookworm/main i386 libicu-dev i386 72.1-3 [10.6 MB] Get: 41 http://deb.debian.org/debian bookworm/main i386 libboost-regex1.74-dev i386 1.74.0+ds1-21 [585 kB] Get: 42 http://deb.debian.org/debian bookworm/main i386 libboost-iostreams1.74-dev i386 1.74.0+ds1-21 [250 kB] Get: 43 http://deb.debian.org/debian bookworm/main i386 libboost-iostreams-dev i386 1.74.0.3 [4320 B] Get: 44 http://deb.debian.org/debian bookworm/main i386 libboost-program-options1.74.0 i386 1.74.0+ds1-21 [338 kB] Get: 45 http://deb.debian.org/debian bookworm/main i386 libboost-program-options1.74-dev i386 1.74.0+ds1-21 [369 kB] Get: 46 http://deb.debian.org/debian bookworm/main i386 libboost-program-options-dev i386 1.74.0.3 [4344 B] Get: 47 http://deb.debian.org/debian bookworm/main i386 libboost-system-dev i386 1.74.0.3 [4472 B] Get: 48 http://deb.debian.org/debian bookworm/main i386 libgenome0 i386 1.3.11+svn20110227.4616-5 [134 kB] Get: 49 http://deb.debian.org/debian bookworm/main i386 libgenome-dev i386 1.3.11+svn20110227.4616-5 [205 kB] Get: 50 http://deb.debian.org/debian bookworm/main i386 libmuscle1 i386 3.7+4565-7 [235 kB] Get: 51 http://deb.debian.org/debian bookworm/main i386 libmems1 i386 1.6.0+4725-9+b1 [686 kB] Get: 52 http://deb.debian.org/debian bookworm/main i386 libmuscle-dev i386 3.7+4565-7 [294 kB] Get: 53 http://deb.debian.org/debian bookworm/main i386 libmems-dev i386 1.6.0+4725-9+b1 [980 kB] Get: 54 http://deb.debian.org/debian bookworm/main i386 libpkgconf3 i386 1.8.1-1 [38.3 kB] Get: 55 http://deb.debian.org/debian bookworm/main i386 pkgconf-bin i386 1.8.1-1 [29.8 kB] Get: 56 http://deb.debian.org/debian bookworm/main i386 pkgconf i386 1.8.1-1 [25.9 kB] Fetched 45.0 MB in 1s (30.1 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 ... 19599 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_i386.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../02-libmagic1_1%3a5.44-3_i386.deb ... Unpacking libmagic1:i386 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_i386.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_i386.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../05-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_i386.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_i386.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../08-libpipeline1_1.5.7-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_i386.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_i386.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 libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-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 .../19-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 .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../22-libelf1_0.188-2.1_i386.deb ... Unpacking libelf1:i386 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_i386.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../24-libicu72_72.1-3_i386.deb ... Unpacking libicu72:i386 (72.1-3) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.2_i386.deb ... Unpacking libxml2:i386 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-12_i386.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../30-icu-devtools_72.1-3_i386.deb ... Unpacking icu-devtools (72.1-3) ... Selecting previously unselected package libboost1.74-dev:i386. Preparing to unpack .../31-libboost1.74-dev_1.74.0+ds1-21_i386.deb ... Unpacking libboost1.74-dev:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-dev:i386. Preparing to unpack .../32-libboost-dev_1.74.0.3_i386.deb ... Unpacking libboost-dev:i386 (1.74.0.3) ... Selecting previously unselected package libboost-filesystem1.74.0:i386. Preparing to unpack .../33-libboost-filesystem1.74.0_1.74.0+ds1-21_i386.deb ... Unpacking libboost-filesystem1.74.0:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-system1.74.0:i386. Preparing to unpack .../34-libboost-system1.74.0_1.74.0+ds1-21_i386.deb ... Unpacking libboost-system1.74.0:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-system1.74-dev:i386. Preparing to unpack .../35-libboost-system1.74-dev_1.74.0+ds1-21_i386.deb ... Unpacking libboost-system1.74-dev:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-filesystem1.74-dev:i386. Preparing to unpack .../36-libboost-filesystem1.74-dev_1.74.0+ds1-21_i386.deb ... Unpacking libboost-filesystem1.74-dev:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-filesystem-dev:i386. Preparing to unpack .../37-libboost-filesystem-dev_1.74.0.3_i386.deb ... Unpacking libboost-filesystem-dev:i386 (1.74.0.3) ... Selecting previously unselected package libboost-regex1.74.0:i386. Preparing to unpack .../38-libboost-regex1.74.0_1.74.0+ds1-21_i386.deb ... Unpacking libboost-regex1.74.0:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libicu-dev:i386. Preparing to unpack .../39-libicu-dev_72.1-3_i386.deb ... Unpacking libicu-dev:i386 (72.1-3) ... Selecting previously unselected package libboost-regex1.74-dev:i386. Preparing to unpack .../40-libboost-regex1.74-dev_1.74.0+ds1-21_i386.deb ... Unpacking libboost-regex1.74-dev:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-iostreams1.74-dev:i386. Preparing to unpack .../41-libboost-iostreams1.74-dev_1.74.0+ds1-21_i386.deb ... Unpacking libboost-iostreams1.74-dev:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-iostreams-dev:i386. Preparing to unpack .../42-libboost-iostreams-dev_1.74.0.3_i386.deb ... Unpacking libboost-iostreams-dev:i386 (1.74.0.3) ... Selecting previously unselected package libboost-program-options1.74.0:i386. Preparing to unpack .../43-libboost-program-options1.74.0_1.74.0+ds1-21_i386.deb ... Unpacking libboost-program-options1.74.0:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-program-options1.74-dev:i386. Preparing to unpack .../44-libboost-program-options1.74-dev_1.74.0+ds1-21_i386.deb ... Unpacking libboost-program-options1.74-dev:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-program-options-dev:i386. Preparing to unpack .../45-libboost-program-options-dev_1.74.0.3_i386.deb ... Unpacking libboost-program-options-dev:i386 (1.74.0.3) ... Selecting previously unselected package libboost-system-dev:i386. Preparing to unpack .../46-libboost-system-dev_1.74.0.3_i386.deb ... Unpacking libboost-system-dev:i386 (1.74.0.3) ... Selecting previously unselected package libgenome0:i386. Preparing to unpack .../47-libgenome0_1.3.11+svn20110227.4616-5_i386.deb ... Unpacking libgenome0:i386 (1.3.11+svn20110227.4616-5) ... Selecting previously unselected package libgenome-dev:i386. Preparing to unpack .../48-libgenome-dev_1.3.11+svn20110227.4616-5_i386.deb ... Unpacking libgenome-dev:i386 (1.3.11+svn20110227.4616-5) ... Selecting previously unselected package libmuscle1. Preparing to unpack .../49-libmuscle1_3.7+4565-7_i386.deb ... Unpacking libmuscle1 (3.7+4565-7) ... Selecting previously unselected package libmems1:i386. Preparing to unpack .../50-libmems1_1.6.0+4725-9+b1_i386.deb ... Unpacking libmems1:i386 (1.6.0+4725-9+b1) ... Selecting previously unselected package libmuscle-dev. Preparing to unpack .../51-libmuscle-dev_3.7+4565-7_i386.deb ... Unpacking libmuscle-dev (3.7+4565-7) ... Selecting previously unselected package libmems-dev. Preparing to unpack .../52-libmems-dev_1.6.0+4725-9+b1_i386.deb ... Unpacking libmems-dev (1.6.0+4725-9+b1) ... Selecting previously unselected package libpkgconf3:i386. Preparing to unpack .../53-libpkgconf3_1.8.1-1_i386.deb ... Unpacking libpkgconf3:i386 (1.8.1-1) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../54-pkgconf-bin_1.8.1-1_i386.deb ... Unpacking pkgconf-bin (1.8.1-1) ... Selecting previously unselected package pkgconf:i386. Preparing to unpack .../55-pkgconf_1.8.1-1_i386.deb ... Unpacking pkgconf:i386 (1.8.1-1) ... Setting up libpipeline1:i386 (1.5.7-1) ... Setting up libboost-system1.74.0:i386 (1.74.0+ds1-21) ... Setting up libboost1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libicu72:i386 (72.1-3) ... Setting up libgenome0:i386 (1.3.11+svn20110227.4616-5) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmuscle1 (3.7+4565-7) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libgenome-dev:i386 (1.3.11+svn20110227.4616-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libboost-program-options1.74.0:i386 (1.74.0+ds1-21) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:i386 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up libboost-filesystem1.74.0:i386 (1.74.0+ds1-21) ... Setting up file (1:5.44-3) ... Setting up libmems1:i386 (1.6.0+4725-9+b1) ... Setting up libboost-program-options1.74-dev:i386 (1.74.0+ds1-21) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:i386 (1.8.1-1) ... Setting up libboost-program-options-dev:i386 (1.74.0.3) ... Setting up libboost-system1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libboost-regex1.74.0:i386 (1.74.0+ds1-21) ... Setting up libmuscle-dev (3.7+4565-7) ... Setting up autopoint (0.21-12) ... Setting up icu-devtools (72.1-3) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up autoconf (2.71-3) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libboost-dev:i386 (1.74.0.3) ... Setting up libboost-filesystem1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libelf1:i386 (0.188-2.1) ... Setting up libicu-dev:i386 (72.1-3) ... Setting up libxml2:i386 (2.9.14+dfsg-1.2) ... Setting up libboost-filesystem-dev:i386 (1.74.0.3) ... 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 libboost-system-dev:i386 (1.74.0.3) ... Setting up pkgconf:i386 (1.8.1-1) ... 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 libboost-regex1.74-dev:i386 (1.74.0+ds1-21) ... 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 libboost-iostreams1.74-dev:i386 (1.74.0+ds1-21) ... Setting up debhelper (13.11.4) ... Setting up libmems-dev (1.6.0+4725-9+b1) ... Setting up libboost-iostreams-dev:i386 (1.74.0.3) ... Processing triggers for libc-bin (2.36-9) ... 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 Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/65045/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/65045/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/progressivemauve-1.2.0+4713+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../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 -j15 make[1]: Entering directory '/build/progressivemauve-1.2.0+4713+dfsg' Making all in src make[2]: Entering directory '/build/progressivemauve-1.2.0+4713+dfsg/src' make all-am make[3]: Entering directory '/build/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/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/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/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/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/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/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/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/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/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/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/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mauveToXMFA.o mauveToXMFA.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/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/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o progressiveMauve.o progressiveMauve.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/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UniqueMatchFinder.o UniqueMatchFinder.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/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o extractBCITrees.o extractBCITrees.cpp In file included from /usr/include/c++/12/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++/12/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/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++/12/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++/12/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++/12/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++/12/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++/12/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++/12/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; | ^~~~~~~~ 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; | ^~~~~~~~ In file included from /usr/include/c++/12/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++/12/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/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/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alignmentProjector.o alignmentProjector.cpp In file included from /usr/include/c++/12/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++/12/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++/12/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++/12/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++/12/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++/12/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/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/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++/12/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++/12/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/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/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++/12/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++/12/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/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/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bbFilter.o bbFilter.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/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bbAnalyze.o bbAnalyze.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/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++/12/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++/12/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/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o xmfa2maf.o xmfa2maf.cpp In file included from /usr/include/c++/12/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++/12/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++/12/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++/12/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++/12/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++/12/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++/12/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++/12/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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 g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/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/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/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/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/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/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/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/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/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/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/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/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 g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/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 make[3]: Leaving directory '/build/progressivemauve-1.2.0+4713+dfsg/src' make[2]: Leaving directory '/build/progressivemauve-1.2.0+4713+dfsg/src' make[2]: Entering directory '/build/progressivemauve-1.2.0+4713+dfsg' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/progressivemauve-1.2.0+4713+dfsg' make[1]: Leaving directory '/build/progressivemauve-1.2.0+4713+dfsg' dh_auto_test make -j15 check "TESTSUITEFLAGS=-j15 --verbose" VERBOSE=1 make[1]: Entering directory '/build/progressivemauve-1.2.0+4713+dfsg' Making check in src make[2]: Entering directory '/build/progressivemauve-1.2.0+4713+dfsg/src' make[2]: Leaving directory '/build/progressivemauve-1.2.0+4713+dfsg/src' make[2]: Entering directory '/build/progressivemauve-1.2.0+4713+dfsg' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/build/progressivemauve-1.2.0+4713+dfsg' make[1]: Leaving directory '/build/progressivemauve-1.2.0+4713+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/progressivemauve/ make -j15 install DESTDIR=/build/progressivemauve-1.2.0\+4713\+dfsg/debian/progressivemauve AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/progressivemauve-1.2.0+4713+dfsg' Making install in src make[2]: Entering directory '/build/progressivemauve-1.2.0+4713+dfsg/src' make[3]: Entering directory '/build/progressivemauve-1.2.0+4713+dfsg/src' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/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/progressivemauve-1.2.0+4713+dfsg/debian/progressivemauve/usr/bin' make[3]: Leaving directory '/build/progressivemauve-1.2.0+4713+dfsg/src' make[2]: Leaving directory '/build/progressivemauve-1.2.0+4713+dfsg/src' make[2]: Entering directory '/build/progressivemauve-1.2.0+4713+dfsg' make[3]: Entering directory '/build/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/progressivemauve-1.2.0+4713+dfsg' make[2]: Leaving directory '/build/progressivemauve-1.2.0+4713+dfsg' make[1]: Leaving directory '/build/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: user script /srv/workspace/pbuilder/65045/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/65045/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/65045 and its subdirectories I: Current time: Fri Jul 12 00:55:24 +14 2024 I: pbuilder-time-stamp: 1720695324