I: pbuilder: network access will be disabled during build I: Current time: Sun Jul 17 22:47:09 +14 2022 I: pbuilder-time-stamp: 1658047629 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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 [clustalo_1.2.4-7.dsc] I: copying [./clustalo_1.2.4.orig.tar.gz] I: copying [./clustalo_1.2.4-7.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.dL66LvhG/trustedkeys.kbx': General error gpgv: Signature made Mon Nov 23 22:15:40 2020 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./clustalo_1.2.4-7.dsc dpkg-source: info: extracting clustalo in clustalo-1.2.4 dpkg-source: info: unpacking clustalo_1.2.4.orig.tar.gz dpkg-source: info: unpacking clustalo_1.2.4-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying clustalo-log-format-calls.patch dpkg-source: info: applying array_out_of_bounds.patch dpkg-source: info: applying memory_leak.patch dpkg-source: info: applying fix_syntax.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/64289/tmp/hooks/D01_modify_environment starting debug: Running on ionos6-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 Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/64289/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/64289/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.1.4(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,-fixfilepath parallel=18' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=dc640ea89fe84ce091c434d2f87005ea 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=64289 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/tmp.yKyl5kh2jc/pbuilderrc_WEa9 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.yKyl5kh2jc/b2 --logfile b2/build.log --extrapackages usrmerge clustalo_1.2.4-7.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 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux I: ls -l /bin total 5776 -rwxr-xr-x 1 root root 1367848 Feb 25 2021 bash -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 17768 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 38824 Sep 23 2020 cat -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp -rwxr-xr-x 1 root root 128724 Dec 11 2020 dash -rwxr-xr-x 1 root root 124904 Sep 23 2020 date -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd -rwxr-xr-x 1 root root 100752 Sep 23 2020 df -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir -rwxr-xr-x 1 root root 83644 Feb 8 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 34664 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 71928 Feb 8 2021 findmnt -rwsr-xr-x 1 root root 30112 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe -rwxr-xr-x 1 root root 100952 Mar 3 2021 gzip -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln -rwxr-xr-x 1 root root 55572 Feb 8 2020 login -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls -rwxr-xr-x 1 root root 153124 Feb 8 2021 lsblk -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 58920 Feb 8 2021 more -rwsr-xr-x 1 root root 50720 Feb 8 2021 mount -rwxr-xr-x 1 root root 13856 Feb 8 2021 mountpoint -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Feb 25 2021 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jul 17 22:47 sh -> bash lrwxrwxrwx 1 root root 4 Jul 17 05:47 sh.distrib -> dash -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty -rwsr-xr-x 1 root root 79396 Feb 8 2021 su -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync -rwxr-xr-x 1 root root 602584 Feb 17 2021 tar -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch -rwxr-xr-x 1 root root 34664 Sep 23 2020 true -rwxr-xr-x 1 root root 17768 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 30236 Feb 8 2021 umount -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63024 Feb 8 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew I: user script /srv/workspace/pbuilder/64289/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), libargtable2-dev, doxygen, graphviz, sphinx-common dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19675 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 libargtable2-dev; however: Package libargtable2-dev is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on graphviz; however: Package graphviz is not installed. pbuilder-satisfydepends-dummy depends on sphinx-common; however: Package sphinx-common 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} doxygen{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} graphviz{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libargtable2-0{a} libargtable2-dev{a} libargtable2-docs{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcdt5{a} libcgraph6{a} libclang-cpp11{a} libclang1-11{a} libdatrie1{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgd3{a} libglib2.0-0{a} libgraphite2-3{a} libgts-0.7-5{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libice6{a} libicu67{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} liblab-gamut1{a} libllvm11{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpathplan4{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libsigsegv2{a} libsm6{a} libsub-override-perl{a} libthai-data{a} libthai0{a} libtiff5{a} libtool{a} libuchardet0{a} libwebp6{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6{a} libz3-4{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} sphinx-common{a} ucf{a} x11-common{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-liberation javascript-common libarchive-cpio-perl libglib2.0-data libgts-bin libltdl-dev libmail-sendmail-perl lynx python3-sphinx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 98 newly installed, 0 to remove and 0 not upgraded. Need to get 81.8 MB of archives. After unpacking 298 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-7 [148 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 ucf all 3.0043 [74.0 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-6 [8776 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libmd0 i386 1.0.3-3 [28.9 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 libbsd0 i386 0.11.3-1 [111 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 libedit2 i386 3.1-20191231-2+b1 [101 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 libz3-4 i386 4.8.10-1 [7737 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 libllvm11 i386 1:11.0.1-2 [17.7 MB] Get: 38 http://deb.debian.org/debian bullseye/main i386 libclang-cpp11 i386 1:11.0.1-2 [9562 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 libclang1-11 i386 1:11.0.1-2 [5429 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 doxygen i386 1.9.1-1 [4426 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 libexpat1 i386 2.2.10-2 [98.8 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 libpng16-16 i386 1.6.37-3 [303 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 libfreetype6 i386 2.10.4+dfsg-1 [429 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 libfontconfig1 i386 2.13.1-4.2 [358 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 fontconfig i386 2.13.1-4.2 [417 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 libcdt5 i386 2.42.2-5 [62.6 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 libcgraph6 i386 2.42.2-5 [89.8 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 libjpeg62-turbo i386 1:2.0.6-4 [160 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 libdeflate0 i386 1.7-1 [48.4 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 libjbig0 i386 2.1-3.1+b2 [31.5 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 libwebp6 i386 0.6.1-2+b1 [274 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 libtiff5 i386 4.2.0-1 [305 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 libxcb1 i386 1.14-3 [144 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 libx11-data all 2:1.7.1-1 [310 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 libx11-6 i386 2:1.7.1-1 [796 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 libxpm4 i386 1:3.5.12-1 [50.9 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 libgd3 i386 2.3.0-2 [142 kB] Get: 63 http://deb.debian.org/debian bullseye/main i386 libglib2.0-0 i386 2.66.8-1 [1437 kB] Get: 64 http://deb.debian.org/debian bullseye/main i386 libgts-0.7-5 i386 0.7.6+darcs121130-4+b1 [161 kB] Get: 65 http://deb.debian.org/debian bullseye/main i386 libpixman-1-0 i386 0.40.0-1 [545 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 libxcb-render0 i386 1.14-3 [112 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 libxcb-shm0 i386 1.14-3 [102 kB] Get: 68 http://deb.debian.org/debian bullseye/main i386 libxext6 i386 2:1.3.3-1.1 [55.2 kB] Get: 69 http://deb.debian.org/debian bullseye/main i386 libxrender1 i386 1:0.9.10-1 [34.1 kB] Get: 70 http://deb.debian.org/debian bullseye/main i386 libcairo2 i386 1.16.0-5 [746 kB] Get: 71 http://deb.debian.org/debian bullseye/main i386 libltdl7 i386 2.4.6-15 [392 kB] Get: 72 http://deb.debian.org/debian bullseye/main i386 libfribidi0 i386 1.0.8-2 [65.4 kB] Get: 73 http://deb.debian.org/debian bullseye/main i386 libgraphite2-3 i386 1.3.14-1 [84.0 kB] Get: 74 http://deb.debian.org/debian bullseye/main i386 libharfbuzz0b i386 2.7.4-1 [1490 kB] Get: 75 http://deb.debian.org/debian bullseye/main i386 libthai-data all 0.1.28-3 [170 kB] Get: 76 http://deb.debian.org/debian bullseye/main i386 libdatrie1 i386 0.2.13-1 [44.5 kB] Get: 77 http://deb.debian.org/debian bullseye/main i386 libthai0 i386 0.1.28-3 [55.3 kB] Get: 78 http://deb.debian.org/debian bullseye/main i386 libpango-1.0-0 i386 1.46.2-3 [197 kB] Get: 79 http://deb.debian.org/debian bullseye/main i386 libpangoft2-1.0-0 i386 1.46.2-3 [65.1 kB] Get: 80 http://deb.debian.org/debian bullseye/main i386 libpangocairo-1.0-0 i386 1.46.2-3 [51.9 kB] Get: 81 http://deb.debian.org/debian bullseye/main i386 libpathplan4 i386 2.42.2-5 [64.5 kB] Get: 82 http://deb.debian.org/debian bullseye/main i386 libgvc6 i386 2.42.2-5 [728 kB] Get: 83 http://deb.debian.org/debian bullseye/main i386 libgvpr2 i386 2.42.2-5 [221 kB] Get: 84 http://deb.debian.org/debian bullseye/main i386 liblab-gamut1 i386 2.42.2-5 [221 kB] Get: 85 http://deb.debian.org/debian bullseye/main i386 x11-common all 1:7.7+22 [252 kB] Get: 86 http://deb.debian.org/debian bullseye/main i386 libice6 i386 2:1.0.10-1 [60.8 kB] Get: 87 http://deb.debian.org/debian bullseye/main i386 libsm6 i386 2:1.2.3-1 [35.7 kB] Get: 88 http://deb.debian.org/debian bullseye/main i386 libxt6 i386 1:1.2.0-1 [195 kB] Get: 89 http://deb.debian.org/debian bullseye/main i386 libxmu6 i386 2:1.1.2-2+b3 [62.8 kB] Get: 90 http://deb.debian.org/debian bullseye/main i386 libxaw7 i386 2:1.0.13-1.1 [210 kB] Get: 91 http://deb.debian.org/debian bullseye/main i386 graphviz i386 2.42.2-5 [594 kB] Get: 92 http://deb.debian.org/debian bullseye/main i386 libargtable2-0 i386 13-1.1 [18.5 kB] Get: 93 http://deb.debian.org/debian bullseye/main i386 libargtable2-docs all 13-1.1 [2622 kB] Get: 94 http://deb.debian.org/debian bullseye/main i386 libargtable2-dev i386 13-1.1 [58.5 kB] Get: 95 http://deb.debian.org/debian bullseye/main i386 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 96 http://deb.debian.org/debian bullseye/main i386 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 97 http://deb.debian.org/debian bullseye/main i386 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 98 http://deb.debian.org/debian bullseye/main i386 sphinx-common all 3.4.3-2 [578 kB] Fetched 81.8 MB in 1s (93.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19675 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7_i386.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../01-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_i386.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../03-libpipeline1_1.5.3-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_i386.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_i386.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../07-libmagic1_1%3a5.39-3_i386.deb ... Unpacking libmagic1:i386 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_i386.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. 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Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.21-4_i386.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package libmd0:i386. Preparing to unpack .../32-libmd0_1.0.3-3_i386.deb ... Unpacking libmd0:i386 (1.0.3-3) ... Selecting previously unselected package libbsd0:i386. Preparing to unpack .../33-libbsd0_0.11.3-1_i386.deb ... Unpacking libbsd0:i386 (0.11.3-1) ... Selecting previously unselected package libedit2:i386. 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Preparing to unpack .../52-libjbig0_2.1-3.1+b2_i386.deb ... Unpacking libjbig0:i386 (2.1-3.1+b2) ... Selecting previously unselected package libwebp6:i386. Preparing to unpack .../53-libwebp6_0.6.1-2+b1_i386.deb ... Unpacking libwebp6:i386 (0.6.1-2+b1) ... Selecting previously unselected package libtiff5:i386. Preparing to unpack .../54-libtiff5_4.2.0-1_i386.deb ... Unpacking libtiff5:i386 (4.2.0-1) ... Selecting previously unselected package libxau6:i386. Preparing to unpack .../55-libxau6_1%3a1.0.9-1_i386.deb ... Unpacking libxau6:i386 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:i386. Preparing to unpack .../56-libxdmcp6_1%3a1.1.2-3_i386.deb ... Unpacking libxdmcp6:i386 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:i386. Preparing to unpack .../57-libxcb1_1.14-3_i386.deb ... Unpacking libxcb1:i386 (1.14-3) ... Selecting previously unselected package libx11-data. Preparing to unpack .../58-libx11-data_2%3a1.7.1-1_all.deb ... Unpacking libx11-data (2:1.7.1-1) ... Selecting previously unselected package libx11-6:i386. Preparing to unpack .../59-libx11-6_2%3a1.7.1-1_i386.deb ... Unpacking libx11-6:i386 (2:1.7.1-1) ... Selecting previously unselected package libxpm4:i386. Preparing to unpack .../60-libxpm4_1%3a3.5.12-1_i386.deb ... Unpacking libxpm4:i386 (1:3.5.12-1) ... Selecting previously unselected package libgd3:i386. Preparing to unpack .../61-libgd3_2.3.0-2_i386.deb ... Unpacking libgd3:i386 (2.3.0-2) ... Selecting previously unselected package libglib2.0-0:i386. Preparing to unpack .../62-libglib2.0-0_2.66.8-1_i386.deb ... Unpacking libglib2.0-0:i386 (2.66.8-1) ... Selecting previously unselected package libgts-0.7-5:i386. Preparing to unpack .../63-libgts-0.7-5_0.7.6+darcs121130-4+b1_i386.deb ... Unpacking libgts-0.7-5:i386 (0.7.6+darcs121130-4+b1) ... Selecting previously unselected package libpixman-1-0:i386. Preparing to unpack .../64-libpixman-1-0_0.40.0-1_i386.deb ... Unpacking libpixman-1-0:i386 (0.40.0-1) ... Selecting previously unselected package libxcb-render0:i386. Preparing to unpack .../65-libxcb-render0_1.14-3_i386.deb ... Unpacking libxcb-render0:i386 (1.14-3) ... Selecting previously unselected package libxcb-shm0:i386. Preparing to unpack .../66-libxcb-shm0_1.14-3_i386.deb ... Unpacking libxcb-shm0:i386 (1.14-3) ... Selecting previously unselected package libxext6:i386. Preparing to unpack .../67-libxext6_2%3a1.3.3-1.1_i386.deb ... Unpacking libxext6:i386 (2:1.3.3-1.1) ... Selecting previously unselected package libxrender1:i386. Preparing to unpack .../68-libxrender1_1%3a0.9.10-1_i386.deb ... Unpacking libxrender1:i386 (1:0.9.10-1) ... Selecting previously unselected package libcairo2:i386. Preparing to unpack .../69-libcairo2_1.16.0-5_i386.deb ... Unpacking libcairo2:i386 (1.16.0-5) ... Selecting previously unselected package libltdl7:i386. Preparing to unpack .../70-libltdl7_2.4.6-15_i386.deb ... Unpacking libltdl7:i386 (2.4.6-15) ... Selecting previously unselected package libfribidi0:i386. Preparing to unpack .../71-libfribidi0_1.0.8-2_i386.deb ... Unpacking libfribidi0:i386 (1.0.8-2) ... Selecting previously unselected package libgraphite2-3:i386. Preparing to unpack .../72-libgraphite2-3_1.3.14-1_i386.deb ... Unpacking libgraphite2-3:i386 (1.3.14-1) ... Selecting previously unselected package libharfbuzz0b:i386. Preparing to unpack .../73-libharfbuzz0b_2.7.4-1_i386.deb ... Unpacking libharfbuzz0b:i386 (2.7.4-1) ... Selecting previously unselected package libthai-data. Preparing to unpack .../74-libthai-data_0.1.28-3_all.deb ... Unpacking libthai-data (0.1.28-3) ... Selecting previously unselected package libdatrie1:i386. Preparing to unpack .../75-libdatrie1_0.2.13-1_i386.deb ... Unpacking libdatrie1:i386 (0.2.13-1) ... Selecting previously unselected package libthai0:i386. Preparing to unpack .../76-libthai0_0.1.28-3_i386.deb ... Unpacking libthai0:i386 (0.1.28-3) ... Selecting previously unselected package libpango-1.0-0:i386. Preparing to unpack .../77-libpango-1.0-0_1.46.2-3_i386.deb ... Unpacking libpango-1.0-0:i386 (1.46.2-3) ... Selecting previously unselected package libpangoft2-1.0-0:i386. Preparing to unpack .../78-libpangoft2-1.0-0_1.46.2-3_i386.deb ... Unpacking libpangoft2-1.0-0:i386 (1.46.2-3) ... Selecting previously unselected package libpangocairo-1.0-0:i386. Preparing to unpack .../79-libpangocairo-1.0-0_1.46.2-3_i386.deb ... Unpacking libpangocairo-1.0-0:i386 (1.46.2-3) ... Selecting previously unselected package libpathplan4:i386. Preparing to unpack .../80-libpathplan4_2.42.2-5_i386.deb ... Unpacking libpathplan4:i386 (2.42.2-5) ... Selecting previously unselected package libgvc6. Preparing to unpack .../81-libgvc6_2.42.2-5_i386.deb ... Unpacking libgvc6 (2.42.2-5) ... Selecting previously unselected package libgvpr2:i386. Preparing to unpack .../82-libgvpr2_2.42.2-5_i386.deb ... Unpacking libgvpr2:i386 (2.42.2-5) ... Selecting previously unselected package liblab-gamut1:i386. Preparing to unpack .../83-liblab-gamut1_2.42.2-5_i386.deb ... Unpacking liblab-gamut1:i386 (2.42.2-5) ... Selecting previously unselected package x11-common. Preparing to unpack .../84-x11-common_1%3a7.7+22_all.deb ... Unpacking x11-common (1:7.7+22) ... Selecting previously unselected package libice6:i386. Preparing to unpack .../85-libice6_2%3a1.0.10-1_i386.deb ... Unpacking libice6:i386 (2:1.0.10-1) ... Selecting previously unselected package libsm6:i386. Preparing to unpack .../86-libsm6_2%3a1.2.3-1_i386.deb ... Unpacking libsm6:i386 (2:1.2.3-1) ... Selecting previously unselected package libxt6:i386. Preparing to unpack .../87-libxt6_1%3a1.2.0-1_i386.deb ... Unpacking libxt6:i386 (1:1.2.0-1) ... Selecting previously unselected package libxmu6:i386. Preparing to unpack .../88-libxmu6_2%3a1.1.2-2+b3_i386.deb ... Unpacking libxmu6:i386 (2:1.1.2-2+b3) ... Selecting previously unselected package libxaw7:i386. Preparing to unpack .../89-libxaw7_2%3a1.0.13-1.1_i386.deb ... Unpacking libxaw7:i386 (2:1.0.13-1.1) ... Selecting previously unselected package graphviz. Preparing to unpack .../90-graphviz_2.42.2-5_i386.deb ... Unpacking graphviz (2.42.2-5) ... Selecting previously unselected package libargtable2-0. Preparing to unpack .../91-libargtable2-0_13-1.1_i386.deb ... Unpacking libargtable2-0 (13-1.1) ... Selecting previously unselected package libargtable2-docs. Preparing to unpack .../92-libargtable2-docs_13-1.1_all.deb ... Unpacking libargtable2-docs (13-1.1) ... Selecting previously unselected package libargtable2-dev. Preparing to unpack .../93-libargtable2-dev_13-1.1_i386.deb ... Unpacking libargtable2-dev (13-1.1) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../94-libjs-jquery_3.5.1+dfsg+~3.5.5-7_all.deb ... Unpacking libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../95-libjs-underscore_1.9.1~dfsg-3_all.deb ... Unpacking libjs-underscore (1.9.1~dfsg-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../96-libjs-sphinxdoc_3.4.3-2_all.deb ... Unpacking libjs-sphinxdoc (3.4.3-2) ... Selecting previously unselected package sphinx-common. Preparing to unpack .../97-sphinx-common_3.4.3-2_all.deb ... Unpacking sphinx-common (3.4.3-2) ... Setting up libexpat1:i386 (2.2.10-2) ... Setting up libpipeline1:i386 (1.5.3-1) ... Setting up libgraphite2-3:i386 (1.3.14-1) ... Setting up libpixman-1-0:i386 (0.40.0-1) ... Setting up libxau6:i386 (1:1.0.9-1) ... Setting up bsdextrautils (2.36.1-7) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:i386 (67.1-6) ... Setting up libdatrie1:i386 (0.2.13-1) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:i386 (2.66.8-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:i386 (1.0.9-2+b2) ... Setting up liblab-gamut1:i386 (2.42.2-5) ... Setting up x11-common (1:7.7+22) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libmagic1:i386 (1:5.39-3) ... Setting up libdeflate0:i386 (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up libargtable2-docs (13-1.1) ... Setting up file (1:5.39-3) ... Setting up libjbig0:i386 (2.1-3.1+b2) ... Setting up libgts-0.7-5:i386 (0.7.6+darcs121130-4+b1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libz3-4:i386 (4.8.10-1) ... Setting up libjpeg62-turbo:i386 (1:2.0.6-4) ... Setting up libx11-data (2:1.7.1-1) ... Setting up libpathplan4:i386 (2.42.2-5) ... Setting up libsigsegv2:i386 (2.13-1) ... Setting up libfribidi0:i386 (1.0.8-2) ... Setting up libpng16-16:i386 (1.6.37-3) ... Setting up autopoint (0.21-4) ... Setting up libwebp6:i386 (0.6.1-2+b1) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up libltdl7:i386 (2.4.6-15) ... Setting up libmd0:i386 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libthai-data (0.1.28-3) ... Setting up libcdt5:i386 (2.42.2-5) ... Setting up libcgraph6:i386 (2.42.2-5) ... Setting up libtiff5:i386 (4.2.0-1) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up libbsd0:i386 (0.11.3-1) ... Setting up libelf1:i386 (0.183-1) ... Setting up libxml2:i386 (2.9.10+dfsg-6.7) ... Setting up libargtable2-0 (13-1.1) ... Setting up libjs-underscore (1.9.1~dfsg-3) ... Setting up libfile-stripnondeterminism-perl (1.11.0-1) ... Setting up libice6:i386 (2:1.0.10-1) ... Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up libxcb1:i386 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libxcb-render0:i386 (1.14-3) ... Setting up libedit2:i386 (3.1-20191231-2+b1) ... Setting up m4 (1.4.18-5) ... Setting up libxcb-shm0:i386 (1.14-3) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libthai0:i386 (0.1.28-3) ... Setting up libllvm11:i386 (1:11.0.1-2) ... Setting up libfreetype6:i386 (2.10.4+dfsg-1) ... Setting up libclang1-11 (1:11.0.1-2) ... Setting up libargtable2-dev (13-1.1) ... Setting up ucf (3.0043) ... Setting up libjs-sphinxdoc (3.4.3-2) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.11.0-1) ... Setting up libgvpr2:i386 (2.42.2-5) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libx11-6:i386 (2:1.7.1-1) ... Setting up libharfbuzz0b:i386 (2.7.4-1) ... Setting up libsm6:i386 (2:1.2.3-1) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libxpm4:i386 (1:3.5.12-1) ... Setting up libxrender1:i386 (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:i386 (2:1.3.3-1.1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libclang-cpp11 (1:11.0.1-2) ... Setting up dh-autoreconf (20) ... Setting up doxygen (1.9.1-1) ... Setting up sphinx-common (3.4.3-2) ... Setting up libxt6:i386 (1:1.2.0-1) ... Setting up libfontconfig1:i386 (2.13.1-4.2) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libxmu6:i386 (2:1.1.2-2+b3) ... Setting up libpango-1.0-0:i386 (1.46.2-3) ... Setting up debhelper (13.3.4) ... Setting up libxaw7:i386 (2:1.0.13-1.1) ... Setting up libcairo2:i386 (1.16.0-5) ... Setting up libgd3:i386 (2.3.0-2) ... Setting up libpangoft2-1.0-0:i386 (1.46.2-3) ... Setting up libpangocairo-1.0-0:i386 (1.46.2-3) ... Setting up libgvc6 (2.42.2-5) ... Setting up graphviz (2.42.2-5) ... Processing triggers for libc-bin (2.31-12) ... 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... The following additional packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl The following NEW packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 59.5 kB of archives. After this operation, 157 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main i386 libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 25 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 0s (4866 kB/s) Selecting previously unselected package libnumber-compare-perl. (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 ... 23032 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... Unpacking libnumber-compare-perl (0.03-1.1) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... Unpacking libtext-glob-perl (0.11-1) ... Selecting previously unselected package libfile-find-rule-perl. Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... Unpacking libfile-find-rule-perl (0.34-1) ... Selecting previously unselected package usrmerge. Preparing to unpack .../archives/usrmerge_25_all.deb ... Unpacking usrmerge (25) ... Setting up libtext-glob-perl (0.11-1) ... Setting up libnumber-compare-perl (0.03-1.1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up usrmerge (25) ... The system has been successfully converted. Processing triggers for man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. I: Building the package I: Running cd /build/clustalo-1.2.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package clustalo dpkg-buildpackage: info: source version 1.2.4-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/clustalo-1.2.4' dh_clean rm -f _configs.sed rm -rf doc make[1]: Leaving directory '/build/clustalo-1.2.4' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf configure.ac:150: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from... m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from... m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from... m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from... m4/libtool.m4:138: _LT_SETUP is expanded from... m4/libtool.m4:67: LT_INIT is expanded from... configure.ac:150: the top level configure.ac:150: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from... m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from... m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from... m4/libtool.m4:138: _LT_SETUP is expanded from... m4/libtool.m4:67: LT_INIT is expanded from... configure.ac:150: the top level configure.ac:172: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from... m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from... m4/libtool.m4:5356: _LT_LANG_CXX_CONFIG is expanded from... m4/libtool.m4:785: _LT_LANG is expanded from... m4/libtool.m4:768: LT_LANG is expanded from... configure.ac:172: the top level configure.ac:150: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from... m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from... m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from... m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from... m4/libtool.m4:138: _LT_SETUP is expanded from... m4/libtool.m4:67: LT_INIT is expanded from... configure.ac:150: the top level configure.ac:150: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from... m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from... m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from... m4/libtool.m4:138: _LT_SETUP is expanded from... m4/libtool.m4:67: LT_INIT is expanded from... configure.ac:150: the top level configure.ac:172: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from... m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from... m4/libtool.m4:5356: _LT_LANG_CXX_CONFIG is expanded from... m4/libtool.m4:785: _LT_LANG is expanded from... m4/libtool.m4:768: LT_LANG is expanded from... configure.ac:172: the top level configure.ac:150: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from... m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from... m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from... m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from... m4/libtool.m4:138: _LT_SETUP is expanded from... m4/libtool.m4:67: LT_INIT is expanded from... configure.ac:150: the top level configure.ac:150: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from... m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from... m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from... m4/libtool.m4:138: _LT_SETUP is expanded from... m4/libtool.m4:67: LT_INIT is expanded from... configure.ac:150: the top level configure.ac:172: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from... m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from... m4/libtool.m4:5356: _LT_LANG_CXX_CONFIG is expanded from... m4/libtool.m4:785: _LT_LANG is expanded from... m4/libtool.m4:768: LT_LANG is expanded from... configure.ac:172: the top level libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:133: installing './compile' configure.ac:115: installing './missing' src/Makefile.am: installing './depcomp' 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 configure: Welcome to Clustal Omega - version 1.2.4 (AndreaGiacomo) +NMMMMMMMMMS= MMMMM? :MMMMM8 IMMMMS MMMMM, ~MMMMN ,MMMMM =MMMMM MMMMM ?MMMMM +MMMMM MMMMMS MMMMM MMMMM MMMMM: MMMMM MMMMM+ MMMMM MMMMM~ MMMMM MMMMM MMMMMZ MMMMM MMMMM ,MMMMZ MMMM8 MMMM+ MMMMS MMMM, MMMMO MMMM ,N SMMM MMM8 +8 ,M7 M+ M+ :M8 ,MMMMMMMMMMMMI MMMMMMMMMMMM8 ,MMMMMMMMMMMM8 MMMMMMMMMMMM8 ,MMMMMMMMMMMMN MMMMMMMMMMMM8 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking whether make sets $(MAKE)... (cached) yes checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop checking how to convert i686-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) none checking how to run the C preprocessor... gcc -E checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking how to run the C++ preprocessor... g++ -E checking for ANSI C header files... (cached) yes checking assert.h usability... yes checking assert.h presence... yes checking for assert.h... yes checking ctype.h usability... yes checking ctype.h presence... yes checking for ctype.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking for memory.h... (cached) yes checking stdarg.h usability... yes checking stdarg.h presence... yes checking for stdarg.h... yes checking stdio.h usability... yes checking stdio.h presence... yes checking for stdio.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking time.h usability... yes checking time.h presence... yes checking for time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking for inline... inline checking for log in -lm... yes checking for log2 in -lm... yes checking argtable2.h usability... yes checking argtable2.h presence... yes checking for argtable2.h... yes checking for arg_parse in -largtable2... yes checking for OpenMP flag of C compiler... -fopenmp checking whether byte ordering is bigendian... no checking for ntohs... yes checking for ntohl... yes checking for ntons... no checking for ntonl... no checking size of unsigned short... 2 checking size of unsigned int... 4 checking size of unsigned long... 4 checking size of unsigned long long... 8 checking for stroul... no checking for strtoull... yes checking for ftello... yes checking for fseeko... yes checking for ftello64... yes checking for fseeko64... yes checking for ftell64... no checking for fseek64... no checking for off_t... yes checking size of fpos_t... 12 checking if malloc debugging is wanted... no checking whether to build with debug information... 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 clustalo.pc config.status: creating Doxyfile config.status: creating src/clustal/Makefile config.status: creating src/hhalign/Makefile config.status: creating src/kmpp/Makefile config.status: creating src/squid/Makefile config.status: creating src/config.h config.status: executing src/clustal-omega-config.h commands config.status: creating src/clustal-omega-config.h - prefix CLUSTAL_OMEGA for src/config.h defines config.status: executing depfiles commands config.status: executing libtool commands debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/clustalo-1.2.4' # nothing to do here make[1]: Leaving directory '/build/clustalo-1.2.4' dh_auto_build -Nlibclustalo-doc make -j18 make[1]: Entering directory '/build/clustalo-1.2.4' Making all in src make[2]: Entering directory '/build/clustalo-1.2.4/src' make all-recursive make[3]: Entering directory '/build/clustalo-1.2.4/src' Making all in hhalign make[4]: Entering directory '/build/clustalo-1.2.4/src/hhalign' /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hhalign.lo hhalign.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c hhalign.cpp -fPIC -DPIC -o .libs/hhalign.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c hhalign.cpp -o hhalign.o >/dev/null 2>&1 /bin/sh ../../libtool --tag=CXX --mode=link g++ -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o libhhalign.la hhalign.lo -largtable2 -lm libtool: link: ar cr .libs/libhhalign.a .libs/hhalign.o libtool: link: ranlib .libs/libhhalign.a libtool: link: ( cd ".libs" && rm -f "libhhalign.la" && ln -s "../libhhalign.la" "libhhalign.la" ) make[4]: Leaving directory '/build/clustalo-1.2.4/src/hhalign' Making all in squid make[4]: Entering directory '/build/clustalo-1.2.4/src/squid' /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o a2m.lo a2m.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o aligneval.lo aligneval.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alignio.lo alignio.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o clustal.lo clustal.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cluster.lo cluster.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o dayhoff.lo dayhoff.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o eps.lo eps.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o file.lo file.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o getopt.lo getopt.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gki.lo gki.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsi.lo gsi.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsi64.lo gsi64.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hsregex.lo hsregex.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o iupac.lo iupac.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o msa.lo msa.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o msf.lo msf.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylip.lo phylip.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o revcomp.lo revcomp.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c alignio.c -fPIC -DPIC -o .libs/alignio.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 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-O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c dayhoff.c -fPIC -DPIC -o .libs/dayhoff.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c gsi.c -fPIC -DPIC -o .libs/gsi.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c iupac.c -fPIC -DPIC -o .libs/iupac.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c msa.c -fPIC -DPIC -o .libs/msa.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c gsi64.c -fPIC -DPIC -o .libs/gsi64.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c phylip.c -fPIC -DPIC -o .libs/phylip.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c eps.c -fPIC -DPIC -o .libs/eps.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c revcomp.c -fPIC -DPIC -o .libs/revcomp.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g 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hhalign_wrapper.lo hhalign_wrapper.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ktuple_pair.lo ktuple_pair.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o list.lo list.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o log.lo log.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o muscle_upgma.lo muscle_upgma.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o muscle_tree.lo muscle_tree.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mbed.lo mbed.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pair_dist.lo pair_dist.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o progress.lo progress.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o seq.lo seq.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o symmatrix.lo symmatrix.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tree.lo tree.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.lo util.c /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o weights.lo weights.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c log.c -fPIC -DPIC -o .libs/log.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c muscle_upgma.c -fPIC -DPIC -o .libs/muscle_upgma.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c mbed.c -fPIC -DPIC -o .libs/mbed.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c hhalign_wrapper.c -fPIC -DPIC -o .libs/hhalign_wrapper.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c ktuple_pair.c -fPIC -DPIC -o .libs/ktuple_pair.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c list.c -fPIC -DPIC -o .libs/list.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c muscle_tree.c -fPIC -DPIC -o .libs/muscle_tree.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c weights.c -fPIC -DPIC -o .libs/weights.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c pair_dist.c -fPIC -DPIC -o .libs/pair_dist.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c seq.c -fPIC -DPIC -o .libs/seq.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c tree.c -fPIC -DPIC -o .libs/tree.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c progress.c -fPIC -DPIC -o .libs/progress.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c symmatrix.c -fPIC -DPIC -o .libs/symmatrix.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c util.c -fPIC -DPIC -o .libs/util.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c list.c -o list.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c log.c -o log.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c progress.c -o progress.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c weights.c -o weights.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c util.c -o util.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c tree.c -o tree.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c pair_dist.c -o pair_dist.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c symmatrix.c -o symmatrix.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c muscle_upgma.c -o muscle_upgma.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c ktuple_pair.c -o ktuple_pair.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c mbed.c -o mbed.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c seq.c -o seq.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c muscle_tree.c -o muscle_tree.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c hhalign_wrapper.c -o hhalign_wrapper.o >/dev/null 2>&1 /bin/sh ../../libtool --tag=CC --mode=link gcc -fopenmp -O3 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o libclustal.la hhalign_wrapper.lo ktuple_pair.lo list.lo log.lo muscle_upgma.lo muscle_tree.lo mbed.lo pair_dist.lo progress.lo seq.lo symmatrix.lo tree.lo util.lo weights.lo -largtable2 -lm libtool: link: ar cr .libs/libclustal.a .libs/hhalign_wrapper.o .libs/ktuple_pair.o .libs/list.o .libs/log.o .libs/muscle_upgma.o .libs/muscle_tree.o .libs/mbed.o .libs/pair_dist.o .libs/progress.o .libs/seq.o .libs/symmatrix.o .libs/tree.o .libs/util.o .libs/weights.o libtool: link: ranlib .libs/libclustal.a libtool: link: ( cd ".libs" && rm -f "libclustal.la" && ln -s "../libclustal.la" "libclustal.la" ) make[4]: Leaving directory '/build/clustalo-1.2.4/src/clustal' make[4]: Entering directory '/build/clustalo-1.2.4/src' g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.cpp gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mymain.o mymain.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o clustal-omega.lo clustal-omega.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c clustal-omega.c -fPIC -DPIC -o .libs/clustal-omega.o clustal-omega.c: In function 'PrintLongVersion': clustal-omega.c:152:49: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 152 | PACKAGE_VERSION, PACKAGE_CODENAME, __DATE__); | ^~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c clustal-omega.c -o clustal-omega.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=link gcc -O3 -fopenmp -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -static -Wl,-z,relro -Wl,-z,now -o libclustalo.la -rpath /usr/lib/i386-linux-gnu clustal-omega.lo clustal/libclustal.la hhalign/libhhalign.la squid/libsquid.la kmpp/libkmpp.la -largtable2 -lm libtool: link: (cd .libs/libclustalo.lax/libclustal.a && ar x "/build/clustalo-1.2.4/src/clustal/.libs/libclustal.a") libtool: link: (cd .libs/libclustalo.lax/libhhalign.a && ar x "/build/clustalo-1.2.4/src/hhalign/.libs/libhhalign.a") libtool: link: (cd .libs/libclustalo.lax/libsquid.a && ar x "/build/clustalo-1.2.4/src/squid/.libs/libsquid.a") libtool: link: (cd .libs/libclustalo.lax/libkmpp.a && ar x "/build/clustalo-1.2.4/src/kmpp/.libs/libkmpp.a") libtool: link: ar cr .libs/libclustalo.a clustal-omega.o .libs/libclustalo.lax/libclustal.a/hhalign_wrapper.o .libs/libclustalo.lax/libclustal.a/ktuple_pair.o .libs/libclustalo.lax/libclustal.a/list.o .libs/libclustalo.lax/libclustal.a/log.o .libs/libclustalo.lax/libclustal.a/mbed.o .libs/libclustalo.lax/libclustal.a/muscle_tree.o .libs/libclustalo.lax/libclustal.a/muscle_upgma.o .libs/libclustalo.lax/libclustal.a/pair_dist.o .libs/libclustalo.lax/libclustal.a/progress.o .libs/libclustalo.lax/libclustal.a/seq.o .libs/libclustalo.lax/libclustal.a/symmatrix.o .libs/libclustalo.lax/libclustal.a/tree.o .libs/libclustalo.lax/libclustal.a/util.o .libs/libclustalo.lax/libclustal.a/weights.o .libs/libclustalo.lax/libhhalign.a/hhalign.o .libs/libclustalo.lax/libsquid.a/a2m.o .libs/libclustalo.lax/libsquid.a/aligneval.o .libs/libclustalo.lax/libsquid.a/alignio.o .libs/libclustalo.lax/libsquid.a/clustal.o .libs/libclustalo.lax/libsquid.a/cluster.o .libs/libclustalo.lax/libsquid.a/dayhoff.o .libs/libclustalo.lax/libsquid.a/eps.o .libs/libclustalo.lax/libsquid.a/file.o .libs/libclustalo.lax/libsquid.a/getopt.o .libs/libclustalo.lax/libsquid.a/gki.o .libs/libclustalo.lax/libsquid.a/gsi.o .libs/libclustalo.lax/libsquid.a/gsi64.o .libs/libclustalo.lax/libsquid.a/hsregex.o .libs/libclustalo.lax/libsquid.a/iupac.o .libs/libclustalo.lax/libsquid.a/msa.o .libs/libclustalo.lax/libsquid.a/msf.o .libs/libclustalo.lax/libsquid.a/phylip.o .libs/libclustalo.lax/libsquid.a/revcomp.o .libs/libclustalo.lax/libsquid.a/rk.o .libs/libclustalo.lax/libsquid.a/selex.o .libs/libclustalo.lax/libsquid.a/seqencode.o .libs/libclustalo.lax/libsquid.a/shuffle.o .libs/libclustalo.lax/libsquid.a/sqerror.o .libs/libclustalo.lax/libsquid.a/sqio.o .libs/libclustalo.lax/libsquid.a/squidcore.o .libs/libclustalo.lax/libsquid.a/sre_ctype.o .libs/libclustalo.lax/libsquid.a/sre_math.o .libs/libclustalo.lax/libsquid.a/sre_random.o .libs/libclustalo.lax/libsquid.a/sre_string.o .libs/libclustalo.lax/libsquid.a/ssi.o .libs/libclustalo.lax/libsquid.a/stack.o .libs/libclustalo.lax/libsquid.a/stockholm.o .libs/libclustalo.lax/libsquid.a/stopwatch.o .libs/libclustalo.lax/libsquid.a/translate.o .libs/libclustalo.lax/libsquid.a/types.o .libs/libclustalo.lax/libsquid.a/vectorops.o .libs/libclustalo.lax/libsquid.a/weight.o .libs/libclustalo.lax/libkmpp.a/KMeans.o .libs/libclustalo.lax/libkmpp.a/KmTree.o .libs/libclustalo.lax/libkmpp.a/KmUtils.o libtool: link: ranlib .libs/libclustalo.a libtool: link: rm -fr .libs/libclustalo.lax libtool: link: ( cd ".libs" && rm -f "libclustalo.la" && ln -s "../libclustalo.la" "libclustalo.la" ) /bin/sh ../libtool --tag=CXX --mode=link g++ -O3 -fopenmp -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o clustalo main.o mymain.o libclustalo.la -largtable2 -lm libtool: link: g++ -O3 -fopenmp -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o clustalo main.o mymain.o ./.libs/libclustalo.a /usr/lib/i386-linux-gnu/libargtable2.so -lm -fopenmp /usr/bin/ld: ./.libs/libclustalo.a(clustal-omega.o): in function `AlnToHHMFile': ./src/clustal-omega.c:393: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' make[4]: Leaving directory '/build/clustalo-1.2.4/src' make[3]: Leaving directory '/build/clustalo-1.2.4/src' make[2]: Leaving directory '/build/clustalo-1.2.4/src' make[2]: Entering directory '/build/clustalo-1.2.4' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/clustalo-1.2.4' make[1]: Leaving directory '/build/clustalo-1.2.4' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/clustalo-1.2.4' dh_auto_test -a make -j18 check VERBOSE=1 make[2]: Entering directory '/build/clustalo-1.2.4' Making check in src make[3]: Entering directory '/build/clustalo-1.2.4/src' Making check in hhalign make[4]: Entering directory '/build/clustalo-1.2.4/src/hhalign' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/clustalo-1.2.4/src/hhalign' Making check in squid make[4]: Entering directory '/build/clustalo-1.2.4/src/squid' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/clustalo-1.2.4/src/squid' Making check in kmpp make[4]: Entering directory '/build/clustalo-1.2.4/src/kmpp' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/clustalo-1.2.4/src/kmpp' Making check in clustal make[4]: Entering directory '/build/clustalo-1.2.4/src/clustal' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/clustalo-1.2.4/src/clustal' make[4]: Entering directory '/build/clustalo-1.2.4/src' make[4]: Leaving directory '/build/clustalo-1.2.4/src' make[3]: Leaving directory '/build/clustalo-1.2.4/src' make[3]: Entering directory '/build/clustalo-1.2.4' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/clustalo-1.2.4' make[2]: Leaving directory '/build/clustalo-1.2.4' # Run additional test from python-biopython package to verify that # this will work as well src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal --force rm temp_test.aln temp_test.dnd make[1]: Leaving directory '/build/clustalo-1.2.4' debian/rules override_dh_auto_test-indep make[1]: Entering directory '/build/clustalo-1.2.4' echo "Do not run build time test" Do not run build time test make[1]: Leaving directory '/build/clustalo-1.2.4' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/clustalo-1.2.4' dh_auto_install -a make -j1 install DESTDIR=/build/clustalo-1.2.4/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/clustalo-1.2.4' Making install in src make[3]: Entering directory '/build/clustalo-1.2.4/src' Making install in hhalign make[4]: Entering directory '/build/clustalo-1.2.4/src/hhalign' make[5]: Entering directory '/build/clustalo-1.2.4/src/hhalign' make[5]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/clustalo-1.2.4/debian/tmp/usr/include/clustalo/hhalign' /usr/bin/install -c -m 644 general.h hhfunc.h '/build/clustalo-1.2.4/debian/tmp/usr/include/clustalo/hhalign' make[5]: Leaving directory '/build/clustalo-1.2.4/src/hhalign' make[4]: Leaving directory '/build/clustalo-1.2.4/src/hhalign' Making install in squid make[4]: Entering directory '/build/clustalo-1.2.4/src/squid' make[5]: Entering directory '/build/clustalo-1.2.4/src/squid' make[5]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/clustalo-1.2.4/debian/tmp/usr/include/clustalo/squid' /usr/bin/install -c -m 644 gki.h gsi64.h msa.h rk.h squid.h stopwatch.h sqfuncs.h sre_random.h ssi.h stockholm.h vectorops.h version.h '/build/clustalo-1.2.4/debian/tmp/usr/include/clustalo/squid' make[5]: Leaving directory '/build/clustalo-1.2.4/src/squid' make[4]: Leaving directory '/build/clustalo-1.2.4/src/squid' Making install in kmpp make[4]: Entering directory '/build/clustalo-1.2.4/src/kmpp' make[5]: Entering directory '/build/clustalo-1.2.4/src/kmpp' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/build/clustalo-1.2.4/src/kmpp' make[4]: Leaving directory '/build/clustalo-1.2.4/src/kmpp' Making install in clustal make[4]: Entering directory '/build/clustalo-1.2.4/src/clustal' make[5]: Entering directory '/build/clustalo-1.2.4/src/clustal' make[5]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/clustalo-1.2.4/debian/tmp/usr/include/clustalo/clustal' /usr/bin/install -c -m 644 hhalign_wrapper.h ktuple_pair.h log.h mbed.h muscle_tree.h pair_dist.h progress.h seq.h symmatrix.h tree.h util.h weights.h '/build/clustalo-1.2.4/debian/tmp/usr/include/clustalo/clustal' make[5]: Leaving directory '/build/clustalo-1.2.4/src/clustal' make[4]: Leaving directory '/build/clustalo-1.2.4/src/clustal' make[4]: Entering directory '/build/clustalo-1.2.4/src' make[5]: Entering directory '/build/clustalo-1.2.4/src' /usr/bin/mkdir -p '/build/clustalo-1.2.4/debian/tmp/usr/lib/i386-linux-gnu' /bin/sh ../libtool --mode=install /usr/bin/install -c libclustalo.la '/build/clustalo-1.2.4/debian/tmp/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/libclustalo.lai /build/clustalo-1.2.4/debian/tmp/usr/lib/i386-linux-gnu/libclustalo.la libtool: install: /usr/bin/install -c .libs/libclustalo.a /build/clustalo-1.2.4/debian/tmp/usr/lib/i386-linux-gnu/libclustalo.a libtool: install: chmod 644 /build/clustalo-1.2.4/debian/tmp/usr/lib/i386-linux-gnu/libclustalo.a libtool: install: ranlib /build/clustalo-1.2.4/debian/tmp/usr/lib/i386-linux-gnu/libclustalo.a libtool: warning: remember to run 'libtool --finish /usr/lib/i386-linux-gnu' /usr/bin/mkdir -p '/build/clustalo-1.2.4/debian/tmp/usr/bin' /bin/sh ../libtool --mode=install /usr/bin/install -c clustalo '/build/clustalo-1.2.4/debian/tmp/usr/bin' libtool: install: /usr/bin/install -c clustalo /build/clustalo-1.2.4/debian/tmp/usr/bin/clustalo /usr/bin/mkdir -p '/build/clustalo-1.2.4/debian/tmp/usr/include/clustalo/' /usr/bin/install -c -m 644 clustal-omega-config.h clustal-omega.h '/build/clustalo-1.2.4/debian/tmp/usr/include/clustalo/' make[5]: Leaving directory '/build/clustalo-1.2.4/src' make[4]: Leaving directory '/build/clustalo-1.2.4/src' make[3]: Leaving directory '/build/clustalo-1.2.4/src' make[3]: Entering directory '/build/clustalo-1.2.4' make[4]: Entering directory '/build/clustalo-1.2.4' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/clustalo-1.2.4/debian/tmp/usr/share/doc/clustal-omega' /usr/bin/install -c -m 644 README '/build/clustalo-1.2.4/debian/tmp/usr/share/doc/clustal-omega' /usr/bin/mkdir -p '/build/clustalo-1.2.4/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 clustalo.pc '/build/clustalo-1.2.4/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig' make[4]: Leaving directory '/build/clustalo-1.2.4' make[3]: Leaving directory '/build/clustalo-1.2.4' make[2]: Leaving directory '/build/clustalo-1.2.4' rm -rf debian/tmp/usr/lib/pkgconfig rm -f debian/tmp/usr/lib/*/libclustalo.la mv debian/tmp/usr/include debian/libclustalo-dev/usr mv debian/tmp/usr/lib debian/libclustalo-dev/usr mv debian/tmp/usr/bin debian/clustalo/usr make[1]: Leaving directory '/build/clustalo-1.2.4' debian/rules override_dh_auto_install-indep make[1]: Entering directory '/build/clustalo-1.2.4' # Generate doxygen doc mkdir -p doc doxygen Doxyfile warning: Tag 'SYMBOL_CACHE_SIZE' at line 289 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'SHOW_DIRECTORIES' at line 473 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'COLS_IN_ALPHA_INDEX' at line 744 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'HTML_ALIGN_MEMBERS' at line 799 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'XML_SCHEMA' at line 1136 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'XML_DTD' at line 1142 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'PERL_PATH' at line 1307 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'MSCGEN_PATH' at line 1329 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: argument 'a4wide' for option PAPER_TYPE is not a valid enum value Using the default: a4! warning: doxygen no longer ships with the FreeSans font. You may want to clear or change DOT_FONTNAME. Otherwise you run the risk that the wrong font is being used for dot generated graphs. /build/clustalo-1.2.4/src/clustal-omega.c:755: warning: argument 'pdSeqWeights_p' from the argument list of AlignmentOrder has multiple @param documentation sections /build/clustalo-1.2.4/src/clustal-omega.c:755: warning: The following parameters of AlignmentOrder(int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq, int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile, int iClusteringType, int iClustersizes, char *pcGuidetreeInfile, char *pcGuidetreeOutfile, char *pcClusterFile, bool bUseMbed, bool bPercID) are not documented: parameter 'iClustersizes' parameter 'pcClusterFile' parameter 'bPercID' /build/clustalo-1.2.4/src/clustal-omega.h:169: warning: argument 'pdSeqWeights_p' from the argument list of AlignmentOrder has multiple @param documentation sections /build/clustalo-1.2.4/src/clustal-omega.h:169: warning: The following parameters of AlignmentOrder(int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq, int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile, int iClusteringType, int iClustersizes, char *pcGuidetreeInfile, char *pcGuidetreeOutfile, char *pcClusterFile, bool bUseMbed, bool bPercID) are not documented: parameter 'iClustersizes' parameter 'pcClusterFile' parameter 'bPercID' /build/clustalo-1.2.4/src/clustal/mbed.c:666: warning: The following parameter of BisectingKmeans(bisecting_kmeans_result_t **prKMeansResult_p, const int iNObjs, const int iDim, double **ppdVectors, const int iMinRequiredObjsPerCluster, const int iMaxAllowedObjsPerCluster, char ***ppcClusterSplits_p) is not documented: parameter 'ppcClusterSplits_p' /build/clustalo-1.2.4/src/clustal/mbed.c:1162: warning: The following parameters of Mbed(tree_t **prMbedTree_p, mseq_t *prMSeq, const int iPairDistType, const char *pcGuidetreeOut, int iClustersizes, const char *pcClusterFile) are not documented: parameter 'iClustersizes' parameter 'pcClusterFile' /build/clustalo-1.2.4/src/clustal/mbed.h:27: warning: The following parameters of Mbed(tree_t **prMbedTree_p, mseq_t *prMSeq, const int iPairDistType, const char *pcGuidetreeOut, int iClustersizes, const char *pcClusterFile) are not documented: parameter 'iClustersizes' parameter 'pcClusterFile' /build/clustalo-1.2.4/src/clustal/pair_dist.c:264: warning: Unsupported xml/html tag found /build/clustalo-1.2.4/src/clustal/pair_dist.c:270: warning: Unsupported xml/html tag found /build/clustalo-1.2.4/src/clustal/pair_dist.c:277: warning: The following parameter of PairDistances(symmatrix_t **distmat, mseq_t *mseq, int pairdist_type, bool bPercID, int istart, const unsigned long int iend, int jstart, const unsigned long int jend, char *fdist_in, char *fdist_out) is not documented: parameter 'bPercID' /build/clustalo-1.2.4/src/clustal/pair_dist.c:264: warning: Unsupported xml/html tag found /build/clustalo-1.2.4/src/clustal/pair_dist.c:270: warning: Unsupported xml/html tag found /build/clustalo-1.2.4/src/clustal/pair_dist.h:36: warning: The following parameter of PairDistances(symmatrix_t **distmat, mseq_t *mseq, int pairdist_type, bool bPercID, int istart, const unsigned long int iend, int jstart, const unsigned long int jend, char *fdist_in, char *fdist_out) is not documented: parameter 'bPercID' /build/clustalo-1.2.4/src/clustal/seq.c:420: warning: The following parameters of ReadSequences(mseq_t *prMSeq, char *seqfile, int iSeqType, int iSeqFmt, bool bIsProfile, bool bDealignInputSeqs, int iMaxNumSeq, int iMaxSeqLen, char *pcHMMBatch) are not documented: parameter 'iSeqFmt' parameter 'bIsProfile' parameter 'bDealignInputSeqs' parameter 'pcHMMBatch' /build/clustalo-1.2.4/src/clustal/seq.c:1112: warning: The following parameters of SeqsAreAligned(mseq_t *prMSeq, bool bIsProfile, bool bDealignInputSeqs) are not documented: parameter 'bIsProfile' parameter 'bDealignInputSeqs' /build/clustalo-1.2.4/src/clustal/seq.c:884: warning: The following parameter of WriteAlignment(mseq_t *mseq, const char *pcAlnOutfile, int outfmt, int iWrap, bool bResno) is not documented: parameter 'bResno' /build/clustalo-1.2.4/src/clustal/seq.h:136: warning: The following parameters of ReadSequences(mseq_t *prMSeq, char *seqfile, int iSeqType, int iSeqFmt, bool bIsProfile, bool bDealignInputSeqs, int iMaxNumSeq, int iMaxSeqLen, char *pcHMMBatch) are not documented: parameter 'iSeqFmt' parameter 'bIsProfile' parameter 'bDealignInputSeqs' parameter 'pcHMMBatch' /build/clustalo-1.2.4/src/clustal/seq.h:171: warning: The following parameters of SeqsAreAligned(mseq_t *prMSeq, bool bIsProfile, bool bDealignInputSeqs) are not documented: parameter 'bIsProfile' parameter 'bDealignInputSeqs' /build/clustalo-1.2.4/src/clustal/seq.h:156: warning: The following parameter of WriteAlignment(mseq_t *mseq, const char *pcAlnOutfile, int outfmt, int iWrap, bool bResno) is not documented: parameter 'bResno' /build/clustalo-1.2.4/src/clustal/symmatrix.c:248: warning: documented empty return type of SymMatrixGetValueP /build/clustalo-1.2.4/src/clustal/symmatrix.c:316: warning: The following parameter of SymMatrixPrint(symmatrix_t *symmat, char **labels, const char *path, bool bPercID) is not documented: parameter 'bPercID' /build/clustalo-1.2.4/src/clustal/symmatrix.h:74: warning: documented empty return type of SymMatrixGetValueP /build/clustalo-1.2.4/src/clustal/symmatrix.h:80: warning: The following parameter of SymMatrixPrint(symmatrix_t *symmat, char **labels, const char *path, bool bPercID) is not documented: parameter 'bPercID' find doc -name "*.md5" -delete make[1]: Leaving directory '/build/clustalo-1.2.4' dh_install dh_installdocs dh_installchangelogs dh_installexamples 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 dpkg-gencontrol: warning: Depends field of package libclustalo-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libclustalo-doc: substitution variable ${js:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'clustalo' in '../clustalo_1.2.4-7_i386.deb'. dpkg-deb: building package 'clustalo-dbgsym' in '../clustalo-dbgsym_1.2.4-7_i386.deb'. dpkg-deb: building package 'libclustalo-dev' in '../libclustalo-dev_1.2.4-7_i386.deb'. dpkg-deb: building package 'libclustalo-doc' in '../libclustalo-doc_1.2.4-7_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../clustalo_1.2.4-7_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) I: copying local configuration I: user script /srv/workspace/pbuilder/64289/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/64289/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/64289 and its subdirectories I: Current time: Sun Jul 17 22:48:23 +14 2022 I: pbuilder-time-stamp: 1658047703