I: pbuilder: network access will be disabled during build I: Current time: Sun Feb 19 13:58:13 +14 2023 I: pbuilder-time-stamp: 1676764693 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: 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.2KHye51B/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/501559/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. 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/501559/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/501559/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]="x86_64-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=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=333373c9b0c347d38a2d2ea6e37754d6 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-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=501559 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.CvlnFXicAN/pbuilderrc_yKUi --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.CvlnFXicAN/b2 --logfile b2/build.log clustalo_1.2.4-7.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 5 2021 bash -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38984 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 38984 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 18424 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 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jul 29 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 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 29 2021 findmnt -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 203072 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 98048 Mar 3 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 8 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jul 29 2021 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 29 2021 more -rwsr-xr-x 1 root root 55528 Jul 29 2021 mount -rwxr-xr-x 1 root root 18664 Jul 29 2021 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 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 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Aug 5 2021 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Feb 19 13:58 sh -> bash lrwxrwxrwx 1 root root 4 Feb 10 05:47 sh.distrib -> dash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jul 29 2021 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 29 2021 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 29 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/501559/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19655 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} libann0{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, 99 newly installed, 0 to remove and 0 not upgraded. Need to get 80.5 MB of archives. After unpacking 310 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libedit2 amd64 3.1-20191231-2+b1 [96.7 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libz3-4 amd64 4.8.10-1 [6949 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libllvm11 amd64 1:11.0.1-2 [17.9 MB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libclang-cpp11 amd64 1:11.0.1-2 [9632 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libclang1-11 amd64 1:11.0.1-2 [5521 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 doxygen amd64 1.9.1-1 [4232 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2 [96.9 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1 [418 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 fontconfig amd64 2.13.1-4.2 [417 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 libann0 amd64 1.1.2+doc-7 [25.3 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libcdt5 amd64 2.42.2-5 [62.2 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 libcgraph6 amd64 2.42.2-5 [85.5 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1 [258 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1 [289 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1 [311 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1 [772 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 libxpm4 amd64 1:3.5.12-1 [49.1 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 libgd3 amd64 2.3.0-2 [137 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1 [1370 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 libgts-0.7-5 amd64 0.7.6+darcs121130-4+b1 [158 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 libpixman-1-0 amd64 0.40.0-1 [543 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 libxcb-render0 amd64 1.14-3 [111 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 libxcb-shm0 amd64 1.14-3 [101 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libcairo2 amd64 1.16.0-5 [694 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libltdl7 amd64 2.4.6-15 [391 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libfribidi0 amd64 1.0.8-2 [64.8 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libharfbuzz0b amd64 2.7.4-1 [1471 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libthai-data all 0.1.28-3 [170 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 libdatrie1 amd64 0.2.13-1 [42.7 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 libthai0 amd64 0.1.28-3 [54.2 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libpango-1.0-0 amd64 1.46.2-3 [191 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 libpangoft2-1.0-0 amd64 1.46.2-3 [62.2 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 libpangocairo-1.0-0 amd64 1.46.2-3 [50.6 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 libpathplan4 amd64 2.42.2-5 [64.3 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 libgvc6 amd64 2.42.2-5 [695 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 libgvpr2 amd64 2.42.2-5 [212 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 liblab-gamut1 amd64 2.42.2-5 [221 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 x11-common all 1:7.7+22 [252 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get: 88 http://deb.debian.org/debian bullseye/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 libxt6 amd64 1:1.2.0-1 [189 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 libxmu6 amd64 2:1.1.2-2+b3 [60.8 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 libxaw7 amd64 2:1.0.13-1.1 [202 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 graphviz amd64 2.42.2-5 [632 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 libargtable2-0 amd64 13-1.1 [17.9 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 libargtable2-docs all 13-1.1 [2622 kB] Get: 95 http://deb.debian.org/debian bullseye/main amd64 libargtable2-dev amd64 13-1.1 [57.7 kB] Get: 96 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 97 http://deb.debian.org/debian bullseye/main amd64 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 sphinx-common all 3.4.3-2 [578 kB] Fetched 80.5 MB in 2s (34.6 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 ... 19655 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_amd64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_amd64.deb ... 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Setting up bsdextrautils (2.36.1-8) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-7) ... Setting up libdatrie1:amd64 (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:amd64 (2.66.8-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up liblab-gamut1:amd64 (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:amd64 (1:5.39-3) ... Setting up libdeflate0:amd64 (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:amd64 (2.1-3.1+b2) ... Setting up libgts-0.7-5:amd64 (0.7.6+darcs121130-4+b1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libz3-4:amd64 (4.8.10-1) ... Setting up libjpeg62-turbo:amd64 (1:2.0.6-4) ... Setting up libx11-data (2:1.7.2-1) ... Setting up libpathplan4:amd64 (2.42.2-5) ... Setting up libann0 (1.1.2+doc-7) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up libfribidi0:amd64 (1.0.8-2) ... Setting up libpng16-16:amd64 (1.6.37-3) ... Setting up autopoint (0.21-4) ... Setting up libwebp6:amd64 (0.6.1-2.1) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up libltdl7:amd64 (2.4.6-15) ... Setting up libmd0:amd64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libthai-data (0.1.28-3) ... Setting up libcdt5:amd64 (2.42.2-5) ... Setting up libcgraph6:amd64 (2.42.2-5) ... Setting up libtiff5:amd64 (4.2.0-1) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up libbsd0:amd64 (0.11.3-1) ... Setting up libelf1:amd64 (0.183-1) ... Setting up libxml2:amd64 (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 (1.12.0-1) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libxcb1:amd64 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libxcb-render0:amd64 (1.14-3) ... Setting up libedit2:amd64 (3.1-20191231-2+b1) ... Setting up m4 (1.4.18-5) ... Setting up libxcb-shm0:amd64 (1.14-3) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libthai0:amd64 (0.1.28-3) ... Setting up libllvm11:amd64 (1:11.0.1-2) ... Setting up libfreetype6:amd64 (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 (1.12.0-1) ... Setting up libgvpr2:amd64 (2.42.2-5) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libx11-6:amd64 (2:1.7.2-1) ... Setting up libharfbuzz0b:amd64 (2.7.4-1) ... Setting up libsm6:amd64 (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:amd64 (1:3.5.12-1) ... Setting up libxrender1:amd64 (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:amd64 (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:amd64 (1:1.2.0-1) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libxmu6:amd64 (2:1.1.2-2+b3) ... Setting up libpango-1.0-0:amd64 (1.46.2-3) ... Setting up debhelper (13.3.4) ... Setting up libxaw7:amd64 (2:1.0.13-1.1) ... Setting up libcairo2:amd64 (1.16.0-5) ... Setting up libgd3:amd64 (2.3.0-2) ... Setting up libpangoft2-1.0-0:amd64 (1.46.2-3) ... Setting up libpangocairo-1.0-0:amd64 (1.46.2-3) ... Setting up libgvc6 (2.42.2-5) ... Setting up graphviz (2.42.2-5) ... Processing triggers for libc-bin (2.31-13+deb11u2) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package hostname: Name or service not known 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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../clustalo_1.2.4-7_source.changes 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 amd64 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=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking 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... /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... /bin/grep checking for egrep... /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... x86_64-pc-linux-gnu checking host system type... x86_64-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... /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking 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 -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking 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... 8 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... 16 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 -j16 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 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 cluster.c -fPIC -DPIC -o .libs/cluster.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 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 -g -O2 -fdebug-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c a2m.c -fPIC -DPIC -o .libs/a2m.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 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-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 file.c -o file.o >/dev/null 2>&1 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 a2m.c -o a2m.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 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-fstack-protector-strong -Wformat -Werror=format-security -c -o 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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/x86_64-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/x86_64-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 -j16 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'. /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'. /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'. /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' /bin/mkdir -p '/build/clustalo-1.2.4/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/sh ../libtool --mode=install /usr/bin/install -c libclustalo.la '/build/clustalo-1.2.4/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libclustalo.lai /build/clustalo-1.2.4/debian/tmp/usr/lib/x86_64-linux-gnu/libclustalo.la libtool: install: /usr/bin/install -c .libs/libclustalo.a /build/clustalo-1.2.4/debian/tmp/usr/lib/x86_64-linux-gnu/libclustalo.a libtool: install: chmod 644 /build/clustalo-1.2.4/debian/tmp/usr/lib/x86_64-linux-gnu/libclustalo.a libtool: install: ranlib /build/clustalo-1.2.4/debian/tmp/usr/lib/x86_64-linux-gnu/libclustalo.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /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 /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'. /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' /bin/mkdir -p '/build/clustalo-1.2.4/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 clustalo.pc '/build/clustalo-1.2.4/debian/tmp/usr/lib/x86_64-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_amd64.deb'. dpkg-deb: building package 'clustalo-dbgsym' in '../clustalo-dbgsym_1.2.4-7_amd64.deb'. dpkg-deb: building package 'libclustalo-dev' in '../libclustalo-dev_1.2.4-7_amd64.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_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/501559/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/501559/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/501559 and its subdirectories I: Current time: Sun Feb 19 14:02:09 +14 2023 I: pbuilder-time-stamp: 1676764929