I: pbuilder: network access will be disabled during build I: Current time: Sat May 30 09:12:01 -12 2020 I: pbuilder-time-stamp: 1590873122 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-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_1.2.4-2.dsc] I: copying [./clustalo_1.2.4.orig.tar.gz] I: copying [./clustalo_1.2.4-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Jul 18 07:15:32 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./clustalo_1.2.4-2.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_1.2.4-2.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3031/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='da42f21c16a24a6fbacf7e727eb591a5' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3031' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.dOblE9DHj1/pbuilderrc_Fq4Y --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.dOblE9DHj1/b1 --logfile b1/build.log clustalo_1.2.4-2.dsc' SUDO_GID='115' SUDO_UID='111' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux cbxi4pro0 4.19.0-9-armmp #1 SMP Debian 4.19.118-2 (2020-04-29) armv7l GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 22432 Feb 28 2019 cat -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash -rwxr-xr-x 1 root root 71648 Feb 28 2019 date -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd -rwxr-xr-x 1 root root 55672 Feb 28 2019 df -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir -rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 22364 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 18260 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 124508 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln -rwxr-xr-x 1 root root 34932 Jul 26 2018 login -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 9 2019 more -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 84284 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 May 17 20:27 sh -> dash -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty -rwsr-xr-x 1 root root 42472 Jan 9 2019 su -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch -rwxr-xr-x 1 root root 18260 Feb 28 2019 true -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir -rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/3031/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: armhf 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 (>= 11~), dh-linktree, 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 ... 18932 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 (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on dh-linktree; however: Package dh-linktree 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} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-linktree{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} libbsd0{a} libcairo2{a} libcdt5{a} libcgraph6{a} libclang1-6.0{a} libcroco3{a} libdatrie1{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} libicu63{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} liblab-gamut1{a} libllvm6.0{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libncurses6{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} 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} libxdot4{a} libxext6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6{a} lsb-base{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 libgpm2 libgts-bin libltdl-dev libmail-sendmail-perl lynx python-sphinx python3-sphinx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 96 newly installed, 0 to remove and 0 not upgraded. Need to get 55.7 MB of archives. After unpacking 170 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 10 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 11 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 12 http://deb.debian.org/debian buster/main armhf ucf all 3.0038+nmu1 [69.0 kB] Get: 13 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 14 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 15 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 16 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 17 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 18 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 19 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 20 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 21 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 23 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 24 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 25 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 26 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 27 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 29 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 30 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 31 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 32 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 33 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 34 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 35 http://deb.debian.org/debian buster/main armhf dh-linktree all 0.6 [10.7 kB] Get: 36 http://deb.debian.org/debian buster/main armhf libedit2 armhf 3.1-20181209-1 [79.5 kB] Get: 37 http://deb.debian.org/debian buster/main armhf libllvm6.0 armhf 1:6.0.1-10 [13.1 MB] Get: 38 http://deb.debian.org/debian buster/main armhf libclang1-6.0 armhf 1:6.0.1-10 [6029 kB] Get: 39 http://deb.debian.org/debian buster/main armhf doxygen armhf 1.8.13-10 [3568 kB] Get: 40 http://deb.debian.org/debian buster/main armhf libexpat1 armhf 2.2.6-2+deb10u1 [78.0 kB] Get: 41 http://deb.debian.org/debian buster/main armhf libpng16-16 armhf 1.6.36-6 [275 kB] Get: 42 http://deb.debian.org/debian buster/main armhf libfreetype6 armhf 2.9.1-3+deb10u1 [322 kB] Get: 43 http://deb.debian.org/debian buster/main armhf fonts-dejavu-core all 2.37-1 [1068 kB] Get: 44 http://deb.debian.org/debian buster/main armhf fontconfig-config all 2.13.1-2 [280 kB] Get: 45 http://deb.debian.org/debian buster/main armhf libfontconfig1 armhf 2.13.1-2 [328 kB] Get: 46 http://deb.debian.org/debian buster/main armhf fontconfig armhf 2.13.1-2 [404 kB] Get: 47 http://deb.debian.org/debian buster/main armhf libpixman-1-0 armhf 0.36.0-1 [465 kB] Get: 48 http://deb.debian.org/debian buster/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB] Get: 49 http://deb.debian.org/debian buster/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 50 http://deb.debian.org/debian buster/main armhf libxcb1 armhf 1.13.1-2 [132 kB] Get: 51 http://deb.debian.org/debian buster/main armhf libx11-data all 2:1.6.7-1 [298 kB] Get: 52 http://deb.debian.org/debian buster/main armhf libx11-6 armhf 2:1.6.7-1 [698 kB] Get: 53 http://deb.debian.org/debian buster/main armhf libxcb-render0 armhf 1.13.1-2 [108 kB] Get: 54 http://deb.debian.org/debian buster/main armhf libxcb-shm0 armhf 1.13.1-2 [99.0 kB] Get: 55 http://deb.debian.org/debian buster/main armhf libxext6 armhf 2:1.3.3-1+b2 [48.1 kB] Get: 56 http://deb.debian.org/debian buster/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB] Get: 57 http://deb.debian.org/debian buster/main armhf libcairo2 armhf 1.16.0-4 [616 kB] Get: 58 http://deb.debian.org/debian buster/main armhf libcdt5 armhf 2.40.1-6 [58.1 kB] Get: 59 http://deb.debian.org/debian buster/main armhf libcgraph6 armhf 2.40.1-6 [77.3 kB] Get: 60 http://deb.debian.org/debian buster/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [112 kB] Get: 61 http://deb.debian.org/debian buster/main armhf libjbig0 armhf 2.1-3.1+b2 [28.4 kB] Get: 62 http://deb.debian.org/debian buster/main armhf libwebp6 armhf 0.6.1-2 [229 kB] Get: 63 http://deb.debian.org/debian buster/main armhf libtiff5 armhf 4.1.0+git191117-2~deb10u1 [252 kB] Get: 64 http://deb.debian.org/debian buster/main armhf libxpm4 armhf 1:3.5.12-1 [44.0 kB] Get: 65 http://deb.debian.org/debian buster/main armhf libgd3 armhf 2.2.5-5.2 [117 kB] Get: 66 http://deb.debian.org/debian buster/main armhf libgts-0.7-5 armhf 0.7.6+darcs121130-4 [137 kB] Get: 67 http://deb.debian.org/debian buster/main armhf libltdl7 armhf 2.4.6-9 [387 kB] Get: 68 http://deb.debian.org/debian buster/main armhf libfribidi0 armhf 1.0.5-3.1+deb10u1 [61.7 kB] Get: 69 http://deb.debian.org/debian buster/main armhf libthai-data all 0.1.28-2 [170 kB] Get: 70 http://deb.debian.org/debian buster/main armhf libdatrie1 armhf 0.2.12-2 [35.8 kB] Get: 71 http://deb.debian.org/debian buster/main armhf libthai0 armhf 0.1.28-2 [50.7 kB] Get: 72 http://deb.debian.org/debian buster/main armhf libpango-1.0-0 armhf 1.42.4-8~deb10u1 [169 kB] Get: 73 http://deb.debian.org/debian buster/main armhf libgraphite2-3 armhf 1.3.13-7 [70.3 kB] Get: 74 http://deb.debian.org/debian buster/main armhf libharfbuzz0b armhf 2.3.1-1 [1151 kB] Get: 75 http://deb.debian.org/debian buster/main armhf libpangoft2-1.0-0 armhf 1.42.4-8~deb10u1 [62.7 kB] Get: 76 http://deb.debian.org/debian buster/main armhf libpangocairo-1.0-0 armhf 1.42.4-8~deb10u1 [52.2 kB] Get: 77 http://deb.debian.org/debian buster/main armhf libpathplan4 armhf 2.40.1-6 [61.3 kB] Get: 78 http://deb.debian.org/debian buster/main armhf libxdot4 armhf 2.40.1-6 [55.4 kB] Get: 79 http://deb.debian.org/debian buster/main armhf libgvc6 armhf 2.40.1-6 [556 kB] Get: 80 http://deb.debian.org/debian buster/main armhf libgvpr2 armhf 2.40.1-6 [189 kB] Get: 81 http://deb.debian.org/debian buster/main armhf lsb-base all 10.2019051400 [28.4 kB] Get: 82 http://deb.debian.org/debian buster/main armhf x11-common all 1:7.7+19 [251 kB] Get: 83 http://deb.debian.org/debian buster/main armhf libice6 armhf 2:1.0.9-2 [51.7 kB] Get: 84 http://deb.debian.org/debian buster/main armhf liblab-gamut1 armhf 2.40.1-6 [220 kB] Get: 85 http://deb.debian.org/debian buster/main armhf libsm6 armhf 2:1.2.3-1 [33.0 kB] Get: 86 http://deb.debian.org/debian buster/main armhf libxt6 armhf 1:1.1.5-1+b3 [159 kB] Get: 87 http://deb.debian.org/debian buster/main armhf libxmu6 armhf 2:1.1.2-2+b3 [52.7 kB] Get: 88 http://deb.debian.org/debian buster/main armhf libxaw7 armhf 2:1.0.13-1+b2 [167 kB] Get: 89 http://deb.debian.org/debian buster/main armhf graphviz armhf 2.40.1-6 [518 kB] Get: 90 http://deb.debian.org/debian buster/main armhf libargtable2-0 armhf 13-1 [15.8 kB] Get: 91 http://deb.debian.org/debian buster/main armhf libargtable2-docs all 13-1 [2621 kB] Get: 92 http://deb.debian.org/debian buster/main armhf libargtable2-dev armhf 13-1 [55.6 kB] Get: 93 http://deb.debian.org/debian buster/main armhf libjs-jquery all 3.3.1~dfsg-3 [332 kB] Get: 94 http://deb.debian.org/debian buster/main armhf libjs-underscore all 1.9.1~dfsg-1 [99.4 kB] Get: 95 http://deb.debian.org/debian buster/main armhf libjs-sphinxdoc all 1.8.4-1 [95.9 kB] Get: 96 http://deb.debian.org/debian buster/main armhf sphinx-common all 1.8.4-1 [500 kB] Fetched 55.7 MB in 6s (8754 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (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 ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ... 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Setting up x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libmagic1:armhf (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libargtable2-docs (13-1) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libjbig0:armhf (2.1-3.1+b2) ... Setting up libicu63:armhf (63.1-6+deb10u1) ... Setting up libgts-0.7-5:armhf (0.7.6+darcs121130-4) ... Setting up autotools-dev (20180224.1) ... Setting up libjpeg62-turbo:armhf (1:1.5.2-2+b1) ... Setting up libx11-data (2:1.6.7-1) ... Setting up libpathplan4 (2.40.1-6) ... Setting up libncurses6:armhf (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up libfribidi0:armhf (1.0.5-3.1+deb10u1) ... Setting up libpng16-16:armhf (1.6.36-6) ... Setting up autopoint (0.19.8.1-9) ... Setting up libwebp6:armhf (0.6.1-2) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libltdl7:armhf (2.4.6-9) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up libthai-data (0.1.28-2) ... Setting up libcdt5 (2.40.1-6) ... Setting up libcgraph6 (2.40.1-6) ... Setting up libtiff5:armhf (4.1.0+git191117-2~deb10u1) ... Setting up libjs-jquery (3.3.1~dfsg-3) ... Setting up libbsd0:armhf (0.9.1-2) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up libxml2:armhf (2.9.4+dfsg1-7+b3) ... Setting up libargtable2-0 (13-1) ... Setting up libjs-underscore (1.9.1~dfsg-1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libice6:armhf (2:1.0.9-2) ... Setting up libxdmcp6:armhf (1:1.1.2-3) ... Setting up libxcb1:armhf (1.13.1-2) ... Setting up libtool (2.4.6-9) ... Setting up libxcb-render0:armhf (1.13.1-2) ... Setting up libedit2:armhf (3.1-20181209-1) ... Setting up m4 (1.4.18-2) ... Setting up libxcb-shm0:armhf (1.13.1-2) ... Setting up libllvm6.0:armhf (1:6.0.1-10) ... Setting up libclang1-6.0:armhf (1:6.0.1-10) ... Setting up libthai0:armhf (0.1.28-2) ... Setting up doxygen (1.8.13-10) ... Setting up libfreetype6:armhf (2.9.1-3+deb10u1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:armhf (0.6.12-3) ... Setting up libargtable2-dev (13-1) ... Setting up ucf (3.0038+nmu1) ... Setting up libjs-sphinxdoc (1.8.4-1) ... Setting up autoconf (2.69-11) ... Setting up libgvpr2 (2.40.1-6) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libx11-6:armhf (2:1.6.7-1) ... Setting up libharfbuzz0b:armhf (2.3.1-1) ... Setting up libsm6:armhf (2:1.2.3-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libxpm4:armhf (1:3.5.12-1) ... Setting up libxrender1:armhf (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libxext6:armhf (2:1.3.3-1+b2) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up sphinx-common (1.8.4-1) ... Setting up libxt6:armhf (1:1.1.5-1+b3) ... Setting up libfontconfig1:armhf (2.13.1-2) ... Setting up fontconfig (2.13.1-2) ... Regenerating fonts cache... done. Setting up libxmu6:armhf (2:1.1.2-2+b3) ... Setting up po-debconf (1.0.21) ... Setting up libpango-1.0-0:armhf (1.42.4-8~deb10u1) ... Setting up libxaw7:armhf (2:1.0.13-1+b2) ... Setting up libcairo2:armhf (1.16.0-4) ... Setting up libgd3:armhf (2.2.5-5.2) ... Setting up libpangoft2-1.0-0:armhf (1.42.4-8~deb10u1) ... Setting up libpangocairo-1.0-0:armhf (1.42.4-8~deb10u1) ... Setting up libgvc6 (2.40.1-6) ... Setting up graphviz (2.40.1-6) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up dh-linktree (0.6) ... Processing triggers for libc-bin (2.28-10) ... 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... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/clustalo-1.2.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package clustalo dpkg-buildpackage: info: source version 1.2.4-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean --with linktree 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 build dh build --with linktree 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=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode 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... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf 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 arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop checking how to convert arm-unknown-linux-gnueabihf 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) 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 configure: WARNING: unrecognized options: --disable-maintainer-mode 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 -j3 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/bash ../../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 -ffile-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 -ffile-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 -ffile-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/bash ../../libtool --tag=CXX --mode=link g++ -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -ffile-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 cru .libs/libhhalign.a .libs/hhalign.o ar: `u' modifier ignored since `D' is the default (see `U') 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/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o a2m.lo a2m.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o aligneval.lo aligneval.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alignio.lo alignio.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong 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-ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mbed.lo mbed.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-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 -ffile-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 -ffile-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 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-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 -ffile-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 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pair_dist.lo pair_dist.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-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 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o progress.lo progress.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-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 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c progress.c -fPIC -DPIC -o .libs/progress.o /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o seq.lo seq.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-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 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c progress.c -o progress.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o symmatrix.lo symmatrix.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tree.lo tree.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c seq.c -o seq.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.lo util.c /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c weights.c -o weights.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=link gcc -fopenmp -O3 -g -O2 -ffile-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 cru .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 ar: `u' modifier ignored since `D' is the default (see `U') 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 -ffile-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 -ffile-prefix-map=/build/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mymain.o mymain.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -ffile-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 -ffile-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] PACKAGE_VERSION, PACKAGE_CODENAME, __DATE__); ^~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -ffile-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/bash ../libtool --tag=CC --mode=link gcc -O3 -fopenmp -g -O2 -ffile-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/arm-linux-gnueabihf 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 cru .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 ar: `u' modifier ignored since `D' is the default (see `U') 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/bash ../libtool --tag=CXX --mode=link g++ -O3 -fopenmp -g -O2 -ffile-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 -ffile-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/arm-linux-gnueabihf/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-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_test -Nlibclustalo-doc make -j3 check VERBOSE=1 make[1]: Entering directory '/build/clustalo-1.2.4' Making check in src make[2]: Entering directory '/build/clustalo-1.2.4/src' Making check in hhalign make[3]: Entering directory '/build/clustalo-1.2.4/src/hhalign' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/clustalo-1.2.4/src/hhalign' Making check in squid make[3]: Entering directory '/build/clustalo-1.2.4/src/squid' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/clustalo-1.2.4/src/squid' Making check in kmpp make[3]: Entering directory '/build/clustalo-1.2.4/src/kmpp' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/clustalo-1.2.4/src/kmpp' Making check in clustal make[3]: Entering directory '/build/clustalo-1.2.4/src/clustal' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/clustalo-1.2.4/src/clustal' make[3]: Entering 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 'check-am'. make[2]: Leaving directory '/build/clustalo-1.2.4' make[1]: Leaving directory '/build/clustalo-1.2.4' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with linktree dh_testroot 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/arm-linux-gnueabihf' /bin/bash ../libtool --mode=install /usr/bin/install -c libclustalo.la '/build/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/libclustalo.lai /build/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.la libtool: install: /usr/bin/install -c .libs/libclustalo.a /build/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.a libtool: install: chmod 644 /build/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.a libtool: install: ranlib /build/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.a libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf' /bin/mkdir -p '/build/clustalo-1.2.4/debian/tmp/usr/bin' /bin/bash ../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/arm-linux-gnueabihf/pkgconfig' /usr/bin/install -c -m 644 clustalo.pc '/build/clustalo-1.2.4/debian/tmp/usr/lib/arm-linux-gnueabihf/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 `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: 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: 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: 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 parameters 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) are 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:262: warning: Unsupported xml/html tag found /build/clustalo-1.2.4/src/clustal/pair_dist.c:268: warning: Unsupported xml/html tag found /build/clustalo-1.2.4/src/clustal/pair_dist.c:277: warning: The following parameters 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) are not documented: parameter 'bPercID' /build/clustalo-1.2.4/src/clustal/pair_dist.c:262: warning: Unsupported xml/html tag found /build/clustalo-1.2.4/src/clustal/pair_dist.c:268: warning: Unsupported xml/html tag found /build/clustalo-1.2.4/src/clustal/pair_dist.h:36: warning: The following parameters 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) are 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 parameters of WriteAlignment(mseq_t *mseq, const char *pcAlnOutfile, int outfmt, int iWrap, bool bResno) are 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 parameters of WriteAlignment(mseq_t *mseq, const char *pcAlnOutfile, int outfmt, int iWrap, bool bResno) are not documented: parameter 'bResno' /build/clustalo-1.2.4/src/clustal/symmatrix.c:316: warning: The following parameters of SymMatrixPrint(symmatrix_t *symmat, char **labels, const char *path, bool bPercID) are not documented: parameter 'bPercID' /build/clustalo-1.2.4/src/clustal/symmatrix.h:80: warning: The following parameters of SymMatrixPrint(symmatrix_t *symmat, char **labels, const char *path, bool bPercID) are 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_linktree dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: debian/clustalo/usr/bin/clustalo contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libclustalo-doc: substitution variable ${js:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libclustalo-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'clustalo' in '../clustalo_1.2.4-2_armhf.deb'. dpkg-deb: building package 'libclustalo-dev' in '../libclustalo-dev_1.2.4-2_armhf.deb'. dpkg-deb: building package 'clustalo-dbgsym' in '../clustalo-dbgsym_1.2.4-2_armhf.deb'. dpkg-deb: building package 'libclustalo-doc' in '../libclustalo-doc_1.2.4-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../clustalo_1.2.4-2_armhf.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: 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/3031 and its subdirectories I: Current time: Sat May 30 09:24:55 -12 2020 I: pbuilder-time-stamp: 1590873895