I: pbuilder: network access will be disabled during build I: Current time: Thu May 5 05:13:57 +14 2022 I: pbuilder-time-stamp: 1651677237 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 [librostlab-blast_1.0.1-10.dsc] I: copying [./librostlab-blast_1.0.1.orig.tar.gz] I: copying [./librostlab-blast_1.0.1-10.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 Mon Mar 18 23:52:25 2019 +14 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 ./librostlab-blast_1.0.1-10.dsc dpkg-source: info: extracting librostlab-blast in librostlab-blast-1.0.1 dpkg-source: info: unpacking librostlab-blast_1.0.1.orig.tar.gz dpkg-source: info: unpacking librostlab-blast_1.0.1-10.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying reproducible.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/33388/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-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/33388/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/33388/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]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.0.3(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 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=3d6e2c914f9c48d190200147dcb5b594 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=33388 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.adjvJ2s1G8/pbuilderrc_Ardq --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.adjvJ2s1G8/b2 --logfile b2/build.log librostlab-blast_1.0.1-10.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-0.bpo.3-amd64 #1 SMP Debian 5.10.13-1~bpo10+1 (2021-02-11) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash -rwxr-xr-x 1 root root 109408 Mar 1 2019 date -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd -rwxr-xr-x 1 root root 93744 Mar 1 2019 df -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 35424 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln -rwxr-xr-x 1 root root 56760 Jul 27 2018 login -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 10 2019 more -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 May 5 05:14 sh -> bash lrwxrwxrwx 1 root root 4 Apr 24 04:46 sh.distrib -> dash -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty -rwsr-xr-x 1 root root 63568 Jan 10 2019 su -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch -rwxr-xr-x 1 root root 35424 Mar 1 2019 true -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/33388/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 (>= 11~), d-shlibs, bison, doxygen, flex, graphviz, texlive-latex-recommended, librostlab-dev, texlive-fonts-recommended, texlive-latex-extra dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 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 d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on bison; however: Package bison is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on flex; however: Package flex is not installed. pbuilder-satisfydepends-dummy depends on graphviz; however: Package graphviz is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-recommended; however: Package texlive-latex-recommended is not installed. pbuilder-satisfydepends-dummy depends on librostlab-dev; however: Package librostlab-dev is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra 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} bison{a} bsdmainutils{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} doxygen{a} dwz{a} file{a} flex{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-lmodern{a} gettext{a} gettext-base{a} graphviz{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbison-dev{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcdt5{a} libcgraph6{a} libclang1-6.0{a} libcroco3{a} libcups2{a} libcupsimage2{a} libdatrie1{a} libdbus-1-3{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} libgs9{a} libgs9-common{a} libgssapi-krb5-2{a} libgts-0.7-5{a} libgvc6{a} libgvpr2{a} libharfbuzz-icu0{a} libharfbuzz0b{a} libice6{a} libicu63{a} libidn11{a} libijs-0.35{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblab-gamut1{a} liblcms2-2{a} libllvm6.0{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libopenjp2-7{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpathplan4{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libpotrace0{a} libptexenc1{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} librostlab3{a} librostlab3-dev{a} libsigsegv2{a} libsm6{a} libssl1.1{a} libsynctex2{a} libteckit0{a} libtexlua52{a} libtexlua53{a} libtexluajit2{a} libthai-data{a} libthai0{a} libtiff5{a} libtool{a} libuchardet0{a} libwebp6{a} libwoff1{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} libxi6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6{a} libxxhash0{a} libzzip-0-13{a} lsb-base{a} m4{a} man-db{a} mime-support{a} po-debconf{a} poppler-data{a} preview-latex-style{a} python{a} python-minimal{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} readline-common{a} sensible-utils{a} t1utils{a} tex-common{a} texlive-base{a} texlive-binaries{a} texlive-fonts-recommended{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} ucf{a} x11-common{a} xdg-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl dbus fonts-droid-fallback fonts-liberation krb5-locales libarchive-cpio-perl libcupsfilters1 libfile-mimeinfo-perl libfl-dev libglib2.0-data libgpm2 libgts-bin libltdl-dev libmail-sendmail-perl libnet-dbus-perl libx11-protocol-perl lmodern lynx ruby shared-mime-info tex-gyre texlive-plain-generic tipa tk wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 155 newly installed, 0 to remove and 0 not upgraded. Need to get 156 MB of archives. After unpacking 543 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u5 [1539 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 flex amd64 2.6.4-6.2 [456 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 poppler-data all 0.4.9-2 [1473 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 tex-common all 6.11 [53.1 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 libbison-dev amd64 2:3.3.2.dfsg-1 [500 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 bison amd64 2:3.3.2.dfsg-1 [871 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 d-shlibs all 0.84 [17.2 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u2 [1258 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u1 [689 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 libedit2 amd64 3.1-20181209-1 [94.0 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 libllvm6.0 amd64 1:6.0.1-10 [14.7 MB] Get: 58 http://deb.debian.org/debian buster/main amd64 libclang1-6.0 amd64 1:6.0.1-10 [6951 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 doxygen amd64 1.8.13-10 [3985 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u2 [380 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 fontconfig amd64 2.13.1-2 [405 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 fonts-lmodern all 2.004.5-6 [4539 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 libpixman-1-0 amd64 0.36.0-1 [537 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 libx11-data all 2:1.6.7-1+deb10u1 [294 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 libx11-6 amd64 2:1.6.7-1+deb10u1 [757 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 libxcb-render0 amd64 1.13.1-2 [109 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libxcb-shm0 amd64 1.13.1-2 [99.2 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 libcairo2 amd64 1.16.0-4+deb10u1 [688 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 libcdt5 amd64 2.40.1-6 [60.6 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 libcgraph6 amd64 2.40.1-6 [84.1 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 libwebp6 amd64 0.6.1-2 [263 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 libtiff5 amd64 4.1.0+git191117-2~deb10u2 [271 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 libxpm4 amd64 1:3.5.12-1 [49.1 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 libgd3 amd64 2.2.5-5.2 [136 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 libgts-0.7-5 amd64 0.7.6+darcs121130-4 [158 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 libltdl7 amd64 2.4.6-9 [390 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 libfribidi0 amd64 1.0.5-3.1+deb10u1 [63.7 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 libthai-data all 0.1.28-2 [170 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 libdatrie1 amd64 0.2.12-2 [39.3 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 libthai0 amd64 0.1.28-2 [54.1 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 libpango-1.0-0 amd64 1.42.4-8~deb10u1 [186 kB] Get: 93 http://deb.debian.org/debian buster/main amd64 libgraphite2-3 amd64 1.3.13-7 [80.7 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 libharfbuzz0b amd64 2.3.1-1 [1187 kB] Get: 95 http://deb.debian.org/debian buster/main amd64 libpangoft2-1.0-0 amd64 1.42.4-8~deb10u1 [68.3 kB] Get: 96 http://deb.debian.org/debian buster/main amd64 libpangocairo-1.0-0 amd64 1.42.4-8~deb10u1 [55.7 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 libpathplan4 amd64 2.40.1-6 [63.5 kB] Get: 98 http://deb.debian.org/debian buster/main amd64 libxdot4 amd64 2.40.1-6 [56.9 kB] Get: 99 http://deb.debian.org/debian buster/main amd64 libgvc6 amd64 2.40.1-6 [646 kB] Get: 100 http://deb.debian.org/debian buster/main amd64 libgvpr2 amd64 2.40.1-6 [213 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 x11-common all 1:7.7+19 [251 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get: 104 http://deb.debian.org/debian buster/main amd64 liblab-gamut1 amd64 2.40.1-6 [220 kB] Get: 105 http://deb.debian.org/debian buster/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 106 http://deb.debian.org/debian buster/main amd64 libxt6 amd64 1:1.1.5-1+b3 [190 kB] Get: 107 http://deb.debian.org/debian buster/main amd64 libxmu6 amd64 2:1.1.2-2+b3 [60.8 kB] Get: 108 http://deb.debian.org/debian buster/main amd64 libxaw7 amd64 2:1.0.13-1+b2 [201 kB] Get: 109 http://deb.debian.org/debian buster/main amd64 graphviz amd64 2.40.1-6 [594 kB] Get: 110 http://deb.debian.org/debian buster/main amd64 libavahi-common-data amd64 0.7-4+deb10u1 [122 kB] Get: 111 http://deb.debian.org/debian buster/main amd64 libavahi-common3 amd64 0.7-4+deb10u1 [54.4 kB] Get: 112 http://deb.debian.org/debian buster/main amd64 libdbus-1-3 amd64 1.12.20-0+deb10u1 [215 kB] Get: 113 http://deb.debian.org/debian buster/main amd64 libavahi-client3 amd64 0.7-4+deb10u1 [58.2 kB] Get: 114 http://deb.debian.org/debian buster/main amd64 libbrotli1 amd64 1.0.7-2+deb10u1 [269 kB] Get: 115 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 116 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u1 [65.8 kB] Get: 117 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u1 [122 kB] Get: 118 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u1 [369 kB] Get: 119 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u1 [158 kB] Get: 120 http://deb.debian.org/debian buster/main amd64 libcups2 amd64 2.2.10-6+deb10u4 [324 kB] Get: 121 http://deb.debian.org/debian buster/main amd64 libcupsimage2 amd64 2.2.10-6+deb10u4 [133 kB] Get: 122 http://deb.debian.org/debian buster/main amd64 libgs9-common all 9.27~dfsg-2+deb10u4 [5136 kB] Get: 123 http://deb.debian.org/debian buster/main amd64 libidn11 amd64 1.33-2.2 [116 kB] Get: 124 http://deb.debian.org/debian buster/main amd64 libijs-0.35 amd64 0.35-14 [18.3 kB] Get: 125 http://deb.debian.org/debian buster/main amd64 libjbig2dec0 amd64 0.16-1 [62.0 kB] Get: 126 http://deb.debian.org/debian buster/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get: 127 http://deb.debian.org/debian buster/main amd64 libopenjp2-7 amd64 2.3.0-2+deb10u1 [158 kB] Get: 128 http://deb.debian.org/debian buster/main amd64 libpaper1 amd64 1.1.28 [21.3 kB] Get: 129 http://deb.debian.org/debian buster/main amd64 libgs9 amd64 9.27~dfsg-2+deb10u4 [2195 kB] Get: 130 http://deb.debian.org/debian buster/main amd64 libharfbuzz-icu0 amd64 2.3.1-1 [834 kB] Get: 131 http://deb.debian.org/debian buster/main amd64 libkpathsea6 amd64 2018.20181218.49446-1 [167 kB] Get: 132 http://deb.debian.org/debian buster/main amd64 libpaper-utils amd64 1.1.28 [18.0 kB] Get: 133 http://deb.debian.org/debian buster/main amd64 libpotrace0 amd64 1.15-1 [26.3 kB] Get: 134 http://deb.debian.org/debian buster/main amd64 libptexenc1 amd64 2018.20181218.49446-1 [61.0 kB] Get: 135 http://deb.debian.org/debian buster/main amd64 librostlab3 amd64 1.0.20-8 [6180 B] Get: 136 http://deb.debian.org/debian buster/main amd64 librostlab3-dev amd64 1.0.20-8 [13.6 kB] Get: 137 http://deb.debian.org/debian buster/main amd64 libsynctex2 amd64 2018.20181218.49446-1 [80.5 kB] Get: 138 http://deb.debian.org/debian buster/main amd64 libteckit0 amd64 2.5.8+ds2-5 [318 kB] Get: 139 http://deb.debian.org/debian buster/main amd64 libtexlua52 amd64 2018.20181218.49446-1 [112 kB] Get: 140 http://deb.debian.org/debian buster/main amd64 libtexlua53 amd64 2018.20181218.49446-1 [126 kB] Get: 141 http://deb.debian.org/debian buster/main amd64 libtexluajit2 amd64 2018.20181218.49446-1 [256 kB] Get: 142 http://deb.debian.org/debian buster/main amd64 libwoff1 amd64 1.0.2-1 [43.2 kB] Get: 143 http://deb.debian.org/debian buster/main amd64 libxi6 amd64 2:1.7.9-1 [82.6 kB] Get: 144 http://deb.debian.org/debian buster/main amd64 libxxhash0 amd64 0.6.5-2 [7156 B] Get: 145 http://deb.debian.org/debian buster/main amd64 libzzip-0-13 amd64 0.13.62-3.2 [55.4 kB] Get: 146 http://deb.debian.org/debian buster/main amd64 preview-latex-style all 11.91-2 [201 kB] Get: 147 http://deb.debian.org/debian buster/main amd64 t1utils amd64 1.41-3 [62.3 kB] Get: 148 http://deb.debian.org/debian buster/main amd64 texlive-binaries amd64 2018.20181218.49446-1 [11.3 MB] Get: 149 http://deb.debian.org/debian buster/main amd64 xdg-utils all 1.1.3-1+deb10u1 [73.7 kB] Get: 150 http://deb.debian.org/debian buster/main amd64 texlive-base all 2018.20190227-2 [19.7 MB] Get: 151 http://deb.debian.org/debian buster/main amd64 texlive-fonts-recommended all 2018.20190227-2 [5228 kB] Get: 152 http://deb.debian.org/debian buster/main amd64 texlive-latex-base all 2018.20190227-2 [984 kB] Get: 153 http://deb.debian.org/debian buster/main amd64 texlive-latex-recommended all 2018.20190227-2 [15.2 MB] Get: 154 http://deb.debian.org/debian buster/main amd64 texlive-pictures all 2018.20190227-2 [8201 kB] Get: 155 http://deb.debian.org/debian buster/main amd64 texlive-latex-extra all 2018.20190227-2 [12.3 MB] Fetched 156 MB in 2s (77.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3+deb10u1_amd64.deb ... Unpacking groff-base (1.22.4-3+deb10u1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libpython2.7-minimal:amd64. Preparing to unpack .../06-libpython2.7-minimal_2.7.16-2+deb10u1_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../07-python2.7-minimal_2.7.16-2+deb10u1_amd64.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u1) ... Selecting previously unselected package python2-minimal. Preparing to unpack .../08-python2-minimal_2.7.16-1_amd64.deb ... Unpacking python2-minimal (2.7.16-1) ... Selecting previously unselected package python-minimal. Preparing to unpack .../09-python-minimal_2.7.16-1_amd64.deb ... Unpacking python-minimal (2.7.16-1) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../10-libssl1.1_1.1.1d-0+deb10u5_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1d-0+deb10u5) ... Selecting previously unselected package mime-support. Preparing to unpack .../11-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../12-libexpat1_2.2.6-2+deb10u1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-2+deb10u1) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:amd64. Preparing to unpack .../14-libreadline7_7.0-5_amd64.deb ... Unpacking libreadline7:amd64 (7.0-5) ... Selecting previously unselected package libpython2.7-stdlib:amd64. Preparing to unpack .../15-libpython2.7-stdlib_2.7.16-2+deb10u1_amd64.deb ... Unpacking libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7. Preparing to unpack .../16-python2.7_2.7.16-2+deb10u1_amd64.deb ... Unpacking python2.7 (2.7.16-2+deb10u1) ... Selecting previously unselected package libpython2-stdlib:amd64. Preparing to unpack .../17-libpython2-stdlib_2.7.16-1_amd64.deb ... Unpacking libpython2-stdlib:amd64 (2.7.16-1) ... Selecting previously unselected package libpython-stdlib:amd64. Preparing to unpack .../18-libpython-stdlib_2.7.16-1_amd64.deb ... Unpacking libpython-stdlib:amd64 (2.7.16-1) ... Setting up libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (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 ... 20658 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_amd64.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (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 ... 20691 files and directories currently installed.) Preparing to unpack .../000-python_2.7.16-1_amd64.deb ... Unpacking python (2.7.16-1) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../001-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../002-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package flex. Preparing to unpack .../003-flex_2.6.4-6.2_amd64.deb ... Unpacking flex (2.6.4-6.2) ... Selecting previously unselected package poppler-data. Preparing to unpack .../004-poppler-data_0.4.9-2_all.deb ... Unpacking poppler-data (0.4.9-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../005-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package ucf. Preparing to unpack .../006-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package tex-common. Preparing to unpack .../007-tex-common_6.11_all.deb ... Unpacking tex-common (6.11) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../008-libmagic-mgc_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../009-libmagic1_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u2) ... Selecting previously unselected package file. Preparing to unpack .../010-file_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking file (1:5.35-4+deb10u2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../011-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package autoconf. Preparing to unpack .../012-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../013-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../014-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../015-autopoint_0.19.8.1-9_all.deb ... 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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/librostlab-blast-1.0.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package librostlab-blast dpkg-buildpackage: info: source version 1.0.1-10 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/librostlab-blast-1.0.1' dh_auto_clean rm -f lib/librostlab-blast.tag make[1]: Leaving directory '/build/librostlab-blast-1.0.1' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf 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:7: installing './compile' configure.ac:5: installing './missing' lib/Makefile.am: installing './depcomp' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/librostlab-blast-1.0.1' dh_auto_configure -- --enable-doxygen-dot --enable-doxygen-pdf=No ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-doxygen-dot --enable-doxygen-pdf=No configure: WARNING: unrecognized options: --disable-maintainer-mode 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 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 whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none 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 build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E 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 how to run the C preprocessor... gcc -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 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 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 for bison... bison -y checking for flex... flex checking lex output file root... lex.yy checking lex library... none needed checking whether yytext is a pointer... no checking rostlab/aux_functions.h usability... yes checking rostlab/aux_functions.h presence... yes checking for rostlab/aux_functions.h... yes checking rostlab/rostlab_stdexcept.h usability... yes checking rostlab/rostlab_stdexcept.h presence... yes checking for rostlab/rostlab_stdexcept.h... yes checking for doxygen... /usr/bin/doxygen checking for perl... /usr/bin/perl checking for dot... /usr/bin/dot checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating lib/Makefile config.status: creating lib/Doxyfile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: unrecognized options: --disable-maintainer-mode make[1]: Leaving directory '/build/librostlab-blast-1.0.1' debian/rules override_dh_auto_build make[1]: Entering directory '/build/librostlab-blast-1.0.1' dh_auto_build make -j16 make[2]: Entering directory '/build/librostlab-blast-1.0.1' make all-recursive make[3]: Entering directory '/build/librostlab-blast-1.0.1' Making all in lib make[4]: Entering directory '/build/librostlab-blast-1.0.1/lib' mkdir -p rostlab /bin/sh ../ylwrap blast-parser-scanner.lpp lex.yy.c blast-parser-scanner.cpp -- flex /bin/sh ../ylwrap blast-parser-parser.ypp y.tab.c blast-parser-parser.cpp y.tab.h rostlab/blast-parser-parser.h y.output blast-parser-parser.output stack.hh rostlab/blast-parser-stack.h location.hh rostlab/blast-parser-location.h position.hh rostlab/blast-parser-position.h -- bison -y /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:1.1-9: warning: POSIX Yacc does not support %skeleton [-Wyacc] %skeleton "lalr1.cc" ^~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:1.11-20: warning: POSIX Yacc does not support string literals [-Wyacc] %skeleton "lalr1.cc" ^~~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:20.1-8: warning: POSIX Yacc does not support %require [-Wyacc] %require "2.4.1" ^~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:20.10-16: warning: POSIX Yacc does not support string literals [-Wyacc] %require "2.4.1" ^~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:21.1-8: warning: POSIX Yacc does not support %defines [-Wyacc] %defines ^~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:22.1-7: warning: POSIX Yacc does not support %define [-Wyacc] %define namespace "rostlab::blast" ^~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:22.19-34: warning: POSIX Yacc does not support string literals [-Wyacc] %define namespace "rostlab::blast" ^~~~~~~~~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:22.1-34: warning: deprecated directive, use '%define api.namespace {rostlab::blast}' [-Wdeprecated] %define namespace "rostlab::blast" ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:24.1-5: warning: POSIX Yacc does not support %code [-Wyacc] %code requires { ^~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:37.1-14: warning: POSIX Yacc does not support %error-verbose [-Wyacc] %error-verbose ^~~~~~~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:37.1-14: warning: deprecated directive, use '%define parse.error verbose' [-Wdeprecated] %error-verbose ^~~~~~~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:39.1-15: warning: POSIX Yacc does not support %initial-action [-Wyacc] %initial-action ^~~~~~~~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:53.1-5: warning: POSIX Yacc does not support %code [-Wyacc] %code { ^~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:59.29-41: warning: POSIX Yacc does not support string literals [-Wyacc] %token END 0 "end of file" ^~~~~~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:72.29-36: warning: POSIX Yacc does not support string literals [-Wyacc] %token QUERYEQ "Query=" ^~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:73.29-39: warning: POSIX Yacc does not support string literals [-Wyacc] %token DATABASECOLON "Database:" ^~~~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:74.29-48: warning: POSIX Yacc does not support string literals [-Wyacc] %token RESFROMROUND "Results from round" ^~~~~~~~~~~~~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:75.29-37: warning: POSIX Yacc does not support string literals [-Wyacc] %token SCOREEQ "Score =" ^~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:76.29-38: warning: POSIX Yacc does not support string literals [-Wyacc] %token EXPECTEQ "Expect =" ^~~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:77.29-37: warning: POSIX Yacc does not support string literals [-Wyacc] %token METHODCOLON "Method:" ^~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:78.29-42: warning: POSIX Yacc does not support string literals [-Wyacc] %token IDENTITIESEQ "Identities =" ^~~~~~~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:79.29-41: warning: POSIX Yacc does not support string literals [-Wyacc] %token POSITIVESEQ "Positives =" ^~~~~~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:80.29-36: warning: POSIX Yacc does not support string literals [-Wyacc] %token GAPSEQ "Gaps =" ^~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:81.29-38: warning: POSIX Yacc does not support string literals [-Wyacc] %token STRANDEQ "Strand =" ^~~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:82.29-37: warning: POSIX Yacc does not support string literals [-Wyacc] %token FRAMEEQ "Frame =" ^~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:83.29-36: warning: POSIX Yacc does not support string literals [-Wyacc] %token QUERYCOLON "Query:" ^~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:84.29-36: warning: POSIX Yacc does not support string literals [-Wyacc] %token SBJCTCOLON "Sbjct:" ^~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:88.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc] %destructor { delete $$; } ^~~~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:90.1-8: warning: POSIX Yacc does not support %printer [-Wyacc] %printer { debug_stream () << *$$; } ^~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:91.1-8: warning: POSIX Yacc does not support %printer [-Wyacc] %printer { debug_stream () << $$; } ^~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:109.9-16: warning: POSIX Yacc does not support string literals [-Wyacc] query: "Query=" STRING INT ^~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:122.11-21: warning: POSIX Yacc does not support string literals [-Wyacc] database: "Database:" STRING INT INT ^~~~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:137.15-34: warning: POSIX Yacc does not support string literals [-Wyacc] | "Results from round" INT ^~~~~~~~~~~~~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:201.19-27: warning: POSIX Yacc does not support string literals [-Wyacc] hsp_headerfield: "Score =" num INT ^~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:203.19-28: warning: POSIX Yacc does not support string literals [-Wyacc] | "Expect =" num ^~~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:205.19-27: warning: POSIX Yacc does not support string literals [-Wyacc] | "Method:" STRING ^~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:207.19-32: warning: POSIX Yacc does not support string literals [-Wyacc] | "Identities =" INT ^~~~~~~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:209.19-31: warning: POSIX Yacc does not support string literals [-Wyacc] | "Positives =" INT ^~~~~~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:211.19-26: warning: POSIX Yacc does not support string literals [-Wyacc] | "Gaps =" INT ^~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:213.19-28: warning: POSIX Yacc does not support string literals [-Wyacc] | "Strand =" STRING '/' STRING ^~~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:215.19-27: warning: POSIX Yacc does not support string literals [-Wyacc] | "Frame =" INT '/' INT ^~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:217.19-27: warning: POSIX Yacc does not support string literals [-Wyacc] | "Frame =" INT ^~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:224.15-22: warning: POSIX Yacc does not support string literals [-Wyacc] alitriple: "Query:" INT STRING INT STRING "Sbjct:" INT STRING INT ^~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:224.46-53: warning: POSIX Yacc does not support string literals [-Wyacc] alitriple: "Query:" INT STRING INT STRING "Sbjct:" INT STRING INT ^~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:247.15-22: warning: POSIX Yacc does not support string literals [-Wyacc] | "Query:" '0' /* bug as far as I can tell */ ^~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp:22.1-34: warning: %define variable 'api.namespace' requires '{...}' values [-Wdeprecated] %define namespace "rostlab::blast" ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp: warning: fix-its can be applied. Rerun with option '--update'. [-Wother] updating rostlab/blast-parser-location.h updating rostlab/blast-parser-position.h updating rostlab/blast-parser-stack.h updating rostlab/blast-parser-parser.h sed -i -e 's,\by.tab.h\b,rostlab/blast-parser-parser.h,g' blast-parser-parser.cpp sed -i -e 's,\bstack.hh\b,rostlab/blast-parser-stack.h,g;s,\blocation.hh\b,rostlab/blast-parser-location.h,g;' rostlab/blast-parser-parser.h sed -i -e 's,\bposition.hh\b,rostlab/blast-parser-position.h,g;' rostlab/blast-parser-location.h make all-am make[5]: Entering directory '/build/librostlab-blast-1.0.1/lib' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/librostlab-blast-1.0.1=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -c -o librostlab_blast_la-blast-parser-driver.lo `test -f 'blast-parser-driver.cpp' || echo './'`blast-parser-driver.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/librostlab-blast-1.0.1=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -c -o librostlab_blast_la-blast-parser-parser.lo `test -f 'blast-parser-parser.cpp' || echo './'`blast-parser-parser.cpp \ \ /bin/sh ../ylwrap `test -f 'blast-parser-scanner.lpp' || echo './'`blast-parser-scanner.lpp lex.yy.c librostlab_blast_la-blast-parser-scanner.cpp -- flex -Cfe libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/librostlab-blast-1.0.1=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -c blast-parser-parser.cpp -fPIC -DPIC -o .libs/librostlab_blast_la-blast-parser-parser.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/librostlab-blast-1.0.1=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -c blast-parser-driver.cpp -fPIC -DPIC -o .libs/librostlab_blast_la-blast-parser-driver.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/librostlab-blast-1.0.1=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -c -o librostlab_blast_la-librostlab_blast_la-blast-parser-scanner.lo `test -f 'librostlab_blast_la-blast-parser-scanner.cpp' || echo './'`librostlab_blast_la-blast-parser-scanner.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/librostlab-blast-1.0.1=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -c librostlab_blast_la-blast-parser-scanner.cpp -fPIC -DPIC -o .libs/librostlab_blast_la-librostlab_blast_la-blast-parser-scanner.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/librostlab-blast-1.0.1=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -c blast-parser-driver.cpp -o librostlab_blast_la-blast-parser-driver.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/librostlab-blast-1.0.1=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -c blast-parser-parser.cpp -o librostlab_blast_la-blast-parser-parser.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -g -O2 -ffile-prefix-map=/build/librostlab-blast-1.0.1=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -c librostlab_blast_la-blast-parser-scanner.cpp -o librostlab_blast_la-librostlab_blast_la-blast-parser-scanner.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -g -O2 -ffile-prefix-map=/build/librostlab-blast-1.0.1=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -version-info 0:0:0 -Wall -Wl,-z,relro -Wl,-z,now -o librostlab-blast.la -rpath /usr/lib/x86_64-linux-gnu librostlab_blast_la-blast-parser-driver.lo librostlab_blast_la-blast-parser-parser.lo librostlab_blast_la-librostlab_blast_la-blast-parser-scanner.lo libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/8/crtbeginS.o .libs/librostlab_blast_la-blast-parser-driver.o .libs/librostlab_blast_la-blast-parser-parser.o .libs/librostlab_blast_la-librostlab_blast_la-blast-parser-scanner.o -L/usr/lib/gcc/x86_64-linux-gnu/8 -L/usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/8/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/8/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/8/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,librostlab-blast.so.0 -o .libs/librostlab-blast.so.0.0.0 libtool: link: (cd ".libs" && rm -f "librostlab-blast.so.0" && ln -s "librostlab-blast.so.0.0.0" "librostlab-blast.so.0") libtool: link: (cd ".libs" && rm -f "librostlab-blast.so" && ln -s "librostlab-blast.so.0.0.0" "librostlab-blast.so") libtool: link: ar cru .libs/librostlab-blast.a librostlab_blast_la-blast-parser-driver.o librostlab_blast_la-blast-parser-parser.o librostlab_blast_la-librostlab_blast_la-blast-parser-scanner.o ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/librostlab-blast.a libtool: link: ( cd ".libs" && rm -f "librostlab-blast.la" && ln -s "../librostlab-blast.la" "librostlab-blast.la" ) make[5]: Leaving directory '/build/librostlab-blast-1.0.1/lib' make[4]: Leaving directory '/build/librostlab-blast-1.0.1/lib' make[4]: Entering directory '/build/librostlab-blast-1.0.1' make[4]: Leaving directory '/build/librostlab-blast-1.0.1' make[3]: Leaving directory '/build/librostlab-blast-1.0.1' make[2]: Leaving directory '/build/librostlab-blast-1.0.1' /usr/bin/make -C lib doxygen-doc make[2]: Entering directory '/build/librostlab-blast-1.0.1/lib' rm -rf ../doxygen-doc SRCDIR='.' PROJECT='librostlab-blast' DOCDIR='../doxygen-doc' VERSION='1.0.1' PERL_PATH='/usr/bin/perl' HAVE_DOT='YES' DOT_PATH='/usr/bin' GENERATE_MAN='NO' GENERATE_RTF='NO' GENERATE_XML='NO' GENERATE_HTMLHELP='NO' GENERATE_CHI='NO' GENERATE_HTML='YES' GENERATE_LATEX='NO' /usr/bin/doxygen ./Doxyfile warning: Tag `SYMBOL_CACHE_SIZE' at line 290 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 490 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 847 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 `USE_INLINE_TREES' at line 1032 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 1257 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 1263 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. error: Tag file `/usr/share/doc/librostlab-doc/librostlab.tag' does not exist or is not a file. Skipping it... /build/librostlab-blast-1.0.1/lib/rostlab/blast-parser-location.h:34: warning: the name `location.hh' supplied as the second argument in the \file statement is not an input file /build/librostlab-blast-1.0.1/lib/rostlab/blast-parser-parser.h:35: warning: the name `y.tab.h' supplied as the second argument in the \file statement is not an input file Notice: Output directory `../doxygen-doc' does not exist. I have created it for you. Searching for include files... Searching for example files... Searching for files in directory /build/librostlab-blast-1.0.1/examples Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching INPUT for files to process... Searching for files in directory /build/librostlab-blast-1.0.1/lib/rostlab Reading and parsing tag files Parsing files Preprocessing /build/librostlab-blast-1.0.1/lib/rostlab/blast-parser-driver.h... Parsing file /build/librostlab-blast-1.0.1/lib/rostlab/blast-parser-driver.h... Preprocessing /build/librostlab-blast-1.0.1/lib/rostlab/blast-parser-location.h... Parsing file /build/librostlab-blast-1.0.1/lib/rostlab/blast-parser-location.h... Preprocessing /build/librostlab-blast-1.0.1/lib/rostlab/blast-parser-parser.h... Parsing file /build/librostlab-blast-1.0.1/lib/rostlab/blast-parser-parser.h... Preprocessing /build/librostlab-blast-1.0.1/lib/rostlab/blast-parser-position.h... Parsing file /build/librostlab-blast-1.0.1/lib/rostlab/blast-parser-position.h... Preprocessing /build/librostlab-blast-1.0.1/lib/rostlab/blast-parser-stack.h... Parsing file /build/librostlab-blast-1.0.1/lib/rostlab/blast-parser-stack.h... Preprocessing /build/librostlab-blast-1.0.1/lib/rostlab/blast-result.h... Parsing file /build/librostlab-blast-1.0.1/lib/rostlab/blast-result.h... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Associating documentation with classes... Computing nesting relations for classes... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Freeing entry tree Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Computing dependencies between directories... Generating citations page... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file rostlab/blast-parser-driver.h... Generating code for file rostlab/blast-parser-location.h... Generating code for file rostlab/blast-parser-parser.h... Generating code for file rostlab/blast-parser-position.h... Generating code for file rostlab/blast-parser-stack.h... Generating code for file rostlab/blast-result.h... Generating file documentation... Generating docs for file rostlab/blast-parser-driver.h... Generating docs for file rostlab/blast-parser-location.h... Generating docs for file rostlab/blast-parser-parser.h... Generating docs for file rostlab/blast-parser-position.h... Generating docs for file rostlab/blast-parser-stack.h... Generating docs for file rostlab/blast-result.h... Generating page documentation... Generating group documentation... Generating class documentation... Generating namespace index... Generating docs for namespace rostlab Generating docs for namespace rostlab::blast Generating docs for compound rostlab::blast::hit... Generating docs for compound rostlab::blast::hsp... Generating docs for compound rostlab::blast::location... Generating docs for compound rostlab::blast::oneline... Generating docs for compound rostlab::blast::parser... Generating docs for nested compound rostlab::blast::parser::basic_symbol... Generating docs for nested compound rostlab::blast::parser::by_type... Generating docs for nested compound rostlab::blast::parser::semantic_type... Generating docs for nested compound rostlab::blast::parser::stack::slice... Generating docs for nested compound rostlab::blast::parser::symbol_type... Generating docs for nested compound rostlab::blast::parser::syntax_error... Generating docs for nested compound rostlab::blast::parser::token... Generating docs for compound rostlab::blast::parser_driver... Generating docs for compound rostlab::blast::parser_error... Generating docs for compound rostlab::blast::position... Generating docs for compound rostlab::blast::result... Generating docs for compound rostlab::blast::round... Generating graph info page... Generating directory documentation... Generating index page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating graphical class hierarchy... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running dot... Generating dot graphs using 17 parallel threads... Running dot for graph 1/54 Running dot for graph 2/54 Running dot for graph 3/54 Running dot for graph 4/54 Running dot for graph 5/54 Running dot for graph 6/54 Running dot for graph 7/54 Running dot for graph 8/54 Running dot for graph 9/54 Running dot for graph 10/54 Running dot for graph 11/54 Running dot for graph 12/54 Running dot for graph 13/54 Running dot for graph 14/54 Running dot for graph 15/54 Running dot for graph 16/54 Running dot for graph 17/54 Running dot for graph 18/54 Running dot for graph 19/54 Running dot for graph 20/54 Running dot for graph 21/54 Running dot for graph 22/54 Running dot for graph 23/54 Running dot for graph 24/54 Running dot for graph 25/54 Running dot for graph 26/54 Running dot for graph 27/54 Running dot for graph 28/54 Running dot for graph 29/54 Running dot for graph 30/54 Running dot for graph 31/54 Running dot for graph 32/54 Running dot for graph 33/54 Running dot for graph 34/54 Running dot for graph 35/54 Running dot for graph 36/54 Running dot for graph 37/54 Running dot for graph 38/54 Running dot for graph 39/54 Running dot for graph 40/54 Running dot for graph 41/54 Running dot for graph 42/54 Running dot for graph 43/54 Running dot for graph 44/54 Running dot for graph 45/54 Running dot for graph 46/54 Running dot for graph 47/54 Running dot for graph 48/54 Running dot for graph 49/54 Running dot for graph 50/54 Running dot for graph 51/54 Running dot for graph 52/54 Running dot for graph 53/54 Running dot for graph 54/54 Patching output file 1/23 Patching output file 2/23 Patching output file 3/23 Patching output file 4/23 Patching output file 5/23 Patching output file 6/23 Patching output file 7/23 Patching output file 8/23 Patching output file 9/23 Patching output file 10/23 Patching output file 11/23 Patching output file 12/23 Patching output file 13/23 Patching output file 14/23 Patching output file 15/23 Patching output file 16/23 Patching output file 17/23 Patching output file 18/23 Patching output file 19/23 Patching output file 20/23 Patching output file 21/23 Patching output file 22/23 Patching output file 23/23 lookup cache used 541/65536 hits=4560 misses=586 finished... make[2]: Leaving directory '/build/librostlab-blast-1.0.1/lib' make[1]: Leaving directory '/build/librostlab-blast-1.0.1' dh_auto_test make -j16 check VERBOSE=1 make[1]: Entering directory '/build/librostlab-blast-1.0.1' Making check in lib make[2]: Entering directory '/build/librostlab-blast-1.0.1/lib' make check-am make[3]: Entering directory '/build/librostlab-blast-1.0.1/lib' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/librostlab-blast-1.0.1/lib' make[2]: Leaving directory '/build/librostlab-blast-1.0.1/lib' make[2]: Entering directory '/build/librostlab-blast-1.0.1' make[2]: Leaving directory '/build/librostlab-blast-1.0.1' make[1]: Leaving directory '/build/librostlab-blast-1.0.1' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install make -j1 install DESTDIR=/build/librostlab-blast-1.0.1/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/librostlab-blast-1.0.1' Making install in lib make[2]: Entering directory '/build/librostlab-blast-1.0.1/lib' make install-am make[3]: Entering directory '/build/librostlab-blast-1.0.1/lib' make[4]: Entering directory '/build/librostlab-blast-1.0.1/lib' /bin/mkdir -p '/build/librostlab-blast-1.0.1/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/sh ../libtool --mode=install /usr/bin/install -c librostlab-blast.la '/build/librostlab-blast-1.0.1/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/librostlab-blast.so.0.0.0 /build/librostlab-blast-1.0.1/debian/tmp/usr/lib/x86_64-linux-gnu/librostlab-blast.so.0.0.0 libtool: install: (cd /build/librostlab-blast-1.0.1/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f librostlab-blast.so.0.0.0 librostlab-blast.so.0 || { rm -f librostlab-blast.so.0 && ln -s librostlab-blast.so.0.0.0 librostlab-blast.so.0; }; }) libtool: install: (cd /build/librostlab-blast-1.0.1/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f librostlab-blast.so.0.0.0 librostlab-blast.so || { rm -f librostlab-blast.so && ln -s librostlab-blast.so.0.0.0 librostlab-blast.so; }; }) libtool: install: /usr/bin/install -c .libs/librostlab-blast.lai /build/librostlab-blast-1.0.1/debian/tmp/usr/lib/x86_64-linux-gnu/librostlab-blast.la libtool: install: /usr/bin/install -c .libs/librostlab-blast.a /build/librostlab-blast-1.0.1/debian/tmp/usr/lib/x86_64-linux-gnu/librostlab-blast.a libtool: install: chmod 644 /build/librostlab-blast-1.0.1/debian/tmp/usr/lib/x86_64-linux-gnu/librostlab-blast.a libtool: install: ranlib /build/librostlab-blast-1.0.1/debian/tmp/usr/lib/x86_64-linux-gnu/librostlab-blast.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /bin/mkdir -p '/build/librostlab-blast-1.0.1/debian/tmp/usr/include/rostlab' /usr/bin/install -c -m 644 rostlab/blast-parser-driver.h rostlab/blast-result.h '/build/librostlab-blast-1.0.1/debian/tmp/usr/include/rostlab' /bin/mkdir -p '/build/librostlab-blast-1.0.1/debian/tmp/usr/include/rostlab' /usr/bin/install -c -m 644 rostlab/blast-parser-location.h rostlab/blast-parser-parser.h rostlab/blast-parser-position.h rostlab/blast-parser-stack.h '/build/librostlab-blast-1.0.1/debian/tmp/usr/include/rostlab' make[4]: Leaving directory '/build/librostlab-blast-1.0.1/lib' make[3]: Leaving directory '/build/librostlab-blast-1.0.1/lib' make[2]: Leaving directory '/build/librostlab-blast-1.0.1/lib' make[2]: Entering directory '/build/librostlab-blast-1.0.1' make[3]: Entering directory '/build/librostlab-blast-1.0.1' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/librostlab-blast-1.0.1/debian/tmp/usr/share/doc/librostlab-blast/examples' /usr/bin/install -c -m 644 examples/converged.ali examples/parseblast.cpp '/build/librostlab-blast-1.0.1/debian/tmp/usr/share/doc/librostlab-blast/examples' make[3]: Leaving directory '/build/librostlab-blast-1.0.1' make[2]: Leaving directory '/build/librostlab-blast-1.0.1' make[1]: Leaving directory '/build/librostlab-blast-1.0.1' debian/rules override_dh_install make[1]: Entering directory '/build/librostlab-blast-1.0.1' d-shlibmove --commit \ --multiarch \ --exclude-la \ --v5 \ --movedev debian/tmp/usr/include/* usr/include \ debian/tmp/usr/lib/*/*.so Library package automatic movement utility set -e install -d -m 755 debian/librostlab-blast0-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/librostlab-blast0v5/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/librostlab-blast.a debian/librostlab-blast0-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/librostlab-blast.so debian/librostlab-blast0-dev/usr/lib/x86_64-linux-gnu mv /build/librostlab-blast-1.0.1/debian/tmp/usr/lib/x86_64-linux-gnu/librostlab-blast.so.0 debian/librostlab-blast0v5/usr/lib/x86_64-linux-gnu mv /build/librostlab-blast-1.0.1/debian/tmp/usr/lib/x86_64-linux-gnu/librostlab-blast.so.0.0.0 debian/librostlab-blast0v5/usr/lib/x86_64-linux-gnu PKGDEV=librostlab-blast0-dev PKGSHL=librostlab-blast0v5 install -d -m 755 debian/librostlab-blast0-dev/usr/include mv debian/tmp/usr/include/rostlab debian/librostlab-blast0-dev/usr/include make[1]: Leaving directory '/build/librostlab-blast-1.0.1' debian/rules override_dh_installdocs make[1]: Entering directory '/build/librostlab-blast-1.0.1' dh_installdocs dh_installdocs: Cannot auto-detect main package for librostlab-blast-doc. If the default is wrong, please use --doc-main-package find debian -name "*.md5" -delete make[1]: Leaving directory '/build/librostlab-blast-1.0.1' dh_installchangelogs dh_installexamples dh_lintian dh_perl debian/rules override_dh_link make[1]: Entering directory '/build/librostlab-blast-1.0.1' find debian -name jquery.js -delete dh_link make[1]: Leaving directory '/build/librostlab-blast-1.0.1' dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/librostlab-blast-1.0.1' dh_compress -Xlibrostlab-blast.tag make[1]: Leaving directory '/build/librostlab-blast-1.0.1' dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package librostlab-blast-doc: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'librostlab-blast0v5' in '../librostlab-blast0v5_1.0.1-10_amd64.deb'. dpkg-deb: building package 'librostlab-blast0v5-dbgsym' in '../librostlab-blast0v5-dbgsym_1.0.1-10_amd64.deb'. dpkg-deb: building package 'librostlab-blast0-dev' in '../librostlab-blast0-dev_1.0.1-10_amd64.deb'. dpkg-deb: building package 'librostlab-blast-doc' in '../librostlab-blast-doc_1.0.1-10_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../librostlab-blast_1.0.1-10_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) I: copying local configuration I: user script /srv/workspace/pbuilder/33388/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/33388/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/33388 and its subdirectories I: Current time: Thu May 5 05:16:16 +14 2022 I: pbuilder-time-stamp: 1651677376