I: pbuilder: network access will be disabled during build I: Current time: Sat Apr 22 13:44:11 +14 2023 I: pbuilder-time-stamp: 1682120651 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [genomethreader_1.7.3+dfsg-7.dsc] I: copying [./genomethreader_1.7.3+dfsg.orig.tar.xz] I: copying [./genomethreader_1.7.3+dfsg-7.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Oct 9 04:02:29 2022 +14 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./genomethreader_1.7.3+dfsg-7.dsc: no acceptable signature found dpkg-source: info: extracting genomethreader in genomethreader-1.7.3+dfsg dpkg-source: info: unpacking genomethreader_1.7.3+dfsg.orig.tar.xz dpkg-source: info: unpacking genomethreader_1.7.3+dfsg-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying debian-gt-libs.patch dpkg-source: info: applying gt-path-fix.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying search-paths.patch dpkg-source: info: applying m32-m64-ignore.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying disable-fastdp-tests.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/839907/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-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 '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Apr 22 13:44 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/839907/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/839907/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=ab32a10face9498f857836309b45ec08 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=839907 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.jmCH72L6/pbuilderrc_FKiH --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.jmCH72L6/b2 --logfile b2/build.log --extrapackages usrmerge genomethreader_1.7.3+dfsg-7.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://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Feb 13 10:05 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp -rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash -rwxr-xr-x 1 root root 121904 Sep 21 2022 date -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd -rwxr-xr-x 1 root root 102200 Sep 21 2022 df -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir -rwxr-xr-x 1 root root 88656 Mar 24 00:02 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 35664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Feb 13 10:05 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 3 06:31 run-parts -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 Apr 22 13:44 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar -rwxr-xr-x 1 root root 14520 Nov 3 06:31 tempfile -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch -rwxr-xr-x 1 root root 35664 Sep 21 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 24 00:02 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/839907/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), genometools (>= 1.6.1), libgenometools0-dev (>= 1.6.1), libvmatch-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, liblua5.1-0-dev, libtre-dev, asciidoctor dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on genometools (>= 1.6.1); however: Package genometools is not installed. pbuilder-satisfydepends-dummy depends on libgenometools0-dev (>= 1.6.1); however: Package libgenometools0-dev is not installed. pbuilder-satisfydepends-dummy depends on libvmatch-dev; however: Package libvmatch-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libexpat1-dev; however: Package libexpat1-dev is not installed. pbuilder-satisfydepends-dummy depends on liblua5.1-0-dev; however: Package liblua5.1-0-dev is not installed. pbuilder-satisfydepends-dummy depends on libtre-dev; however: Package libtre-dev is not installed. pbuilder-satisfydepends-dummy depends on asciidoctor; however: Package asciidoctor 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: asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} genometools{a} genometools-common{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libbsd0{a} libbz2-dev{a} libcairo2{a} libdatrie1{a} libdebhelper-perl{a} libedit2{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgenometools0{a} libgenometools0-dev{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libicu72{a} liblua5.1-0{a} liblua5.1-0-dev{a} libmagic-mgc{a} libmagic1{a} libncurses-dev{a} libncurses6{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libreadline-dev{a} libreadline8{a} libruby{a} libruby3.1{a} libsub-override-perl{a} libthai-data{a} libthai0{a} libtool{a} libtre-dev{a} libtre5{a} libuchardet0{a} libvmatch-dev{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxrender1{a} libyaml-0-2{a} lua-filesystem{a} lua-lpeg{a} lua-md5{a} m4{a} man-db{a} openssl{a} po-debconf{a} rake{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl fonts-lato libarchive-cpio-perl libglib2.0-data libgpm2 libjs-jquery libltdl-dev libmail-sendmail-perl libtool-bin lynx pkg-config pkgconf shared-mime-info wget xdg-user-dirs zip 0 packages upgraded, 97 newly installed, 0 to remove and 0 not upgraded. Need to get 43.7 MB of archives. After unpacking 152 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.8-1 [1407 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 rubygems-integration all 1.18 [6704 B] Get: 15 http://deb.debian.org/debian bookworm/main amd64 rake all 13.0.6-3 [83.9 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libruby amd64 1:3.1 [4972 B] Get: 20 http://deb.debian.org/debian bookworm/main amd64 ruby-sdbm amd64 1.0.0-5+b1 [15.4 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-2 [103 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libruby3.1 amd64 3.1.2-7 [5401 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 ruby3.1 amd64 3.1.2-7 [663 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 ruby-rubygems all 3.3.15-2 [293 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 ruby amd64 1:3.1 [5868 B] Get: 29 http://deb.debian.org/debian bookworm/main amd64 ruby-asciidoctor all 2.0.18-2 [211 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 asciidoctor all 2.0.18-2 [86.6 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-4 [399 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2 [292 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 liblua5.1-0 amd64 5.1.5-9 [111 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libtre5 amd64 0.8.0-7 [58.1 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 lua-filesystem amd64 1.8.0-3 [11.8 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 lua-lpeg amd64 1.0.2-2 [37.7 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 lua-md5 amd64 1.2+git+1+8d87fee-2 [12.8 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 genometools-common all 1.6.2+ds-3 [194 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 genometools amd64 1.6.2+ds-3 [1627 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libbz2-dev amd64 1.0.8-5+b1 [30.9 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libgenometools0 amd64 1.6.2+ds-3 [1388 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libgenometools0-dev amd64 1.6.2+ds-3 [94.5 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 libncurses-dev amd64 6.4-2 [348 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libreadline-dev amd64 8.2-1.3 [151 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 liblua5.1-0-dev amd64 5.1.5-9 [135 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 libtre-dev amd64 0.8.0-7 [34.3 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libvmatch-dev amd64 2.3.1+dfsg-8 [644 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Fetched 43.7 MB in 1s (59.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package readline-common. (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 ... 19596 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../02-openssl_3.0.8-1_amd64.deb ... 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Unpacking libedit2:amd64 (3.1-20221030-2) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../22-libncurses6_6.4-2_amd64.deb ... Unpacking libncurses6:amd64 (6.4-2) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../23-libyaml-0-2_0.2.5-1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-1) ... Selecting previously unselected package libruby3.1:amd64. Preparing to unpack .../24-libruby3.1_3.1.2-7_amd64.deb ... Unpacking libruby3.1:amd64 (3.1.2-7) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../25-ruby3.1_3.1.2-7_amd64.deb ... Unpacking ruby3.1 (3.1.2-7) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../26-ruby-rubygems_3.3.15-2_all.deb ... Unpacking ruby-rubygems (3.3.15-2) ... Selecting previously unselected package ruby. Preparing to unpack .../27-ruby_1%3a3.1_amd64.deb ... Unpacking ruby (1:3.1) ... 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Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../35-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../36-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../37-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../38-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../39-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../40-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../41-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../42-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../43-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../44-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../45-libxml2_2.9.14+dfsg-1.1+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.1+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../46-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../47-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../48-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../49-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../50-libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../51-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../52-libpng16-16_1.6.39-2_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.39-2) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../53-libfreetype6_2.12.1+dfsg-4_amd64.deb ... Unpacking libfreetype6:amd64 (2.12.1+dfsg-4) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../54-fonts-dejavu-core_2.37-6_all.deb ... Unpacking fonts-dejavu-core (2.37-6) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../55-fontconfig-config_2.14.1-4_amd64.deb ... Unpacking fontconfig-config (2.14.1-4) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../56-libfontconfig1_2.14.1-4_amd64.deb ... Unpacking libfontconfig1:amd64 (2.14.1-4) ... Selecting previously unselected package fontconfig. Preparing to unpack .../57-fontconfig_2.14.1-4_amd64.deb ... Unpacking fontconfig (2.14.1-4) ... Selecting previously unselected package libpixman-1-0:amd64. Preparing to unpack .../58-libpixman-1-0_0.42.2-1_amd64.deb ... Unpacking libpixman-1-0:amd64 (0.42.2-1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../59-libxau6_1%3a1.0.9-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../60-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../61-libxcb1_1.15-1_amd64.deb ... Unpacking libxcb1:amd64 (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../62-libx11-data_2%3a1.8.4-2_all.deb ... Unpacking libx11-data (2:1.8.4-2) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../63-libx11-6_2%3a1.8.4-2_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.4-2) ... Selecting previously unselected package libxcb-render0:amd64. Preparing to unpack .../64-libxcb-render0_1.15-1_amd64.deb ... Unpacking libxcb-render0:amd64 (1.15-1) ... Selecting previously unselected package libxcb-shm0:amd64. Preparing to unpack .../65-libxcb-shm0_1.15-1_amd64.deb ... Unpacking libxcb-shm0:amd64 (1.15-1) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../66-libxext6_2%3a1.3.4-1+b1_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1+b1) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../67-libxrender1_1%3a0.9.10-1.1_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.10-1.1) ... Selecting previously unselected package libcairo2:amd64. Preparing to unpack .../68-libcairo2_1.16.0-7_amd64.deb ... Unpacking libcairo2:amd64 (1.16.0-7) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../69-libglib2.0-0_2.74.6-2_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.74.6-2) ... Selecting previously unselected package liblua5.1-0:amd64. Preparing to unpack .../70-liblua5.1-0_5.1.5-9_amd64.deb ... Unpacking liblua5.1-0:amd64 (5.1.5-9) ... Selecting previously unselected package libfribidi0:amd64. Preparing to unpack .../71-libfribidi0_1.0.8-2.1_amd64.deb ... Unpacking libfribidi0:amd64 (1.0.8-2.1) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../72-libgraphite2-3_1.3.14-1_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.14-1) ... Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../73-libharfbuzz0b_6.0.0+dfsg-3_amd64.deb ... Unpacking libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Selecting previously unselected package libthai-data. Preparing to unpack .../74-libthai-data_0.1.29-1_all.deb ... Unpacking libthai-data (0.1.29-1) ... Selecting previously unselected package libdatrie1:amd64. Preparing to unpack .../75-libdatrie1_0.2.13-2+b1_amd64.deb ... Unpacking libdatrie1:amd64 (0.2.13-2+b1) ... Selecting previously unselected package libthai0:amd64. Preparing to unpack .../76-libthai0_0.1.29-1_amd64.deb ... Unpacking libthai0:amd64 (0.1.29-1) ... Selecting previously unselected package libpango-1.0-0:amd64. Preparing to unpack .../77-libpango-1.0-0_1.50.12+ds-1_amd64.deb ... Unpacking libpango-1.0-0:amd64 (1.50.12+ds-1) ... Selecting previously unselected package libpangoft2-1.0-0:amd64. Preparing to unpack .../78-libpangoft2-1.0-0_1.50.12+ds-1_amd64.deb ... Unpacking libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Selecting previously unselected package libpangocairo-1.0-0:amd64. Preparing to unpack .../79-libpangocairo-1.0-0_1.50.12+ds-1_amd64.deb ... Unpacking libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Selecting previously unselected package libtre5:amd64. Preparing to unpack .../80-libtre5_0.8.0-7_amd64.deb ... Unpacking libtre5:amd64 (0.8.0-7) ... Selecting previously unselected package lua-filesystem:amd64. Preparing to unpack .../81-lua-filesystem_1.8.0-3_amd64.deb ... Unpacking lua-filesystem:amd64 (1.8.0-3) ... Selecting previously unselected package lua-lpeg:amd64. Preparing to unpack .../82-lua-lpeg_1.0.2-2_amd64.deb ... Unpacking lua-lpeg:amd64 (1.0.2-2) ... Selecting previously unselected package lua-md5:amd64. Preparing to unpack .../83-lua-md5_1.2+git+1+8d87fee-2_amd64.deb ... Unpacking lua-md5:amd64 (1.2+git+1+8d87fee-2) ... Selecting previously unselected package genometools-common. Preparing to unpack .../84-genometools-common_1.6.2+ds-3_all.deb ... Unpacking genometools-common (1.6.2+ds-3) ... Selecting previously unselected package genometools. Preparing to unpack .../85-genometools_1.6.2+ds-3_amd64.deb ... Unpacking genometools (1.6.2+ds-3) ... Selecting previously unselected package libbz2-dev:amd64. Preparing to unpack .../86-libbz2-dev_1.0.8-5+b1_amd64.deb ... Unpacking libbz2-dev:amd64 (1.0.8-5+b1) ... Selecting previously unselected package libexpat1-dev:amd64. Preparing to unpack .../87-libexpat1-dev_2.5.0-1_amd64.deb ... Unpacking libexpat1-dev:amd64 (2.5.0-1) ... Selecting previously unselected package libgenometools0. 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Setting up libpango-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.16.0-7) ... Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Setting up debhelper (13.11.4) ... Setting up genometools-common (1.6.2+ds-3) ... Setting up libgenometools0 (1.6.2+ds-3) ... Setting up libgenometools0-dev (1.6.2+ds-3) ... Setting up genometools (1.6.2+ds-3) ... Setting up libruby:amd64 (1:3.1) ... Setting up ruby-rubygems (3.3.15-2) ... Setting up ruby (1:3.1) ... Setting up ruby-asciidoctor (2.0.18-2) ... Setting up rake (13.0.6-3) ... Setting up asciidoctor (2.0.18-2) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b1) ... Setting up libruby3.1:amd64 (3.1.2-7) ... Setting up ruby3.1 (3.1.2-7) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/839907/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/839907/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/genomethreader-1.7.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../genomethreader_1.7.3+dfsg-7_source.changes dpkg-buildpackage: info: source package genomethreader dpkg-buildpackage: info: source version 1.7.3+dfsg-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/genomethreader-1.7.3+dfsg' dh_clean rm -rf bin/bssm debian/bssm bin/gthdata debian/gthdata rm -rf /build/genomethreader-1.7.3+dfsg/debian/man rm -f debian/*substvars make[1]: Leaving directory '/build/genomethreader-1.7.3+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/genomethreader-1.7.3+dfsg' make licensemanager=no opt=yes 64bit=yes make[2]: Entering directory '/build/genomethreader-1.7.3+dfsg' [create obj/gth_config.h] [compile findfile.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/findfile.c -o obj/src/libgenomethreader/findfile.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/findfile.c -o obj/src/libgenomethreader/findfile.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/findfile.o [compile gt_align_dna.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/gt_align_dna.c -o obj/src/libgenomethreader/gt_align_dna.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gt_align_dna.c -o obj/src/libgenomethreader/gt_align_dna.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gt_align_dna.o [compile gt_gthgetseq.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/gt_gthgetseq.c -o obj/src/libgenomethreader/gt_gthgetseq.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gt_gthgetseq.c -o obj/src/libgenomethreader/gt_gthgetseq.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gt_gthgetseq.o [compile gthmkvtree.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/gthmkvtree.c -o obj/src/libgenomethreader/gthmkvtree.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gthmkvtree.c -o obj/src/libgenomethreader/gthmkvtree.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gthmkvtree.o [compile gthpolyafunc.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/gthpolyafunc.c -o obj/src/libgenomethreader/gthpolyafunc.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gthpolyafunc.c -o obj/src/libgenomethreader/gthpolyafunc.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gthpolyafunc.o [compile gthpre.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/gthpre.c -o obj/src/libgenomethreader/gthpre.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gthpre.c -o obj/src/libgenomethreader/gthpre.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gthpre.o [compile gthversionfunc.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/gthversionfunc.c -o obj/src/libgenomethreader/gthversionfunc.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gthversionfunc.c -o obj/src/libgenomethreader/gthversionfunc.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gthversionfunc.o [compile gthvmatch.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/gthvmatch.c -o obj/src/libgenomethreader/gthvmatch.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gthvmatch.c -o obj/src/libgenomethreader/gthvmatch.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gthvmatch.o [compile jt.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/jt.c -o obj/src/libgenomethreader/jt.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/jt.c -o obj/src/libgenomethreader/jt.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/jt.o [compile jt_align_dna.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/jt_align_dna.c -o obj/src/libgenomethreader/jt_align_dna.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/jt_align_dna.c -o obj/src/libgenomethreader/jt_align_dna.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/jt_align_dna.o [compile jt_align_protein.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/jt_align_protein.c -o obj/src/libgenomethreader/jt_align_protein.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/jt_align_protein.c -o obj/src/libgenomethreader/jt_align_protein.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/jt_align_protein.o [compile seq_con_multiseq.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/seq_con_multiseq.c -o obj/src/libgenomethreader/seq_con_multiseq.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/seq_con_multiseq.c -o obj/src/libgenomethreader/seq_con_multiseq.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/seq_con_multiseq.o [compile ags.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/ags.c -o obj/src/gth/ags.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/ags.c -o obj/src/gth/ags.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/ags.o [compile ags_build.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/ags_build.c -o obj/src/gth/ags_build.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/ags_build.c -o obj/src/gth/ags_build.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/ags_build.o [compile align_dna.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/align_dna.c -o obj/src/gth/align_dna.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/align_dna.c -o obj/src/gth/align_dna.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/align_dna.o [compile align_protein.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/align_protein.c -o obj/src/gth/align_protein.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/align_protein.c -o obj/src/gth/align_protein.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/align_protein.o [compile backtrace_path.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/backtrace_path.c -o obj/src/gth/backtrace_path.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/backtrace_path.c -o obj/src/gth/backtrace_path.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/backtrace_path.o [compile bssm_helper.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/bssm_helper.c -o obj/src/gth/bssm_helper.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_helper.c -o obj/src/gth/bssm_helper.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/bssm_helper.o [compile bssm_param.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/bssm_param.c -o obj/src/gth/bssm_param.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_param.c -o obj/src/gth/bssm_param.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/bssm_param.o [compile bssm_param_rmsd.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/bssm_param_rmsd.c -o obj/src/gth/bssm_param_rmsd.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_param_rmsd.c -o obj/src/gth/bssm_param_rmsd.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/bssm_param_rmsd.o [compile bssm_seq_processor.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/bssm_seq_processor.c -o obj/src/gth/bssm_seq_processor.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_seq_processor.c -o obj/src/gth/bssm_seq_processor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/bssm_seq_processor.o [compile bssm_train_stream.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/bssm_train_stream.c -o obj/src/gth/bssm_train_stream.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_train_stream.c -o obj/src/gth/bssm_train_stream.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/bssm_train_stream.o [compile bssm_train_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/bssm_train_visitor.c -o obj/src/gth/bssm_train_visitor.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_train_visitor.c -o obj/src/gth/bssm_train_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/bssm_train_visitor.o [compile call_info.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/call_info.c -o obj/src/gth/call_info.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/call_info.c -o obj/src/gth/call_info.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/call_info.o [compile chain_collection.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/chain_collection.c -o obj/src/gth/chain_collection.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/chain_collection.c -o obj/src/gth/chain_collection.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/chain_collection.o [compile chaining.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/chaining.c -o obj/src/gth/chaining.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/chaining.c -o obj/src/gth/chaining.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/chaining.o [compile compute_scores.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/compute_scores.c -o obj/src/gth/compute_scores.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/compute_scores.c -o obj/src/gth/compute_scores.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/compute_scores.o [compile desc_cache.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/desc_cache.c -o obj/src/gth/desc_cache.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/desc_cache.c -o obj/src/gth/desc_cache.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/desc_cache.o [compile dp_options_core.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/dp_options_core.c -o obj/src/gth/dp_options_core.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/dp_options_core.c -o obj/src/gth/dp_options_core.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/dp_options_core.o [compile dp_options_est.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/dp_options_est.c -o obj/src/gth/dp_options_est.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/dp_options_est.c -o obj/src/gth/dp_options_est.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/dp_options_est.o [compile dp_options_postpro.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/dp_options_postpro.c -o obj/src/gth/dp_options_postpro.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/dp_options_postpro.c -o obj/src/gth/dp_options_postpro.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/dp_options_postpro.o [compile dp_param.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/dp_param.c -o obj/src/gth/dp_param.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/dp_param.c -o obj/src/gth/dp_param.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/dp_param.o [compile dp_scores_protein.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/dp_scores_protein.c -o obj/src/gth/dp_scores_protein.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/dp_scores_protein.c -o obj/src/gth/dp_scores_protein.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/dp_scores_protein.o [compile editoperation.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/editoperation.c -o obj/src/gth/editoperation.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/editoperation.c -o obj/src/gth/editoperation.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/editoperation.o [compile gff3_pgl_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gff3_pgl_visitor.c -o obj/src/gth/gff3_pgl_visitor.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gff3_pgl_visitor.c -o obj/src/gth/gff3_pgl_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gff3_pgl_visitor.o [compile gff3_sa_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gff3_sa_visitor.c -o obj/src/gth/gff3_sa_visitor.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gff3_sa_visitor.c -o obj/src/gth/gff3_sa_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gff3_sa_visitor.o [compile gt_gth.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gt_gth.c -o obj/src/gth/gt_gth.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gth.c -o obj/src/gth/gt_gth.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gth.o [compile gt_gthbssmbuild.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gt_gthbssmbuild.c -o obj/src/gth/gt_gthbssmbuild.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthbssmbuild.c -o obj/src/gth/gt_gthbssmbuild.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthbssmbuild.o [compile gt_gthbssmfileinfo.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gt_gthbssmfileinfo.c -o obj/src/gth/gt_gthbssmfileinfo.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthbssmfileinfo.c -o obj/src/gth/gt_gthbssmfileinfo.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthbssmfileinfo.o [compile gt_gthbssmprint.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gt_gthbssmprint.c -o obj/src/gth/gt_gthbssmprint.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthbssmprint.c -o obj/src/gth/gt_gthbssmprint.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthbssmprint.o [compile gt_gthbssmrmsd.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gt_gthbssmrmsd.c -o obj/src/gth/gt_gthbssmrmsd.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthbssmrmsd.c -o obj/src/gth/gt_gthbssmrmsd.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthbssmrmsd.o [compile gt_gthbssmtrain.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gt_gthbssmtrain.c -o obj/src/gth/gt_gthbssmtrain.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthbssmtrain.c -o obj/src/gth/gt_gthbssmtrain.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthbssmtrain.o [compile gt_gthconsensus.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gt_gthconsensus.c -o obj/src/gth/gt_gthconsensus.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthconsensus.c -o obj/src/gth/gt_gthconsensus.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthconsensus.o [compile gt_gthfilestat.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gt_gthfilestat.c -o obj/src/gth/gt_gthfilestat.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthfilestat.c -o obj/src/gth/gt_gthfilestat.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthfilestat.o [compile gt_gthmkbssmfiles.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gt_gthmkbssmfiles.c -o obj/src/gth/gt_gthmkbssmfiles.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthmkbssmfiles.c -o obj/src/gth/gt_gthmkbssmfiles.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthmkbssmfiles.o [compile gt_gthsplit.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gt_gthsplit.c -o obj/src/gth/gt_gthsplit.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthsplit.c -o obj/src/gth/gt_gthsplit.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthsplit.o [compile gthalignment.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthalignment.c -o obj/src/gth/gthalignment.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthalignment.c -o obj/src/gth/gthalignment.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthalignment.o [compile gthchain.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthchain.c -o obj/src/gth/gthchain.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthchain.c -o obj/src/gth/gthchain.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthchain.o [compile gthcluster.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthcluster.c -o obj/src/gth/gthcluster.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthcluster.c -o obj/src/gth/gthcluster.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthcluster.o [compile gthcutoffsminimal.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthcutoffsminimal.c -o obj/src/gth/gthcutoffsminimal.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthcutoffsminimal.c -o obj/src/gth/gthcutoffsminimal.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthcutoffsminimal.o [compile gthcutoffsrelaxed.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthcutoffsrelaxed.c -o obj/src/gth/gthcutoffsrelaxed.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthcutoffsrelaxed.c -o obj/src/gth/gthcutoffsrelaxed.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthcutoffsrelaxed.o [compile gthcutoffsstrict.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthcutoffsstrict.c -o obj/src/gth/gthcutoffsstrict.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthcutoffsstrict.c -o obj/src/gth/gthcutoffsstrict.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthcutoffsstrict.o [compile gthmatch.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthmatch.c -o obj/src/gth/gthmatch.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthmatch.c -o obj/src/gth/gthmatch.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthmatch.o [compile gthorf.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthorf.c -o obj/src/gth/gthorf.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthorf.c -o obj/src/gth/gthorf.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthorf.o [compile gthoutput.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthoutput.c -o obj/src/gth/gthoutput.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthoutput.c -o obj/src/gth/gthoutput.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthoutput.o [compile gthsadistri.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthsadistri.c -o obj/src/gth/gthsadistri.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthsadistri.c -o obj/src/gth/gthsadistri.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthsadistri.o [compile gthsortags.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthsortags.c -o obj/src/gth/gthsortags.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthsortags.c -o obj/src/gth/gthsortags.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthsortags.o [compile gthsplicesitescr.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthsplicesitescr.c -o obj/src/gth/gthsplicesitescr.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthsplicesitescr.c -o obj/src/gth/gthsplicesitescr.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthsplicesitescr.o [compile gthtrans.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthtrans.c -o obj/src/gth/gthtrans.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthtrans.c -o obj/src/gth/gthtrans.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthtrans.o [compile gthtravalign.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthtravalign.c -o obj/src/gth/gthtravalign.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthtravalign.c -o obj/src/gth/gthtravalign.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthtravalign.o [compile gthverbosefunc.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthverbosefunc.c -o obj/src/gth/gthverbosefunc.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthverbosefunc.c -o obj/src/gth/gthverbosefunc.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthverbosefunc.o [compile gthverbosefuncvm.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthverbosefuncvm.c -o obj/src/gth/gthverbosefuncvm.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthverbosefuncvm.c -o obj/src/gth/gthverbosefuncvm.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthverbosefuncvm.o [compile gthxml.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthxml.c -o obj/src/gth/gthxml.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthxml.c -o obj/src/gth/gthxml.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthxml.o [compile indent.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/indent.c -o obj/src/gth/indent.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/indent.c -o obj/src/gth/indent.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/indent.o [compile input.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/input.c -o obj/src/gth/input.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/input.c -o obj/src/gth/input.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/input.o [compile intermediate.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/intermediate.c -o obj/src/gth/intermediate.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/intermediate.c -o obj/src/gth/intermediate.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/intermediate.o [compile md5_cache.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/md5_cache.c -o obj/src/gth/md5_cache.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/md5_cache.c -o obj/src/gth/md5_cache.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/md5_cache.o [compile parse_options.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/parse_options.c -o obj/src/gth/parse_options.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/parse_options.c -o obj/src/gth/parse_options.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/parse_options.o [compile path_matrix.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/path_matrix.c -o obj/src/gth/path_matrix.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/path_matrix.c -o obj/src/gth/path_matrix.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/path_matrix.o [compile path_walker.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/path_walker.c -o obj/src/gth/path_walker.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/path_walker.c -o obj/src/gth/path_walker.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/path_walker.o [compile pgl.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/pgl.c -o obj/src/gth/pgl.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/pgl.c -o obj/src/gth/pgl.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/pgl.o [compile pgl_collection.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/pgl_collection.c -o obj/src/gth/pgl_collection.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/pgl_collection.c -o obj/src/gth/pgl_collection.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/pgl_collection.o [compile pgl_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/pgl_visitor.c -o obj/src/gth/pgl_visitor.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/pgl_visitor.c -o obj/src/gth/pgl_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/pgl_visitor.o [compile proc_sa_collection.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/proc_sa_collection.c -o obj/src/gth/proc_sa_collection.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/proc_sa_collection.c -o obj/src/gth/proc_sa_collection.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/proc_sa_collection.o [compile region_factory.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/region_factory.c -o obj/src/gth/region_factory.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/region_factory.c -o obj/src/gth/region_factory.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/region_factory.o [compile run_header.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/run_header.c -o obj/src/gth/run_header.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/run_header.c -o obj/src/gth/run_header.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/run_header.o [compile sa.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/sa.c -o obj/src/gth/sa.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/sa.c -o obj/src/gth/sa.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/sa.o [compile sa_cmp.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/sa_cmp.c -o obj/src/gth/sa_cmp.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/sa_cmp.c -o obj/src/gth/sa_cmp.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/sa_cmp.o [compile sa_collection.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/sa_collection.c -o obj/src/gth/sa_collection.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/sa_collection.c -o obj/src/gth/sa_collection.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/sa_collection.o [compile sa_filter.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/sa_filter.c -o obj/src/gth/sa_filter.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/sa_filter.c -o obj/src/gth/sa_filter.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/sa_filter.o [compile sa_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/sa_visitor.c -o obj/src/gth/sa_visitor.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/sa_visitor.c -o obj/src/gth/sa_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/sa_visitor.o [compile seq_con.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/seq_con.c -o obj/src/gth/seq_con.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/seq_con.c -o obj/src/gth/seq_con.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/seq_con.o [compile similarity_filter.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/similarity_filter.c -o obj/src/gth/similarity_filter.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/similarity_filter.c -o obj/src/gth/similarity_filter.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/similarity_filter.o [compile splice_site_model.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/splice_site_model.c -o obj/src/gth/splice_site_model.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/splice_site_model.c -o obj/src/gth/splice_site_model.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/splice_site_model.o [compile spliced_seq.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/spliced_seq.c -o obj/src/gth/spliced_seq.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/spliced_seq.c -o obj/src/gth/spliced_seq.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/spliced_seq.o [compile stat.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/stat.c -o obj/src/gth/stat.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/stat.c -o obj/src/gth/stat.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/stat.o [compile time.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/time.c -o obj/src/gth/time.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/time.c -o obj/src/gth/time.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/time.o [compile txt_pgl_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/txt_pgl_visitor.c -o obj/src/gth/txt_pgl_visitor.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/txt_pgl_visitor.c -o obj/src/gth/txt_pgl_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/txt_pgl_visitor.o [compile txt_sa_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/txt_sa_visitor.c -o obj/src/gth/txt_sa_visitor.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/txt_sa_visitor.c -o obj/src/gth/txt_sa_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/txt_sa_visitor.o [compile xml_final_sa_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/xml_final_sa_visitor.c -o obj/src/gth/xml_final_sa_visitor.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/xml_final_sa_visitor.c -o obj/src/gth/xml_final_sa_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/xml_final_sa_visitor.o [compile xml_inter_sa_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/xml_inter_sa_visitor.c -o obj/src/gth/xml_inter_sa_visitor.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/xml_inter_sa_visitor.c -o obj/src/gth/xml_inter_sa_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/xml_inter_sa_visitor.o [compile xml_pgl_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/xml_pgl_visitor.c -o obj/src/gth/xml_pgl_visitor.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/xml_pgl_visitor.c -o obj/src/gth/xml_pgl_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/xml_pgl_visitor.o [link libgenomethreader.a] ar: `u' modifier ignored since `D' is the default (see `U') ar: creating lib/libgenomethreader.a [compile gth.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth.c -o obj/src/gth.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth.c -o obj/src/gth.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth.o [link gth] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gth.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gth [compile gthconsensus.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gthconsensus.c -o obj/src/gthconsensus.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthconsensus.c -o obj/src/gthconsensus.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthconsensus.o [link gthconsensus] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthconsensus.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthconsensus [compile gthbssmfileinfo.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gthbssmfileinfo.c -o obj/src/gthbssmfileinfo.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthbssmfileinfo.c -o obj/src/gthbssmfileinfo.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthbssmfileinfo.o [link gthbssmfileinfo] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthbssmfileinfo.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthbssmfileinfo [compile gthbssmbuild.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gthbssmbuild.c -o obj/src/gthbssmbuild.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthbssmbuild.c -o obj/src/gthbssmbuild.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthbssmbuild.o [link gthbssmbuild] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthbssmbuild.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthbssmbuild [compile gthbssmprint.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gthbssmprint.c -o obj/src/gthbssmprint.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthbssmprint.c -o obj/src/gthbssmprint.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthbssmprint.o [link gthbssmprint] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthbssmprint.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthbssmprint [compile gthbssmrmsd.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gthbssmrmsd.c -o obj/src/gthbssmrmsd.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthbssmrmsd.c -o obj/src/gthbssmrmsd.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthbssmrmsd.o [link gthbssmrmsd] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthbssmrmsd.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthbssmrmsd [compile gthbssmtrain.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gthbssmtrain.c -o obj/src/gthbssmtrain.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthbssmtrain.c -o obj/src/gthbssmtrain.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthbssmtrain.o [link gthbssmtrain] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthbssmtrain.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthbssmtrain [compile gthfilestat.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gthfilestat.c -o obj/src/gthfilestat.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthfilestat.c -o obj/src/gthfilestat.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthfilestat.o [link gthfilestat] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthfilestat.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthfilestat [compile gthmkbssmfiles.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gthmkbssmfiles.c -o obj/src/gthmkbssmfiles.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthmkbssmfiles.c -o obj/src/gthmkbssmfiles.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthmkbssmfiles.o [link gthmkbssmfiles] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthmkbssmfiles.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthmkbssmfiles [compile gthsplit.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gthsplit.c -o obj/src/gthsplit.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthsplit.c -o obj/src/gthsplit.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthsplit.o [link gthsplit] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthsplit.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthsplit [compile gthunit.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gthunit.c -o obj/src/gthunit.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthunit.c -o obj/src/gthunit.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthunit.o [link gthunit] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthunit.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthunit [compile gthgetseq.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gthgetseq.c -o obj/src/gthgetseq.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthgetseq.c -o obj/src/gthgetseq.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthgetseq.o [link gthgetseq] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthgetseq.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthgetseq [compile align_dna.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/align_dna.c -o obj/src/align_dna.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/align_dna.c -o obj/src/align_dna.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/align_dna.o [link align_dna] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/align_dna.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/align_dna make[2]: Leaving directory '/build/genomethreader-1.7.3+dfsg' make licensemanager=no opt=yes 64bit=yes train make[2]: Entering directory '/build/genomethreader-1.7.3+dfsg' [train arabidopsis.bssm] [train rice.bssm] [train maize.bssm] [train medicago.bssm] [write old BSSMs] [copy gthdata stuff to bin] make[2]: Leaving directory '/build/genomethreader-1.7.3+dfsg' make[1]: Leaving directory '/build/genomethreader-1.7.3+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/genomethreader-1.7.3+dfsg' make licensemanager=no 64bit=yes test make[2]: Entering directory '/build/genomethreader-1.7.3+dfsg' cd testsuite && env -i GTH_MEM_BOOKKEEPING=on MAKE=make PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" \ BSSMDIR=/build/genomethreader-1.7.3+dfsg/bin/bssm GTHDATADIR=/build/genomethreader-1.7.3+dfsg/gthdata/gth \ CCACHE_DISABLE=yes HOME=/nonexistent/second-build GTHTESTDATADIR= \ ruby -I. testsuite.rb \ -testdata /build/genomethreader-1.7.3+dfsg/testdata -bin /build/genomethreader-1.7.3+dfsg/bin -cur /build/genomethreader-1.7.3+dfsg \ -gtruby /build/genomethreader-1.7.3+dfsg/gtruby 1: gth : ok 2: gth -help : ok 3: gth -help+ : ok 4: gth -version : ok 5: gth regression test (assertion in gthsafilter) : ok 6: gth regression test (-gff3out -intermediate) : ok 7: gth regression test (-gff3out -intermediate -fastdp) : ok 8: gth regression test (-gff3out -skipalignmentout) : ok 9: gth regression test (-gff3out -skipalignmentout -fastdp) : ok 10: gth regression test (-gff3out -intermediate -o) : ok 11: gth regression test (-gff3out -skipalignmentout -o) : ok 12: gthconsensus regression test (-gff3out -intermediate) : ok 13: gthconsensus regression test (-gff3out -skipalignmentout) : ok 14: gthconsensus regression test (-gff3out -intermediate -o) : ok 15: gthconsensus regression test (-gff3out -skipalignmentout -o): ok 16: gth regression test (-exondistri) : ok 17: gth regression test (-introndistri) : ok 18: gth regression test (-refseqcovdistri) : ok 19: gth regression test (all distributions) : ok 20: gth regression test (-skipindexcheck) : ok 21: gth regression test (index reconstruction) : ok 22: gth regression test (-createindicesonly & -noautoindex) : ok 23: gth regression test (coverage assertion) : ok 24: gth -gff3out -intermediate (long intron files) : ok 25: gth -gff3out -skipalignmentout (long intron files) : ok 26: gth -gff3out -frompos (correct positions in sequence region): ok 27: gth -gff3out -intermediate (correct reverse positions) : ok 28: gth arabidopsis : ok 29: gth illegal character in protein file : ok 30: align_dna : ok 31: gth -gff3descranges (single exon) : ok 32: gthconsensus -help : ok 33: gthconsensus -help+ : ok 34: gthconsensus empty_file : ok 35: gthconsensus empty_file.gz : ok 36: gthconsensus empty_file.bz2 : ok 37: gthbssmfileinfo (arabidopsis) : ok 38: gthbssmfileinfo (human) : ok 39: gthbssmprint (arabidopsis) : ok 40: gthbssmprint (human) : ok 41: gthbssmrmsd (arabidopsis) : ok 42: gthbssmtrain (examples from manual) : ok 43: gthbssmtrain (file, no introns) : ok 44: gthbssmtrain (file, introns) : ok 45: gthbssmtrain (stdin, no introns) : ok 46: gthbssmtrain (stdin, introns) : ok 47: gthbssmtrain (short intron) : ok 48: gthunit : ok 49: fastdp 01 : ok 50: fastdp (U89959) : ok 51: fastdp (U89959, introncutout) : ok make[2]: Leaving directory '/build/genomethreader-1.7.3+dfsg' make[1]: Leaving directory '/build/genomethreader-1.7.3+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/genomethreader-1.7.3+dfsg' mv bin/bssm debian/bssm mv bin/gthdata debian/gthdata dh_auto_install make[1]: Leaving directory '/build/genomethreader-1.7.3+dfsg' dh_install dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/genomethreader-1.7.3+dfsg' mkdir -p /build/genomethreader-1.7.3+dfsg/debian/man asciidoctor -a docdate='' -b manpage /build/genomethreader-1.7.3+dfsg/debian/man_src/*.adoc cp /build/genomethreader-1.7.3+dfsg/debian/man_src/*.? /build/genomethreader-1.7.3+dfsg/debian/man dh_installman -- make[1]: Leaving directory '/build/genomethreader-1.7.3+dfsg' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/genomethreader-1.7.3+dfsg' echo "libvmatch-dev:Version=2.3.1+dfsg-8" >> debian/genomethreader.substvars dh_gencontrol make[1]: Leaving directory '/build/genomethreader-1.7.3+dfsg' dh_md5sums dh_builddeb dpkg-deb: building package 'genomethreader' in '../genomethreader_1.7.3+dfsg-7_amd64.deb'. dpkg-deb: building package 'genomethreader-dbgsym' in '../genomethreader-dbgsym_1.7.3+dfsg-7_amd64.deb'. dpkg-genbuildinfo --build=binary -O../genomethreader_1.7.3+dfsg-7_amd64.buildinfo dpkg-genchanges --build=binary -O../genomethreader_1.7.3+dfsg-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/839907/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/839907/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/839907 and its subdirectories I: Current time: Sat Apr 22 13:47:21 +14 2023 I: pbuilder-time-stamp: 1682120841