Wed May 31 05:37:08 UTC 2023 I: starting to build genomethreader/bookworm/armhf on jenkins on '2023-05-31 05:36' Wed May 31 05:37:08 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_35/3302/console.log Wed May 31 05:37:08 UTC 2023 I: Downloading source for bookworm/genomethreader=1.7.3+dfsg-7 --2023-05-31 05:37:08-- http://cdn-fastly.deb.debian.org/debian/pool/main/g/genomethreader/genomethreader_1.7.3%2bdfsg-7.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2228 (2.2K) [text/prs.lines.tag] Saving to: ‘genomethreader_1.7.3+dfsg-7.dsc’ 0K .. 100% 172M=0s 2023-05-31 05:37:09 (172 MB/s) - ‘genomethreader_1.7.3+dfsg-7.dsc’ saved [2228/2228] Wed May 31 05:37:09 UTC 2023 I: genomethreader_1.7.3+dfsg-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: genomethreader Binary: genomethreader Architecture: any Version: 1.7.3+dfsg-7 Maintainer: Debian Med Packaging Team Uploaders: Sascha Steinbiss Homepage: http://genomethreader.org Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/genomethreader Vcs-Git: https://salsa.debian.org/med-team/genomethreader.git Testsuite: autopkgtest Testsuite-Triggers: genometools, ruby Build-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 Package-List: genomethreader deb science optional arch=any Checksums-Sha1: 84e7de5ac11ef4305a5e40eddb1c07383c464964 39993616 genomethreader_1.7.3+dfsg.orig.tar.xz c79962d811752f0adcca5295b93fe3c23e30d0c0 13556 genomethreader_1.7.3+dfsg-7.debian.tar.xz Checksums-Sha256: d19808894b1c86312b51f1aeb6e11f5ba0dfc8dcf237bf08fc0615d26b0cf051 39993616 genomethreader_1.7.3+dfsg.orig.tar.xz 41c972fd09c3f8c54bdc1eb031696f922f9d6c31f19c23e9ff0f6fb929dbff81 13556 genomethreader_1.7.3+dfsg-7.debian.tar.xz Files: 62eb8a06280490f22b646147f0e0f444 39993616 genomethreader_1.7.3+dfsg.orig.tar.xz 66e5fa2ed6bff03d8a1d96075014edb3 13556 genomethreader_1.7.3+dfsg-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAmNBgvUACgkQ6NN64vCf SHKriRAAjobpgjBwppFTNUSIkrBIcRFZNyHH0HJFy4ILv8asB5Zjee4rxadPAtdb AaE80x4DlQN6vtQIHwKtZSoBeFHXAX8U7faGxcFfhXYyahqw0slYDkAEZB4Rtrt5 FpSSdVIgwmzLnc8Wg3w+TrvRvjj72lNBy0O2NDQqw+gOLbXYF/bwII0X5K1BCoJ4 EEOJNigMEs+Ivj+B69wecUctIgfZC9ZtFj0MYll3FZwG0PBbyffUObI9wg4zQwLk DE+6o9+pDx8oZY7jCGLYlnmY2+EYACDQhh/OD7YxOZc895nNk0p4NyvQmLudDRoB R31xtE/ssTVgmskCpBnddcoBlEiLkTAcuYXouF+87xVuh+aFCRyKXKP4DheDf8qq LvfyQwPQwUYlSTuDNJuxQrlwC5XcvLNLmZfgl+IsOQfgxYOLmcDfFCUW778LtJbU XOggDww6MCwiddQ3tCZbgOgIiHwyiP0uVuUmtJcI3TK0WVWBED12NrQBAWnHuLBh qkJ+OHw9YnK+KDiKMlojPOVXA20/G7ant9m4ph9//hn6peKb3E9qyDg/rWv4AIRE N2RLINe2vKP4QMMxvegPSJvhjB9xV54dIf1MhaAaEzAh+J7Qd5uCi7dwXWOhsaX6 to3E423PH+EpX/Dg59QONtuTtehN25vJKs8L5rob1T1Qp/1wYWc= =b3bm -----END PGP SIGNATURE----- Wed May 31 05:37:09 UTC 2023 I: Checking whether the package is not for us Wed May 31 05:37:09 UTC 2023 I: Starting 1st build on remote node jtx1c-armhf-rb.debian.net. Wed May 31 05:37:09 UTC 2023 I: Preparing to do remote build '1' on jtx1c-armhf-rb.debian.net. Wed May 31 05:42:25 UTC 2023 I: Deleting $TMPDIR on jtx1c-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue May 30 17:37:22 -12 2023 I: pbuilder-time-stamp: 1685511442 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 Sat Oct 8 02:02:29 2022 -12 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/1293/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='e755320c990e40ac98614ecfa15fa3f0' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1293' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Kuam1qcm/pbuilderrc_p9Uu --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Kuam1qcm/b1 --logfile b1/build.log genomethreader_1.7.3+dfsg-7.dsc' SUDO_GID='114' SUDO_UID='108' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux jtx1c 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash -rwxr-xr-x 1 root root 133220 Sep 20 2022 date -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd -rwxr-xr-x 1 root root 68104 Sep 20 2022 df -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 67548 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch -rwxr-xr-x 1 root root 67548 Sep 20 2022 true -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/1293/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-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 ... 19324 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 41.4 MB of archives. After unpacking 135 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf readline-common all 8.2-1.3 [69.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf openssl armhf 3.0.8-1 [1373 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf ca-certificates all 20230311 [153 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 11 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf rubygems-integration all 1.18 [6704 B] Get: 15 http://deb.debian.org/debian bookworm/main armhf rake all 13.0.6-3 [83.9 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf ruby-webrick all 1.8.1-1 [51.4 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf libruby armhf 1:3.1 [4968 B] Get: 20 http://deb.debian.org/debian bookworm/main armhf ruby-sdbm armhf 1.0.0-5+b1 [13.3 kB] Get: 21 http://deb.debian.org/debian bookworm/main armhf libbsd0 armhf 0.11.7-2 [113 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf libedit2 armhf 3.1-20221030-2 [77.0 kB] Get: 23 http://deb.debian.org/debian bookworm/main armhf libncurses6 armhf 6.4-4 [81.1 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf libyaml-0-2 armhf 0.2.5-1 [46.8 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf libruby3.1 armhf 3.1.2-7 [5065 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf ruby3.1 armhf 3.1.2-7 [663 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf ruby-rubygems all 3.3.15-2 [293 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf ruby armhf 1:3.1 [5868 B] Get: 29 http://deb.debian.org/debian bookworm/main armhf ruby-asciidoctor all 2.0.18-2 [211 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf asciidoctor all 2.0.18-2 [86.6 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 34 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 35 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 41 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 42 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 43 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 44 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 45 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 46 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 47 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 48 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 51 http://deb.debian.org/debian bookworm/main armhf libexpat1 armhf 2.5.0-1 [79.9 kB] Get: 52 http://deb.debian.org/debian bookworm/main armhf libbrotli1 armhf 1.0.9-2+b6 [271 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf libpng16-16 armhf 1.6.39-2 [260 kB] Get: 54 http://deb.debian.org/debian bookworm/main armhf libfreetype6 armhf 2.12.1+dfsg-5 [332 kB] Get: 55 http://deb.debian.org/debian bookworm/main armhf fonts-dejavu-core all 2.37-6 [1068 kB] Get: 56 http://deb.debian.org/debian bookworm/main armhf fontconfig-config armhf 2.14.1-4 [315 kB] Get: 57 http://deb.debian.org/debian bookworm/main armhf libfontconfig1 armhf 2.14.1-4 [368 kB] Get: 58 http://deb.debian.org/debian bookworm/main armhf fontconfig armhf 2.14.1-4 [448 kB] Get: 59 http://deb.debian.org/debian bookworm/main armhf libpixman-1-0 armhf 0.42.2-1 [465 kB] Get: 60 http://deb.debian.org/debian bookworm/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB] Get: 61 http://deb.debian.org/debian bookworm/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 62 http://deb.debian.org/debian bookworm/main armhf libxcb1 armhf 1.15-1 [140 kB] Get: 63 http://deb.debian.org/debian bookworm/main armhf libx11-data all 2:1.8.4-2 [292 kB] Get: 64 http://deb.debian.org/debian bookworm/main armhf libx11-6 armhf 2:1.8.4-2 [695 kB] Get: 65 http://deb.debian.org/debian bookworm/main armhf libxcb-render0 armhf 1.15-1 [114 kB] Get: 66 http://deb.debian.org/debian bookworm/main armhf libxcb-shm0 armhf 1.15-1 [106 kB] Get: 67 http://deb.debian.org/debian bookworm/main armhf libxext6 armhf 2:1.3.4-1+b1 [47.8 kB] Get: 68 http://deb.debian.org/debian bookworm/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.1 kB] Get: 69 http://deb.debian.org/debian bookworm/main armhf libcairo2 armhf 1.16.0-7 [493 kB] Get: 70 http://deb.debian.org/debian bookworm/main armhf libglib2.0-0 armhf 2.74.6-2 [1227 kB] Get: 71 http://deb.debian.org/debian bookworm/main armhf liblua5.1-0 armhf 5.1.5-9 [88.3 kB] Get: 72 http://deb.debian.org/debian bookworm/main armhf libfribidi0 armhf 1.0.8-2.1 [63.1 kB] Get: 73 http://deb.debian.org/debian bookworm/main armhf libgraphite2-3 armhf 1.3.14-1 [70.5 kB] Get: 74 http://deb.debian.org/debian bookworm/main armhf libharfbuzz0b armhf 6.0.0+dfsg-3 [1893 kB] Get: 75 http://deb.debian.org/debian bookworm/main armhf libthai-data all 0.1.29-1 [176 kB] Get: 76 http://deb.debian.org/debian bookworm/main armhf libdatrie1 armhf 0.2.13-2+b1 [39.9 kB] Get: 77 http://deb.debian.org/debian bookworm/main armhf libthai0 armhf 0.1.29-1 [54.3 kB] Get: 78 http://deb.debian.org/debian bookworm/main armhf libpango-1.0-0 armhf 1.50.12+ds-1 [188 kB] Get: 79 http://deb.debian.org/debian bookworm/main armhf libpangoft2-1.0-0 armhf 1.50.12+ds-1 [40.9 kB] Get: 80 http://deb.debian.org/debian bookworm/main armhf libpangocairo-1.0-0 armhf 1.50.12+ds-1 [30.3 kB] Get: 81 http://deb.debian.org/debian bookworm/main armhf libtre5 armhf 0.8.0-7 [51.4 kB] Get: 82 http://deb.debian.org/debian bookworm/main armhf lua-filesystem armhf 1.8.0-3 [11.0 kB] Get: 83 http://deb.debian.org/debian bookworm/main armhf lua-lpeg armhf 1.0.2-2 [33.0 kB] Get: 84 http://deb.debian.org/debian bookworm/main armhf lua-md5 armhf 1.2+git+1+8d87fee-2 [11.5 kB] Get: 85 http://deb.debian.org/debian bookworm/main armhf genometools-common all 1.6.2+ds-3 [194 kB] Get: 86 http://deb.debian.org/debian bookworm/main armhf genometools armhf 1.6.2+ds-3 [1454 kB] Get: 87 http://deb.debian.org/debian bookworm/main armhf libbz2-dev armhf 1.0.8-5+b1 [28.1 kB] Get: 88 http://deb.debian.org/debian bookworm/main armhf libexpat1-dev armhf 2.5.0-1 [134 kB] Get: 89 http://deb.debian.org/debian bookworm/main armhf libgenometools0 armhf 1.6.2+ds-3 [1228 kB] Get: 90 http://deb.debian.org/debian bookworm/main armhf libgenometools0-dev armhf 1.6.2+ds-3 [94.5 kB] Get: 91 http://deb.debian.org/debian bookworm/main armhf libreadline8 armhf 8.2-1.3 [144 kB] Get: 92 http://deb.debian.org/debian bookworm/main armhf libncurses-dev armhf 6.4-4 [311 kB] Get: 93 http://deb.debian.org/debian bookworm/main armhf libreadline-dev armhf 8.2-1.3 [136 kB] Get: 94 http://deb.debian.org/debian bookworm/main armhf liblua5.1-0-dev armhf 5.1.5-9 [123 kB] Get: 95 http://deb.debian.org/debian bookworm/main armhf libtre-dev armhf 0.8.0-7 [28.0 kB] Get: 96 http://deb.debian.org/debian bookworm/main armhf libvmatch-dev armhf 2.3.1+dfsg-8 [602 kB] Get: 97 http://deb.debian.org/debian bookworm/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB] Fetched 41.4 MB in 4s (11.6 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 ... 19324 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_armhf.deb ... Unpacking openssl (3.0.8-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../03-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.44-3_armhf.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../05-libmagic1_1%3a5.44-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.44-3_armhf.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.21-12_armhf.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../08-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.22.4-10_armhf.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.38.1-5+b1_armhf.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../11-libpipeline1_1.5.7-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.11.2-2_armhf.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../13-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package rake. Preparing to unpack .../14-rake_13.0.6-3_all.deb ... Unpacking rake (13.0.6-3) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../15-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../16-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../17-ruby-xmlrpc_0.3.2-2_all.deb ... Unpacking ruby-xmlrpc (0.3.2-2) ... Selecting previously unselected package libruby:armhf. Preparing to unpack .../18-libruby_1%3a3.1_armhf.deb ... Unpacking libruby:armhf (1:3.1) ... Selecting previously unselected package ruby-sdbm:armhf. Preparing to unpack .../19-ruby-sdbm_1.0.0-5+b1_armhf.deb ... Unpacking ruby-sdbm:armhf (1.0.0-5+b1) ... Selecting previously unselected package libbsd0:armhf. Preparing to unpack .../20-libbsd0_0.11.7-2_armhf.deb ... Unpacking libbsd0:armhf (0.11.7-2) ... Selecting previously unselected package libedit2:armhf. Preparing to unpack .../21-libedit2_3.1-20221030-2_armhf.deb ... Unpacking libedit2:armhf (3.1-20221030-2) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../22-libncurses6_6.4-4_armhf.deb ... Unpacking libncurses6:armhf (6.4-4) ... Selecting previously unselected package libyaml-0-2:armhf. Preparing to unpack .../23-libyaml-0-2_0.2.5-1_armhf.deb ... Unpacking libyaml-0-2:armhf (0.2.5-1) ... Selecting previously unselected package libruby3.1:armhf. Preparing to unpack .../24-libruby3.1_3.1.2-7_armhf.deb ... Unpacking libruby3.1:armhf (3.1.2-7) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../25-ruby3.1_3.1.2-7_armhf.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_armhf.deb ... Unpacking ruby (1:3.1) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../28-ruby-asciidoctor_2.0.18-2_all.deb ... Unpacking ruby-asciidoctor (2.0.18-2) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../29-asciidoctor_2.0.18-2_all.deb ... Unpacking asciidoctor (2.0.18-2) ... Selecting previously unselected package m4. Preparing to unpack .../30-m4_1.4.19-3_armhf.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../31-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../32-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../33-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../34-autopoint_0.21-12_all.deb ... 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:armhf. Preparing to unpack .../42-libelf1_0.188-2.1_armhf.deb ... Unpacking libelf1:armhf (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../43-dwz_0.15-1_armhf.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../44-libicu72_72.1-3_armhf.deb ... Unpacking libicu72:armhf (72.1-3) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../45-libxml2_2.9.14+dfsg-1.2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../46-gettext_0.21-12_armhf.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:armhf. Preparing to unpack .../50-libexpat1_2.5.0-1_armhf.deb ... Unpacking libexpat1:armhf (2.5.0-1) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../51-libbrotli1_1.0.9-2+b6_armhf.deb ... Unpacking libbrotli1:armhf (1.0.9-2+b6) ... Selecting previously unselected package libpng16-16:armhf. Preparing to unpack .../52-libpng16-16_1.6.39-2_armhf.deb ... Unpacking libpng16-16:armhf (1.6.39-2) ... Selecting previously unselected package libfreetype6:armhf. Preparing to unpack .../53-libfreetype6_2.12.1+dfsg-5_armhf.deb ... Unpacking libfreetype6:armhf (2.12.1+dfsg-5) ... 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_armhf.deb ... Unpacking fontconfig-config (2.14.1-4) ... Selecting previously unselected package libfontconfig1:armhf. Preparing to unpack .../56-libfontconfig1_2.14.1-4_armhf.deb ... Unpacking libfontconfig1:armhf (2.14.1-4) ... Selecting previously unselected package fontconfig. Preparing to unpack .../57-fontconfig_2.14.1-4_armhf.deb ... Unpacking fontconfig (2.14.1-4) ... Selecting previously unselected package libpixman-1-0:armhf. Preparing to unpack .../58-libpixman-1-0_0.42.2-1_armhf.deb ... Unpacking libpixman-1-0:armhf (0.42.2-1) ... Selecting previously unselected package libxau6:armhf. Preparing to unpack .../59-libxau6_1%3a1.0.9-1_armhf.deb ... Unpacking libxau6:armhf (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:armhf. Preparing to unpack .../60-libxdmcp6_1%3a1.1.2-3_armhf.deb ... Unpacking libxdmcp6:armhf (1:1.1.2-3) ... Selecting previously unselected package libxcb1:armhf. Preparing to unpack .../61-libxcb1_1.15-1_armhf.deb ... Unpacking libxcb1:armhf (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:armhf. Preparing to unpack .../63-libx11-6_2%3a1.8.4-2_armhf.deb ... Unpacking libx11-6:armhf (2:1.8.4-2) ... Selecting previously unselected package libxcb-render0:armhf. Preparing to unpack .../64-libxcb-render0_1.15-1_armhf.deb ... Unpacking libxcb-render0:armhf (1.15-1) ... Selecting previously unselected package libxcb-shm0:armhf. Preparing to unpack .../65-libxcb-shm0_1.15-1_armhf.deb ... Unpacking libxcb-shm0:armhf (1.15-1) ... Selecting previously unselected package libxext6:armhf. Preparing to unpack .../66-libxext6_2%3a1.3.4-1+b1_armhf.deb ... Unpacking libxext6:armhf (2:1.3.4-1+b1) ... Selecting previously unselected package libxrender1:armhf. Preparing to unpack .../67-libxrender1_1%3a0.9.10-1.1_armhf.deb ... Unpacking libxrender1:armhf (1:0.9.10-1.1) ... Selecting previously unselected package libcairo2:armhf. Preparing to unpack .../68-libcairo2_1.16.0-7_armhf.deb ... Unpacking libcairo2:armhf (1.16.0-7) ... Selecting previously unselected package libglib2.0-0:armhf. Preparing to unpack .../69-libglib2.0-0_2.74.6-2_armhf.deb ... Unpacking libglib2.0-0:armhf (2.74.6-2) ... Selecting previously unselected package liblua5.1-0:armhf. Preparing to unpack .../70-liblua5.1-0_5.1.5-9_armhf.deb ... Unpacking liblua5.1-0:armhf (5.1.5-9) ... Selecting previously unselected package libfribidi0:armhf. Preparing to unpack .../71-libfribidi0_1.0.8-2.1_armhf.deb ... Unpacking libfribidi0:armhf (1.0.8-2.1) ... Selecting previously unselected package libgraphite2-3:armhf. Preparing to unpack .../72-libgraphite2-3_1.3.14-1_armhf.deb ... Unpacking libgraphite2-3:armhf (1.3.14-1) ... Selecting previously unselected package libharfbuzz0b:armhf. Preparing to unpack .../73-libharfbuzz0b_6.0.0+dfsg-3_armhf.deb ... Unpacking libharfbuzz0b:armhf (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:armhf. Preparing to unpack .../75-libdatrie1_0.2.13-2+b1_armhf.deb ... Unpacking libdatrie1:armhf (0.2.13-2+b1) ... Selecting previously unselected package libthai0:armhf. Preparing to unpack .../76-libthai0_0.1.29-1_armhf.deb ... Unpacking libthai0:armhf (0.1.29-1) ... Selecting previously unselected package libpango-1.0-0:armhf. Preparing to unpack .../77-libpango-1.0-0_1.50.12+ds-1_armhf.deb ... Unpacking libpango-1.0-0:armhf (1.50.12+ds-1) ... Selecting previously unselected package libpangoft2-1.0-0:armhf. Preparing to unpack .../78-libpangoft2-1.0-0_1.50.12+ds-1_armhf.deb ... Unpacking libpangoft2-1.0-0:armhf (1.50.12+ds-1) ... Selecting previously unselected package libpangocairo-1.0-0:armhf. Preparing to unpack .../79-libpangocairo-1.0-0_1.50.12+ds-1_armhf.deb ... Unpacking libpangocairo-1.0-0:armhf (1.50.12+ds-1) ... Selecting previously unselected package libtre5:armhf. Preparing to unpack .../80-libtre5_0.8.0-7_armhf.deb ... Unpacking libtre5:armhf (0.8.0-7) ... Selecting previously unselected package lua-filesystem:armhf. Preparing to unpack .../81-lua-filesystem_1.8.0-3_armhf.deb ... Unpacking lua-filesystem:armhf (1.8.0-3) ... Selecting previously unselected package lua-lpeg:armhf. 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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 I: Building the package I: Running cd /build/genomethreader-1.7.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-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 armhf 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=no 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=no 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=no 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" \ BSSMDIR=/build/genomethreader-1.7.3+dfsg/bin/bssm GTHDATADIR=/build/genomethreader-1.7.3+dfsg/gthdata/gth \ CCACHE_DISABLE=yes HOME=/nonexistent/first-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-dbgsym' in '../genomethreader-dbgsym_1.7.3+dfsg-7_armhf.deb'. dpkg-deb: building package 'genomethreader' in '../genomethreader_1.7.3+dfsg-7_armhf.deb'. dpkg-genbuildinfo --build=binary -O../genomethreader_1.7.3+dfsg-7_armhf.buildinfo dpkg-genchanges --build=binary -O../genomethreader_1.7.3+dfsg-7_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1293 and its subdirectories I: Current time: Tue May 30 17:41:16 -12 2023 I: pbuilder-time-stamp: 1685511676 Wed May 31 05:42:30 UTC 2023 I: 1st build successful. Starting 2nd build on remote node virt32c-armhf-rb.debian.net. Wed May 31 05:42:30 UTC 2023 I: Preparing to do remote build '2' on virt32c-armhf-rb.debian.net. Wed May 31 05:56:42 UTC 2023 I: Deleting $TMPDIR on virt32c-armhf-rb.debian.net. Wed May 31 05:56:47 UTC 2023 I: genomethreader_1.7.3+dfsg-7_armhf.changes: Format: 1.8 Date: Sat, 08 Oct 2022 13:52:00 +0000 Source: genomethreader Binary: genomethreader genomethreader-dbgsym Architecture: armhf Version: 1.7.3+dfsg-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: genomethreader - software tool to compute gene structure predictions Changes: genomethreader (1.7.3+dfsg-7) unstable; urgency=medium . * Fix watchfile to detect new versions on github * Bump Standards-Version. Checksums-Sha1: 5e9ca925b7bae105f6eb4433261125efcc4c0c31 1583616 genomethreader-dbgsym_1.7.3+dfsg-7_armhf.deb 21be6e9de864ce5f0a66072a3d742eeae7e1b14b 7022 genomethreader_1.7.3+dfsg-7_armhf.buildinfo b1bc7183b4dac477824cd5a32fe6797fea85d79d 1923928 genomethreader_1.7.3+dfsg-7_armhf.deb Checksums-Sha256: 0a982748e8742a996ddfc55ce424d676e1579fef766efe6025771718a650116b 1583616 genomethreader-dbgsym_1.7.3+dfsg-7_armhf.deb c998b52492c5d08d0810c60e9dbdbd9313ede872bc13f1c7ea45f0849169a0c9 7022 genomethreader_1.7.3+dfsg-7_armhf.buildinfo 17a756be7d564ce3cb1c62cc3105f7dee42e644c12d7b84c6a823fc89f0ebd17 1923928 genomethreader_1.7.3+dfsg-7_armhf.deb Files: b0b32bef3674f861f5988c23dc879324 1583616 debug optional genomethreader-dbgsym_1.7.3+dfsg-7_armhf.deb 91ab647f3d368753cfcbad0850f9375c 7022 science optional genomethreader_1.7.3+dfsg-7_armhf.buildinfo b4b2d54219a0ddf596cb597d498bbd87 1923928 science optional genomethreader_1.7.3+dfsg-7_armhf.deb Wed May 31 05:56:48 UTC 2023 I: diffoscope 242 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Kuam1qcm/genomethreader_1.7.3+dfsg-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Kuam1qcm/genomethreader_1.7.3+dfsg-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Kuam1qcm/genomethreader_1.7.3+dfsg-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Kuam1qcm/b1/genomethreader_1.7.3+dfsg-7_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.Kuam1qcm/b2/genomethreader_1.7.3+dfsg-7_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.346s) 0.346s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.052s) 0.052s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Wed May 31 05:56:49 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Wed May 31 05:56:49 UTC 2023 I: genomethreader from bookworm built successfully and reproducibly on armhf. Wed May 31 05:56:50 UTC 2023 I: Submitting .buildinfo files to external archives: Wed May 31 05:56:50 UTC 2023 I: Submitting 8.0K b1/genomethreader_1.7.3+dfsg-7_armhf.buildinfo.asc Wed May 31 05:56:51 UTC 2023 I: Submitting 8.0K b2/genomethreader_1.7.3+dfsg-7_armhf.buildinfo.asc Wed May 31 05:56:52 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed May 31 05:56:52 UTC 2023 I: Done submitting .buildinfo files. Wed May 31 05:56:52 UTC 2023 I: Removing signed genomethreader_1.7.3+dfsg-7_armhf.buildinfo.asc files: removed './b1/genomethreader_1.7.3+dfsg-7_armhf.buildinfo.asc' removed './b2/genomethreader_1.7.3+dfsg-7_armhf.buildinfo.asc'