Mon Jul 26 14:29:37 UTC 2021 I: starting to build genomethreader/bullseye/arm64 on jenkins on '2021-07-26 14:29' Mon Jul 26 14:29:37 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_15/44397/console.log Mon Jul 26 14:29:37 UTC 2021 I: Downloading source for bullseye/genomethreader=1.7.3+dfsg-5 --2021-07-26 14:29:37-- http://cdn-fastly.deb.debian.org/debian/pool/main/g/genomethreader/genomethreader_1.7.3+dfsg-5.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1902 (1.9K) Saving to: ‘genomethreader_1.7.3+dfsg-5.dsc’ 0K . 100% 123M=0s 2021-07-26 14:29:37 (123 MB/s) - ‘genomethreader_1.7.3+dfsg-5.dsc’ saved [1902/1902] Mon Jul 26 14:29:37 UTC 2021 I: genomethreader_1.7.3+dfsg-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: genomethreader Binary: genomethreader Architecture: any Version: 1.7.3+dfsg-5 Maintainer: Debian Med Packaging Team Uploaders: Sascha Steinbiss Homepage: http://genomethreader.org Standards-Version: 4.5.0 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 (>= 12), debhelper-compat (= 12), 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 b46eb0006ad36058176c8f8fa4a5de33b19d0025 13436 genomethreader_1.7.3+dfsg-5.debian.tar.xz Checksums-Sha256: d19808894b1c86312b51f1aeb6e11f5ba0dfc8dcf237bf08fc0615d26b0cf051 39993616 genomethreader_1.7.3+dfsg.orig.tar.xz f4ae49ed7f93ded46f76c8880467691badf2fd7bf6f4be26c05c5be92cb0d466 13436 genomethreader_1.7.3+dfsg-5.debian.tar.xz Files: 62eb8a06280490f22b646147f0e0f444 39993616 genomethreader_1.7.3+dfsg.orig.tar.xz b769b091d4e4ceea6a133e5f827defee 13436 genomethreader_1.7.3+dfsg-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEEhFH5F4Fy5+Lcc/eVUfhKj+zKfgkFAl4+zToACgkQUfhKj+zK fgm/JwgArWjw5m+q6Xneqfq+p3XHuyIOSbfXr7gMpMUw4xGAM+oRTlp5wRxZgSvX s72amkYLfjRv0AXTHlfoYGVtoW05eKyikDRFiCgU7iG22hWp9gyY8s9E7kbCVrxc EIXwvmVNndD8ykW6t6SpzcIoy2j7wXxGGAOEzRwIb0alh94rrCbltclHfkwsI7e8 Uuoo38CiOfvZ05zcE5AMgattPrW7BnXoCjxGnKWokm88+F0ei9lrt+sRarZBuTlu Qx2VAVMplsebbS2sA3g/5/MBtRvxc6o+ReTGNVEganMUo0xtGtokAdO/bWnTLXJg COIfXoQ0RNdhR47ARg8Bkc0JMqG4cA== =fVgI -----END PGP SIGNATURE----- Mon Jul 26 14:29:37 UTC 2021 I: Checking whether the package is not for us Mon Jul 26 14:29:37 UTC 2021 I: Starting 1st build on remote node codethink12-arm64.debian.net. Mon Jul 26 14:29:37 UTC 2021 I: Preparing to do remote build '1' on codethink12-arm64.debian.net. Mon Jul 26 14:34:14 UTC 2021 I: Deleting $TMPDIR on codethink12-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jul 26 02:29:46 -12 2021 I: pbuilder-time-stamp: 1627309786 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [genomethreader_1.7.3+dfsg-5.dsc] I: copying [./genomethreader_1.7.3+dfsg.orig.tar.xz] I: copying [./genomethreader_1.7.3+dfsg-5.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.IkVjrz2p/trustedkeys.kbx': General error gpgv: Signature made Sat Feb 8 03:01:14 2020 -12 gpgv: using RSA key 8451F9178172E7E2DC73F79551F84A8FECCA7E09 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./genomethreader_1.7.3+dfsg-5.dsc 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-5.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: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/5394/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='5394' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.DtTOOoSDm4/pbuilderrc_v8vN --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.DtTOOoSDm4/b1 --logfile b1/build.log genomethreader_1.7.3+dfsg-5.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink12-arm64 4.15.0-151-generic #157-Ubuntu SMP Fri Jul 9 21:03:48 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Jun 21 14:26 bash -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash -rwxr-xr-x 1 root root 101384 Sep 22 2020 date -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd -rwxr-xr-x 1 root root 89824 Sep 22 2020 df -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir -rwxr-xr-x 1 root root 76152 Feb 7 02:38 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 64856 Feb 7 02:38 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe -rwxr-xr-x 1 root root 93744 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln -rwxr-xr-x 1 root root 52720 Feb 7 2020 login -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls -rwxr-xr-x 1 root root 161960 Feb 7 02:38 lsblk -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 51368 Feb 7 02:38 more -rwsr-xr-x 1 root root 51360 Feb 7 02:38 mount -rwxr-xr-x 1 root root 14496 Feb 7 02:38 mountpoint -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Jun 21 14:26 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 24 21:25 sh -> dash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Feb 7 02:38 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 16 21:55 tar -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch -rwxr-xr-x 1 root root 31512 Sep 22 2020 true -rwxr-xr-x 1 root root 14264 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 30880 Feb 7 02:38 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 Feb 7 02:38 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew I: user script /srv/workspace/pbuilder/5394/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: arm64 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 (>= 12), debhelper-compat (= 12), 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 ... 19646 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 (>= 12); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 12); 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} libicu67{a} liblua5.1-0{a} liblua5.1-0-dev{a} libmagic-mgc{a} libmagic1{a} libmd0{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} libpth20{a} libreadline-dev{a} libreadline8{a} libruby2.7{a} libsigsegv2{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-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-rubygems{a} ruby-test-unit{a} ruby-xmlrpc{a} ruby2.7{a} rubygems-integration{a} sensible-utils{a} ucf{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, 101 newly installed, 0 to remove and 0 not upgraded. Need to get 39.2 MB of archives. After unpacking 136 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 openssl arm64 1.1.1k-1 [829 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 ca-certificates all 20210119 [158 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 ucf all 3.0043 [74.0 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 rubygems-integration all 1.18 [6704 B] Get: 17 http://deb.debian.org/debian bullseye/main arm64 rake all 13.0.3-1 [84.7 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 ruby-minitest all 5.13.0-1 [57.3 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 ruby-power-assert all 1.1.7-2 [11.5 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 ruby-test-unit all 3.3.9-1 [86.1 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 libmd0 arm64 1.0.3-3 [27.9 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 libbsd0 arm64 0.11.3-1 [106 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 libedit2 arm64 3.1-20191231-2+b1 [92.1 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 libyaml-0-2 arm64 0.2.2-1 [45.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 libruby2.7 arm64 2.7.4-1 [4031 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 ruby2.7 arm64 2.7.4-1 [747 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 ruby-rubygems all 3.2.5-2 [281 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 ruby arm64 1:2.7+2 [11.7 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 ruby-asciidoctor all 2.0.12-2 [206 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 asciidoctor all 2.0.12-2 [83.9 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 libpng16-16 arm64 1.6.37-3 [289 kB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 libfreetype6 arm64 2.10.4+dfsg-1 [393 kB] Get: 58 http://deb.debian.org/debian bullseye/main arm64 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 59 http://deb.debian.org/debian bullseye/main arm64 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 60 http://deb.debian.org/debian bullseye/main arm64 libfontconfig1 arm64 2.13.1-4.2 [344 kB] Get: 61 http://deb.debian.org/debian bullseye/main arm64 fontconfig arm64 2.13.1-4.2 [416 kB] Get: 62 http://deb.debian.org/debian bullseye/main arm64 libpixman-1-0 arm64 0.40.0-1 [444 kB] Get: 63 http://deb.debian.org/debian bullseye/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 64 http://deb.debian.org/debian bullseye/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 65 http://deb.debian.org/debian bullseye/main arm64 libxcb1 arm64 1.14-3 [138 kB] Get: 66 http://deb.debian.org/debian bullseye/main arm64 libx11-data all 2:1.7.1-1 [310 kB] Get: 67 http://deb.debian.org/debian bullseye/main arm64 libx11-6 arm64 2:1.7.1-1 [747 kB] Get: 68 http://deb.debian.org/debian bullseye/main arm64 libxcb-render0 arm64 1.14-3 [111 kB] Get: 69 http://deb.debian.org/debian bullseye/main arm64 libxcb-shm0 arm64 1.14-3 [101 kB] Get: 70 http://deb.debian.org/debian bullseye/main arm64 libxext6 arm64 2:1.3.3-1.1 [51.6 kB] Get: 71 http://deb.debian.org/debian bullseye/main arm64 libxrender1 arm64 1:0.9.10-1 [30.4 kB] Get: 72 http://deb.debian.org/debian bullseye/main arm64 libcairo2 arm64 1.16.0-5 [648 kB] Get: 73 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-0 arm64 2.66.8-1 [1286 kB] Get: 74 http://deb.debian.org/debian bullseye/main arm64 liblua5.1-0 arm64 5.1.5-8.1+b3 [99.5 kB] Get: 75 http://deb.debian.org/debian bullseye/main arm64 libfribidi0 arm64 1.0.8-2 [64.8 kB] Get: 76 http://deb.debian.org/debian bullseye/main arm64 libgraphite2-3 arm64 1.3.14-1 [75.6 kB] Get: 77 http://deb.debian.org/debian bullseye/main arm64 libharfbuzz0b arm64 2.7.4-1 [1445 kB] Get: 78 http://deb.debian.org/debian bullseye/main arm64 libthai-data all 0.1.28-3 [170 kB] Get: 79 http://deb.debian.org/debian bullseye/main arm64 libdatrie1 arm64 0.2.13-1 [42.1 kB] Get: 80 http://deb.debian.org/debian bullseye/main arm64 libthai0 arm64 0.1.28-3 [53.0 kB] Get: 81 http://deb.debian.org/debian bullseye/main arm64 libpango-1.0-0 arm64 1.46.2-3 [183 kB] Get: 82 http://deb.debian.org/debian bullseye/main arm64 libpangoft2-1.0-0 arm64 1.46.2-3 [59.4 kB] Get: 83 http://deb.debian.org/debian bullseye/main arm64 libpangocairo-1.0-0 arm64 1.46.2-3 [48.6 kB] Get: 84 http://deb.debian.org/debian bullseye/main arm64 libtre5 arm64 0.8.0-6+b1 [54.6 kB] Get: 85 http://deb.debian.org/debian bullseye/main arm64 lua-filesystem arm64 1.8.0-1 [13.1 kB] Get: 86 http://deb.debian.org/debian bullseye/main arm64 lua-lpeg arm64 1.0.2-1 [31.7 kB] Get: 87 http://deb.debian.org/debian bullseye/main arm64 lua-md5 arm64 1.2+git+1+8d87fee-1.1 [12.7 kB] Get: 88 http://deb.debian.org/debian bullseye/main arm64 libpth20 arm64 2.0.7-22 [51.6 kB] Get: 89 http://deb.debian.org/debian bullseye/main arm64 genometools-common all 1.6.1+ds-3 [197 kB] Get: 90 http://deb.debian.org/debian bullseye/main arm64 genometools arm64 1.6.1+ds-3 [1399 kB] Get: 91 http://deb.debian.org/debian bullseye/main arm64 libbz2-dev arm64 1.0.8-4 [31.5 kB] Get: 92 http://deb.debian.org/debian bullseye/main arm64 libexpat1-dev arm64 2.2.10-2 [126 kB] Get: 93 http://deb.debian.org/debian bullseye/main arm64 libgenometools0 arm64 1.6.1+ds-3 [1177 kB] Get: 94 http://deb.debian.org/debian bullseye/main arm64 libgenometools0-dev arm64 1.6.1+ds-3 [97.1 kB] Get: 95 http://deb.debian.org/debian bullseye/main arm64 libncurses6 arm64 6.2+20201114-2 [93.2 kB] Get: 96 http://deb.debian.org/debian bullseye/main arm64 libncurses-dev arm64 6.2+20201114-2 [335 kB] Get: 97 http://deb.debian.org/debian bullseye/main arm64 libreadline-dev arm64 8.1-1 [153 kB] Get: 98 http://deb.debian.org/debian bullseye/main arm64 liblua5.1-0-dev arm64 5.1.5-8.1+b3 [126 kB] Get: 99 http://deb.debian.org/debian bullseye/main arm64 libtre-dev arm64 0.8.0-6+b1 [29.9 kB] Get: 100 http://deb.debian.org/debian bullseye/main arm64 libvmatch-dev arm64 2.3.1+dfsg-6 [638 kB] Get: 101 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Fetched 39.2 MB in 1s (28.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19646 files and directories currently installed.) Preparing to unpack .../000-bsdextrautils_2.36.1-7_arm64.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../001-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../002-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../003-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../004-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../005-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../006-libreadline8_8.1-1_arm64.deb ... Unpacking libreadline8:arm64 (8.1-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../007-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package openssl. Preparing to unpack .../008-openssl_1.1.1k-1_arm64.deb ... Unpacking openssl (1.1.1k-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../009-ca-certificates_20210119_all.deb ... Unpacking ca-certificates (20210119) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../010-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../011-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../012-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../013-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package ucf. Preparing to unpack .../014-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../015-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package rake. Preparing to unpack .../016-rake_13.0.3-1_all.deb ... Unpacking rake (13.0.3-1) ... Selecting previously unselected package ruby-minitest. Preparing to unpack .../017-ruby-minitest_5.13.0-1_all.deb ... Unpacking ruby-minitest (5.13.0-1) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../018-ruby-net-telnet_0.1.1-2_all.deb ... Unpacking ruby-net-telnet (0.1.1-2) ... Selecting previously unselected package ruby-power-assert. Preparing to unpack .../019-ruby-power-assert_1.1.7-2_all.deb ... Unpacking ruby-power-assert (1.1.7-2) ... Selecting previously unselected package ruby-test-unit. Preparing to unpack .../020-ruby-test-unit_3.3.9-1_all.deb ... Unpacking ruby-test-unit (3.3.9-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../021-ruby-xmlrpc_0.3.0-2_all.deb ... Unpacking ruby-xmlrpc (0.3.0-2) ... Selecting previously unselected package libmd0:arm64. Preparing to unpack .../022-libmd0_1.0.3-3_arm64.deb ... Unpacking libmd0:arm64 (1.0.3-3) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../023-libbsd0_0.11.3-1_arm64.deb ... Unpacking libbsd0:arm64 (0.11.3-1) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../024-libedit2_3.1-20191231-2+b1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20191231-2+b1) ... Selecting previously unselected package libyaml-0-2:arm64. Preparing to unpack .../025-libyaml-0-2_0.2.2-1_arm64.deb ... Unpacking libyaml-0-2:arm64 (0.2.2-1) ... Selecting previously unselected package libruby2.7:arm64. Preparing to unpack .../026-libruby2.7_2.7.4-1_arm64.deb ... Unpacking libruby2.7:arm64 (2.7.4-1) ... Selecting previously unselected package ruby2.7. Preparing to unpack .../027-ruby2.7_2.7.4-1_arm64.deb ... Unpacking ruby2.7 (2.7.4-1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../028-ruby-rubygems_3.2.5-2_all.deb ... Unpacking ruby-rubygems (3.2.5-2) ... Selecting previously unselected package ruby. Preparing to unpack .../029-ruby_1%3a2.7+2_arm64.deb ... Unpacking ruby (1:2.7+2) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../030-ruby-asciidoctor_2.0.12-2_all.deb ... Unpacking ruby-asciidoctor (2.0.12-2) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../031-asciidoctor_2.0.12-2_all.deb ... Unpacking asciidoctor (2.0.12-2) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../032-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../033-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../034-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../035-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../036-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../037-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../038-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../039-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../040-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../041-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 .../042-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../043-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../044-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../045-libelf1_0.183-1_arm64.deb ... Unpacking libelf1:arm64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../046-dwz_0.13+20210201-1_arm64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:arm64. Preparing to unpack .../047-libicu67_67.1-7_arm64.deb ... Unpacking libicu67:arm64 (67.1-7) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../048-libxml2_2.9.10+dfsg-6.7_arm64.deb ... Unpacking libxml2:arm64 (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../049-gettext_0.21-4_arm64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../050-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../051-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../052-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../053-libexpat1_2.2.10-2_arm64.deb ... Unpacking libexpat1:arm64 (2.2.10-2) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../054-libbrotli1_1.0.9-2+b2_arm64.deb ... Unpacking libbrotli1:arm64 (1.0.9-2+b2) ... Selecting previously unselected package libpng16-16:arm64. Preparing to unpack .../055-libpng16-16_1.6.37-3_arm64.deb ... Unpacking libpng16-16:arm64 (1.6.37-3) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../056-libfreetype6_2.10.4+dfsg-1_arm64.deb ... Unpacking libfreetype6:arm64 (2.10.4+dfsg-1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../057-fonts-dejavu-core_2.37-2_all.deb ... Unpacking fonts-dejavu-core (2.37-2) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../058-fontconfig-config_2.13.1-4.2_all.deb ... Unpacking fontconfig-config (2.13.1-4.2) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../059-libfontconfig1_2.13.1-4.2_arm64.deb ... Unpacking libfontconfig1:arm64 (2.13.1-4.2) ... Selecting previously unselected package fontconfig. Preparing to unpack .../060-fontconfig_2.13.1-4.2_arm64.deb ... Unpacking fontconfig (2.13.1-4.2) ... Selecting previously unselected package libpixman-1-0:arm64. Preparing to unpack .../061-libpixman-1-0_0.40.0-1_arm64.deb ... Unpacking libpixman-1-0:arm64 (0.40.0-1) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../062-libxau6_1%3a1.0.9-1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../063-libxdmcp6_1%3a1.1.2-3_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../064-libxcb1_1.14-3_arm64.deb ... Unpacking libxcb1:arm64 (1.14-3) ... Selecting previously unselected package libx11-data. Preparing to unpack .../065-libx11-data_2%3a1.7.1-1_all.deb ... Unpacking libx11-data (2:1.7.1-1) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../066-libx11-6_2%3a1.7.1-1_arm64.deb ... Unpacking libx11-6:arm64 (2:1.7.1-1) ... Selecting previously unselected package libxcb-render0:arm64. Preparing to unpack .../067-libxcb-render0_1.14-3_arm64.deb ... Unpacking libxcb-render0:arm64 (1.14-3) ... Selecting previously unselected package libxcb-shm0:arm64. Preparing to unpack .../068-libxcb-shm0_1.14-3_arm64.deb ... Unpacking libxcb-shm0:arm64 (1.14-3) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../069-libxext6_2%3a1.3.3-1.1_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.3-1.1) ... Selecting previously unselected package libxrender1:arm64. Preparing to unpack .../070-libxrender1_1%3a0.9.10-1_arm64.deb ... Unpacking libxrender1:arm64 (1:0.9.10-1) ... Selecting previously unselected package libcairo2:arm64. Preparing to unpack .../071-libcairo2_1.16.0-5_arm64.deb ... Unpacking libcairo2:arm64 (1.16.0-5) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../072-libglib2.0-0_2.66.8-1_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.66.8-1) ... Selecting previously unselected package liblua5.1-0:arm64. Preparing to unpack .../073-liblua5.1-0_5.1.5-8.1+b3_arm64.deb ... Unpacking liblua5.1-0:arm64 (5.1.5-8.1+b3) ... Selecting previously unselected package libfribidi0:arm64. Preparing to unpack .../074-libfribidi0_1.0.8-2_arm64.deb ... Unpacking libfribidi0:arm64 (1.0.8-2) ... Selecting previously unselected package libgraphite2-3:arm64. Preparing to unpack .../075-libgraphite2-3_1.3.14-1_arm64.deb ... Unpacking libgraphite2-3:arm64 (1.3.14-1) ... Selecting previously unselected package libharfbuzz0b:arm64. Preparing to unpack .../076-libharfbuzz0b_2.7.4-1_arm64.deb ... Unpacking libharfbuzz0b:arm64 (2.7.4-1) ... Selecting previously unselected package libthai-data. Preparing to unpack .../077-libthai-data_0.1.28-3_all.deb ... Unpacking libthai-data (0.1.28-3) ... Selecting previously unselected package libdatrie1:arm64. Preparing to unpack .../078-libdatrie1_0.2.13-1_arm64.deb ... Unpacking libdatrie1:arm64 (0.2.13-1) ... Selecting previously unselected package libthai0:arm64. Preparing to unpack .../079-libthai0_0.1.28-3_arm64.deb ... Unpacking libthai0:arm64 (0.1.28-3) ... Selecting previously unselected package libpango-1.0-0:arm64. Preparing to unpack .../080-libpango-1.0-0_1.46.2-3_arm64.deb ... Unpacking libpango-1.0-0:arm64 (1.46.2-3) ... Selecting previously unselected package libpangoft2-1.0-0:arm64. Preparing to unpack .../081-libpangoft2-1.0-0_1.46.2-3_arm64.deb ... Unpacking libpangoft2-1.0-0:arm64 (1.46.2-3) ... 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Setting up ruby-asciidoctor (2.0.12-2) ... Setting up asciidoctor (2.0.12-2) ... Processing triggers for libc-bin (2.31-13) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 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-5_source.changes dpkg-buildpackage: info: source package genomethreader dpkg-buildpackage: info: source version 1.7.3+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot 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 build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/genomethreader-1.7.3+dfsg' make licensemanager=no opt=yes 64bit=yes make[2]: Entering directory '/build/genomethreader-1.7.3+dfsg' [create obj/gth_config.h] [compile findfile.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/findfile.c -o obj/src/libgenomethreader/findfile.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/build/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/align_dna.c -o obj/src/align_dna.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/align_dna.o [link align_dna] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/align_dna.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/align_dna make[2]: Leaving directory '/build/genomethreader-1.7.3+dfsg' make licensemanager=no opt=yes 64bit=yes train make[2]: Entering directory '/build/genomethreader-1.7.3+dfsg' [train arabidopsis.bssm] [train rice.bssm] [train maize.bssm] [train medicago.bssm] [write old BSSMs] [copy gthdata stuff to bin] make[2]: Leaving directory '/build/genomethreader-1.7.3+dfsg' make[1]: Leaving directory '/build/genomethreader-1.7.3+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/genomethreader-1.7.3+dfsg' make licensemanager=no 64bit=yes test make[2]: Entering directory '/build/genomethreader-1.7.3+dfsg' cd testsuite && env -i GTH_MEM_BOOKKEEPING=on MAKE=make PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" \ 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 fakeroot debian/rules binary dh binary dh_testroot 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 dh_strip dh_makeshlibs dh_shlibdeps 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-6" >> 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-5_arm64.deb'. dpkg-deb: building package 'genomethreader' in '../genomethreader_1.7.3+dfsg-5_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../genomethreader_1.7.3+dfsg-5_arm64.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/5394 and its subdirectories I: Current time: Mon Jul 26 02:34:11 -12 2021 I: pbuilder-time-stamp: 1627310051 Mon Jul 26 14:34:15 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink13-arm64.debian.net. Mon Jul 26 14:34:15 UTC 2021 I: Preparing to do remote build '2' on codethink13-arm64.debian.net. Mon Jul 26 14:38:06 UTC 2021 I: Deleting $TMPDIR on codethink13-arm64.debian.net. Mon Jul 26 14:38:07 UTC 2021 I: genomethreader_1.7.3+dfsg-5_arm64.changes: Format: 1.8 Date: Sat, 08 Feb 2020 15:41:00 +0100 Source: genomethreader Binary: genomethreader genomethreader-dbgsym Architecture: arm64 Version: 1.7.3+dfsg-5 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-5) unstable; urgency=medium . * Add autopkgtest. Checksums-Sha1: 5e50bd9e47d1c452e4e5e7a148a4a098f95494b7 1580364 genomethreader-dbgsym_1.7.3+dfsg-5_arm64.deb 80dc509d2caa1b93284f7f3dca4663cbbbd8abb2 6996 genomethreader_1.7.3+dfsg-5_arm64.buildinfo 3b2a4b9fcfa08bd018792d8a5f8841f64457ce8d 1958216 genomethreader_1.7.3+dfsg-5_arm64.deb Checksums-Sha256: 7d1fe835a0ad923ece35d25eeee7768bcd0b8a3852129f79fa191b2a92fe39e6 1580364 genomethreader-dbgsym_1.7.3+dfsg-5_arm64.deb 0e6aa679956189559fb82f97254b90dede742c3a023688fea71eb90d3bb7165c 6996 genomethreader_1.7.3+dfsg-5_arm64.buildinfo 18e7160953805ee2fc984f3f0fa5f51ba4efc12290956cb4ddca42b7b2b89b6f 1958216 genomethreader_1.7.3+dfsg-5_arm64.deb Files: 464a98f7f59a5aca1ede998a53d1d678 1580364 debug optional genomethreader-dbgsym_1.7.3+dfsg-5_arm64.deb 7e95810e9d455b852264798270f05b19 6996 science optional genomethreader_1.7.3+dfsg-5_arm64.buildinfo 6bedac9632e1ac0db46ce97756b12538 1958216 science optional genomethreader_1.7.3+dfsg-5_arm64.deb Mon Jul 26 14:38:08 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.DtTOOoSDm4/genomethreader_1.7.3+dfsg-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.DtTOOoSDm4/genomethreader_1.7.3+dfsg-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.DtTOOoSDm4/genomethreader_1.7.3+dfsg-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.DtTOOoSDm4/b1/genomethreader_1.7.3+dfsg-5_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.DtTOOoSDm4/b2/genomethreader_1.7.3+dfsg-5_arm64.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: 0.269s) 0.269s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.048s) 0.048s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Mon Jul 26 14:38:09 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Mon Jul 26 14:38:09 UTC 2021 I: genomethreader from bullseye built successfully and reproducibly on arm64. Mon Jul 26 14:38:10 UTC 2021 I: Submitting .buildinfo files to external archives: Mon Jul 26 14:38:10 UTC 2021 I: Submitting 8.0K b1/genomethreader_1.7.3+dfsg-5_arm64.buildinfo.asc Mon Jul 26 14:38:12 UTC 2021 I: Submitting 8.0K b2/genomethreader_1.7.3+dfsg-5_arm64.buildinfo.asc Mon Jul 26 14:38:13 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jul 26 14:38:13 UTC 2021 I: Done submitting .buildinfo files. Mon Jul 26 14:38:13 UTC 2021 I: Removing signed genomethreader_1.7.3+dfsg-5_arm64.buildinfo.asc files: removed './b1/genomethreader_1.7.3+dfsg-5_arm64.buildinfo.asc' removed './b2/genomethreader_1.7.3+dfsg-5_arm64.buildinfo.asc'