Running as unit: rb-build-amd64_34-36886.service ==================================================================================== Mon Nov 25 08:41:53 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_34) on jenkins, called using "infom02-amd64 infom01-amd64" as arguments. Mon Nov 25 08:41:53 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-lcd5ujwD" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Nov 25 08:41:54 UTC 2024 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Mon Nov 25 08:41:54 UTC 2024 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-8JNSvc' Mon Nov 25 08:41:54 UTC 2024 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Mon Nov 25 08:41:54 UTC 2024 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-uaHsuD' ok, let's check if genomethreader is building anywhere yet… ok, genomethreader is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of genomethreader in trixie on amd64 on jenkins now. 1st build will be done on infom02-amd64.debian.net. 2nd build will be done on infom01-amd64.debian.net. ============================================================================= Mon Nov 25 08:42:16 UTC 2024 I: starting to build genomethreader/trixie/amd64 on jenkins on '2024-11-25 08:41' Mon Nov 25 08:42:16 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_34/36886/console.log 1732524136 amd64 trixie genomethreader Mon Nov 25 08:42:16 UTC 2024 I: Downloading source for trixie/genomethreader=1.7.3+dfsg-10 --2024-11-25 08:42:16-- http://deb.debian.org/debian/pool/main/g/genomethreader/genomethreader_1.7.3%2bdfsg-10.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2236 (2.2K) [text/prs.lines.tag] Saving to: ‘genomethreader_1.7.3+dfsg-10.dsc’ 0K .. 100% 375M=0s 2024-11-25 08:42:16 (375 MB/s) - ‘genomethreader_1.7.3+dfsg-10.dsc’ saved [2236/2236] --2024-11-25 08:42:16-- http://deb.debian.org/debian/pool/main/g/genomethreader/genomethreader_1.7.3%2bdfsg-10.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2236 (2.2K) [text/prs.lines.tag] Saving to: ‘genomethreader_1.7.3+dfsg-10.dsc’ 0K .. 100% 375M=0s 2024-11-25 08:42:16 (375 MB/s) - ‘genomethreader_1.7.3+dfsg-10.dsc’ saved [2236/2236] Mon Nov 25 08:42:16 UTC 2024 I: genomethreader_1.7.3+dfsg-10.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: genomethreader Binary: genomethreader Architecture: any Version: 1.7.3+dfsg-10 Maintainer: Debian Med Packaging Team Uploaders: Sascha Steinbiss Homepage: https://genomethreader.org Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/genomethreader Vcs-Git: https://salsa.debian.org/med-team/genomethreader.git Testsuite: autopkgtest Testsuite-Triggers: genometools, ruby Build-Depends: debhelper-compat (= 13), genometools, libgenometools0-dev, 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 f890cd97e5199f865f5e5fcaebc7ad3042be82b4 14160 genomethreader_1.7.3+dfsg-10.debian.tar.xz Checksums-Sha256: d19808894b1c86312b51f1aeb6e11f5ba0dfc8dcf237bf08fc0615d26b0cf051 39993616 genomethreader_1.7.3+dfsg.orig.tar.xz 1969812375367ab0c159fe01244cd2ae79d1c1f3bb55bba365ea6f6eb8958664 14160 genomethreader_1.7.3+dfsg-10.debian.tar.xz Files: 62eb8a06280490f22b646147f0e0f444 39993616 genomethreader_1.7.3+dfsg.orig.tar.xz fd558cdc8a120fdbcdb95f32c005a27d 14160 genomethreader_1.7.3+dfsg-10.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmXaQBkRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHWCg/8CMbNR3lDVJwa3N92tciLcuyA9ud0myUJ g//50lobP7OhIcG5rtOcNlKVWW816bEbxebK9MCWrGvLVd2czzZLPFTevYH7yA0i CcxC7U4trLLVDE0bJRNSJLl4HZ18kl/LQal28H7MeZllEoY32ev6EsBUsntAPgLO PO9WWlpRZnvq+FV7jDJamiRojOeCUx486cjp2p9NZGEtRuwnmsK9WGsNuHa9YeXd ZWhNeFq7+P9ks4lmO18L1lr/FGE4DcwpvJSfC6BmjjP6NSE5nxYkv+iuZQrItX3l tas4DpLU4Ba9sD9Omtiq8FI96xf8yWvgCjzcBegeIf8OxESa6ZsQIuM0QV8Z6jC3 VFFUg4XDZEfIblqfRxWG0XvlOeGUjALXsfE0l/zA3yR0fFNXNAIqsXdEML+H3VCu f5VZ1Ej9930GHZzryKF9GnSqAMjtqXQpymlNn688z3EUs5fJcxOjxNBJMdwoLtMF k1iqzv9mOzjhIGl1kch7AxdhxXj0cjLrkjfq6Q7+BG6xnRWTvxO7T1I2vqL5aQuD eF85aR6Xkodj2IrihOtzONbsIXIJrqiWC72E06tjBYGfpqr2lXyFhEs1AXiBxBmV lLH7qXjbSV8X0RxxMioN7rO+3My3llDGov5srvTNdiD5mWZZFQxXPNOq/PF8aQWj KlvVBz/qVWk= =RHrF -----END PGP SIGNATURE----- Mon Nov 25 08:42:16 UTC 2024 I: Checking whether the package is not for us Mon Nov 25 08:42:16 UTC 2024 I: Starting 1st build on remote node infom02-amd64.debian.net. Mon Nov 25 08:42:16 UTC 2024 I: Preparing to do remote build '1' on infom02-amd64.debian.net. Mon Nov 25 08:42:16 UTC 2024 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Mon Nov 25 08:42:16 UTC 2024 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-cP8Xzl' ==================================================================================== Sun Dec 28 15:05:18 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom02-amd64, called using "1 genomethreader trixie /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ 1.7.3+dfsg-10" as arguments. Sun Dec 28 15:05:18 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-RfoBUxW7" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sun Dec 28 15:05:18 UTC 2025 I: Downloading source for trixie/genomethreader=1.7.3+dfsg-10 Reading package lists... NOTICE: 'genomethreader' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/genomethreader.git Please use: git clone https://salsa.debian.org/med-team/genomethreader.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 40.0 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main genomethreader 1.7.3+dfsg-10 (dsc) [2236 B] Get:2 http://deb.debian.org/debian trixie/main genomethreader 1.7.3+dfsg-10 (tar) [40.0 MB] Get:3 http://deb.debian.org/debian trixie/main genomethreader 1.7.3+dfsg-10 (diff) [14.2 kB] Fetched 40.0 MB in 0s (83.1 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'genomethreader' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/genomethreader.git Please use: git clone https://salsa.debian.org/med-team/genomethreader.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 40.0 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main genomethreader 1.7.3+dfsg-10 (dsc) [2236 B] Get:2 http://deb.debian.org/debian trixie/main genomethreader 1.7.3+dfsg-10 (tar) [40.0 MB] Get:3 http://deb.debian.org/debian trixie/main genomethreader 1.7.3+dfsg-10 (diff) [14.2 kB] Fetched 40.0 MB in 0s (83.1 MB/s) Download complete and in download only mode ============================================================================= Building genomethreader in trixie on amd64 on infom02-amd64 now. Date: Sun Dec 28 15:05:19 UTC 2025 Date UTC: Sun Dec 28 15:05:19 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Sun Dec 28 03:05:19 -12 2025 I: pbuilder-time-stamp: 1766934319 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [genomethreader_1.7.3+dfsg-10.dsc] I: copying [./genomethreader_1.7.3+dfsg.orig.tar.xz] I: copying [./genomethreader_1.7.3+dfsg-10.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Feb 24 19:14:33 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./genomethreader_1.7.3+dfsg-10.dsc: no acceptable signature found dpkg-source: info: extracting genomethreader in genomethreader-1.7.3+dfsg dpkg-source: info: unpacking genomethreader_1.7.3+dfsg.orig.tar.xz dpkg-source: info: unpacking genomethreader_1.7.3+dfsg-10.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-ftbfs-with-ruby-3.2.patch 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 dpkg-source: info: applying extend-clean.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2633570/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='e60271d4e60d4f26957210cd35f1f896' 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='2633570' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/pbuilderrc_tsg5 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/b1 --logfile b1/build.log genomethreader_1.7.3+dfsg-10.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom02-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2633570/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), genometools, libgenometools0-dev, 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 ... 19969 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on genometools; however: Package genometools is not installed. pbuilder-satisfydepends-dummy depends on libgenometools0-dev; 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} fonts-dejavu-mono{a} genometools{a} genometools-common{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libbz2-dev{a} libcairo2{a} libdatrie1{a} libdebhelper-perl{a} libedit2{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgenometools0-dev{a} libgenometools0t64{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libicu72{a} liblua5.1-0{a} liblua5.1-0-dev{a} libmagic-mgc{a} libmagic1t64{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} libpng16-16t64{a} libreadline-dev{a} libreadline8t64{a} libruby{a} libruby3.1t64{a} libthai-data{a} libthai0{a} libtool{a} libtre-dev{a} libtre5{a} libuchardet0{a} libvmatch-dev{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxrender1{a} libyaml-0-2{a} lua-filesystem{a} lua-lpeg{a} lua-md5{a} m4{a} man-db{a} openssl{a} po-debconf{a} rake{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl fonts-lato libarchive-cpio-perl libglib2.0-data libgpm2 libjs-jquery libltdl-dev libmail-sendmail-perl libtool-bin lynx pkg-config pkgconf shared-mime-info wget xdg-user-dirs zip 0 packages upgraded, 96 newly installed, 0 to remove and 0 not upgraded. Need to get 43.5 MB of archives. After unpacking 155 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 rubygems-integration all 1.18 [6704 B] Get: 15 http://deb.debian.org/debian trixie/main amd64 rake all 13.2.1-1 [65.2 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libruby amd64 1:3.1+nmu1 [4664 B] Get: 20 http://deb.debian.org/debian trixie/main amd64 ruby-sdbm amd64 1.0.0-5+b5 [15.6 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-1+b2 [52.7 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libruby3.1t64 amd64 3.1.2-8.4 [5411 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 ruby3.1 amd64 3.1.2-8.4 [664 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 ruby-rubygems all 3.4.20-1 [309 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 ruby amd64 1:3.1+nmu1 [5584 B] Get: 28 http://deb.debian.org/debian trixie/main amd64 ruby-asciidoctor all 2.0.23-1 [214 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 asciidoctor all 2.0.23-1 [88.7 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 41 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-2 [1501 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 liblua5.1-0 amd64 5.1.5-9+b3 [109 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [223 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [54.2 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [35.2 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libtre5 amd64 0.8.0-8 [60.5 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 lua-filesystem amd64 1.8.0-3+b2 [11.9 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 lua-lpeg amd64 1.0.2-2+b2 [37.6 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 lua-md5 amd64 1.2+git+1+8d87fee-2+b2 [13.7 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 genometools-common all 1.6.5+ds-2.2 [195 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 genometools amd64 1.6.5+ds-2.2 [1656 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libgenometools0t64 amd64 1.6.5+ds-2.2 [1420 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libgenometools0-dev amd64 1.6.5+ds-2.2 [95.2 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libncurses-dev amd64 6.5-2+b1 [351 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libreadline-dev amd64 8.2-5 [153 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 liblua5.1-0-dev amd64 5.1.5-9+b3 [132 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libtre-dev amd64 0.8.0-8 [35.4 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libvmatch-dev amd64 2.3.1+dfsg-9 [661 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 43.5 MB in 1s (33.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19969 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../02-openssl_3.3.2-2_amd64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../03-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../05-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../08-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.40.2-11_amd64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../11-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../13-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package rake. Preparing to unpack .../14-rake_13.2.1-1_all.deb ... Unpacking rake (13.2.1-1) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../15-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../16-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../17-ruby-xmlrpc_0.3.3-2_all.deb ... Unpacking ruby-xmlrpc (0.3.3-2) ... Selecting previously unselected package libruby:amd64. Preparing to unpack .../18-libruby_1%3a3.1+nmu1_amd64.deb ... Unpacking libruby:amd64 (1:3.1+nmu1) ... Selecting previously unselected package ruby-sdbm:amd64. Preparing to unpack .../19-ruby-sdbm_1.0.0-5+b5_amd64.deb ... Unpacking ruby-sdbm:amd64 (1.0.0-5+b5) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../20-libedit2_3.1-20240808-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20240808-1) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../21-libncurses6_6.5-2+b1_amd64.deb ... Unpacking libncurses6:amd64 (6.5-2+b1) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../22-libyaml-0-2_0.2.5-1+b2_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-1+b2) ... Selecting previously unselected package libruby3.1t64:amd64. Preparing to unpack .../23-libruby3.1t64_3.1.2-8.4_amd64.deb ... Unpacking libruby3.1t64:amd64 (3.1.2-8.4) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../24-ruby3.1_3.1.2-8.4_amd64.deb ... Unpacking ruby3.1 (3.1.2-8.4) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../25-ruby-rubygems_3.4.20-1_all.deb ... Unpacking ruby-rubygems (3.4.20-1) ... Selecting previously unselected package ruby. Preparing to unpack .../26-ruby_1%3a3.1+nmu1_amd64.deb ... Unpacking ruby (1:3.1+nmu1) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../27-ruby-asciidoctor_2.0.23-1_all.deb ... Unpacking ruby-asciidoctor (2.0.23-1) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../28-asciidoctor_2.0.23-1_all.deb ... Unpacking asciidoctor (2.0.23-1) ... Selecting previously unselected package m4. Preparing to unpack .../29-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../30-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../31-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../32-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../33-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../34-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../35-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../36-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../37-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../38-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../39-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../40-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../41-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../42-libicu72_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../43-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../44-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../45-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../46-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../47-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../48-libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../49-libbrotli1_1.1.0-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b6) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../50-libpng16-16t64_1.6.44-2_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.44-2) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../51-libfreetype6_2.13.3+dfsg-1_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../52-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../53-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../54-fontconfig-config_2.15.0-1.1+b1_amd64.deb ... Unpacking fontconfig-config (2.15.0-1.1+b1) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../55-libfontconfig1_2.15.0-1.1+b1_amd64.deb ... Unpacking libfontconfig1:amd64 (2.15.0-1.1+b1) ... Selecting previously unselected package fontconfig. Preparing to unpack .../56-fontconfig_2.15.0-1.1+b1_amd64.deb ... Unpacking fontconfig (2.15.0-1.1+b1) ... Selecting previously unselected package libpixman-1-0:amd64. Preparing to unpack .../57-libpixman-1-0_0.44.0-3_amd64.deb ... Unpacking libpixman-1-0:amd64 (0.44.0-3) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../58-libxau6_1%3a1.0.11-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../59-libxdmcp6_1%3a1.1.5-1_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.5-1) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../60-libxcb1_1.17.0-2+b1_amd64.deb ... Unpacking libxcb1:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../61-libx11-data_2%3a1.8.10-2_all.deb ... Unpacking libx11-data (2:1.8.10-2) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../62-libx11-6_2%3a1.8.10-2_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.10-2) ... Selecting previously unselected package libxcb-render0:amd64. Preparing to unpack .../63-libxcb-render0_1.17.0-2+b1_amd64.deb ... Unpacking libxcb-render0:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-shm0:amd64. Preparing to unpack .../64-libxcb-shm0_1.17.0-2+b1_amd64.deb ... Unpacking libxcb-shm0:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../65-libxext6_2%3a1.3.4-1+b2_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1+b2) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../66-libxrender1_1%3a0.9.10-1.1+b2_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.10-1.1+b2) ... Selecting previously unselected package libcairo2:amd64. Preparing to unpack .../67-libcairo2_1.18.2-2_amd64.deb ... Unpacking libcairo2:amd64 (1.18.2-2) ... Selecting previously unselected package libglib2.0-0t64:amd64. Preparing to unpack .../68-libglib2.0-0t64_2.82.2-2_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.82.2-2) ... Selecting previously unselected package liblua5.1-0:amd64. Preparing to unpack .../69-liblua5.1-0_5.1.5-9+b3_amd64.deb ... Unpacking liblua5.1-0:amd64 (5.1.5-9+b3) ... Selecting previously unselected package libfribidi0:amd64. Preparing to unpack .../70-libfribidi0_1.0.15-1_amd64.deb ... Unpacking libfribidi0:amd64 (1.0.15-1) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../71-libgraphite2-3_1.3.14-2+b1_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.14-2+b1) ... Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../72-libharfbuzz0b_10.0.1-1_amd64.deb ... Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... Selecting previously unselected package libthai-data. Preparing to unpack .../73-libthai-data_0.1.29-2_all.deb ... Unpacking libthai-data (0.1.29-2) ... Selecting previously unselected package libdatrie1:amd64. Preparing to unpack .../74-libdatrie1_0.2.13-3+b1_amd64.deb ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libncurses-dev:amd64. Preparing to unpack .../90-libncurses-dev_6.5-2+b1_amd64.deb ... Unpacking libncurses-dev:amd64 (6.5-2+b1) ... Selecting previously unselected package libreadline-dev:amd64. Preparing to unpack .../91-libreadline-dev_8.2-5_amd64.deb ... Unpacking libreadline-dev:amd64 (8.2-5) ... Selecting previously unselected package liblua5.1-0-dev:amd64. 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Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:amd64 (1.54.0+ds-3) ... Setting up rubygems-integration (1.18) ... Setting up libreadline-dev:amd64 (8.2-5) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.2-2) ... Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... Setting up liblua5.1-0-dev:amd64 (5.1.5-9+b3) ... Setting up debhelper (13.20) ... Setting up genometools-common (1.6.5+ds-2.2) ... Setting up libgenometools0t64 (1.6.5+ds-2.2) ... Setting up genometools (1.6.5+ds-2.2) ... Setting up libgenometools0-dev (1.6.5+ds-2.2) ... Setting up libruby:amd64 (1:3.1+nmu1) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b5) ... Setting up libruby3.1t64:amd64 (3.1.2-8.4) ... Setting up ruby3.1 (3.1.2-8.4) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/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-10_source.changes dpkg-buildpackage: info: source package genomethreader dpkg-buildpackage: info: source version 1.7.3+dfsg-10 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' dh_clean make licensemanager=no opt=yes 64bit=yes cleanup make[2]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' rm -rf obj lib rm -rf testsuite/stest_testsuite testsuite/stest_stest_tests rm -rf bin find gthdata -name '*.des' | xargs rm -f find gthdata -name '*.esq' | xargs rm -f find gthdata -name '*.md5' | xargs rm -f find gthdata -name '*.ois' | xargs rm -f find gthdata -name '*.sds' | xargs rm -f find gthdata -name '*.suf' | xargs rm -f find gthdata -name '*.bck' | xargs rm -f find gthdata -name '*.llv' | xargs rm -f find gthdata -name '*.bwt' | xargs rm -f find gthdata -name '*.tis' | xargs rm -f find gthdata -name '*.ssp' | xargs rm -f find gthdata -name '*.lcp' | xargs rm -f find gthdata -name '*.sti1' | xargs rm -f find testdata -name '*.des' | xargs rm -f find testdata -name '*.esq' | xargs rm -f find testdata -name '*.md5' | xargs rm -f find testdata -name '*.ois' | xargs rm -f find testdata -name '*.sds' | xargs rm -f find testdata -name '*.suf' | xargs rm -f find testdata -name '*.bck' | xargs rm -f find testdata -name '*.llv' | xargs rm -f find testdata -name '*.bwt' | xargs rm -f find testdata -name '*.tis' | xargs rm -f find testdata -name '*.ssp' | xargs rm -f find testdata -name '*.lcp' | xargs rm -f find testdata -name '*.sti1' | xargs rm -f find testdata -name '*.al1' | xargs rm -f find testdata -name '*.prj' | xargs rm -f find testdata -name '*.polya*' | xargs rm -f make[2]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' rm -rf bin/bssm debian/bssm bin/gthdata debian/gthdata rm -rf /build/reproducible-path/genomethreader-1.7.3+dfsg/debian/man rm -f debian/*substvars make[1]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' make licensemanager=no opt=yes 64bit=yes make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg' make licensemanager=no opt=yes 64bit=yes train make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg' make[1]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' make licensemanager=no 64bit=yes test make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/bin/bssm GTHDATADIR=/build/reproducible-path/genomethreader-1.7.3+dfsg/gthdata/gth \ CCACHE_DISABLE=yes HOME=/nonexistent/first-build GTHTESTDATADIR= \ ruby -I. testsuite.rb \ -testdata /build/reproducible-path/genomethreader-1.7.3+dfsg/testdata -bin /build/reproducible-path/genomethreader-1.7.3+dfsg/bin -cur /build/reproducible-path/genomethreader-1.7.3+dfsg \ -gtruby /build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg' make[1]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' mv bin/bssm debian/bssm mv bin/gthdata debian/gthdata dh_auto_install make[1]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' dh_install dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' mkdir -p /build/reproducible-path/genomethreader-1.7.3+dfsg/debian/man asciidoctor -a docdate='' -b manpage /build/reproducible-path/genomethreader-1.7.3+dfsg/debian/man_src/*.adoc cp /build/reproducible-path/genomethreader-1.7.3+dfsg/debian/man_src/*.? /build/reproducible-path/genomethreader-1.7.3+dfsg/debian/man dh_installman -- make[1]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' echo "libvmatch-dev:Version=2.3.1+dfsg-9" >> debian/genomethreader.substvars dh_gencontrol make[1]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' dh_md5sums dh_builddeb dpkg-deb: building package 'genomethreader' in '../genomethreader_1.7.3+dfsg-10_amd64.deb'. dpkg-deb: building package 'genomethreader-dbgsym' in '../genomethreader-dbgsym_1.7.3+dfsg-10_amd64.deb'. dpkg-genbuildinfo --build=binary -O../genomethreader_1.7.3+dfsg-10_amd64.buildinfo dpkg-genchanges --build=binary -O../genomethreader_1.7.3+dfsg-10_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/2633570 and its subdirectories I: Current time: Sun Dec 28 03:08:10 -12 2025 I: pbuilder-time-stamp: 1766934490 Sun Dec 28 15:08:10 UTC 2025 I: Signing ./b1/genomethreader_1.7.3+dfsg-10_amd64.buildinfo as genomethreader_1.7.3+dfsg-10_amd64.buildinfo.asc Sun Dec 28 15:08:10 UTC 2025 I: Signed ./b1/genomethreader_1.7.3+dfsg-10_amd64.buildinfo as ./b1/genomethreader_1.7.3+dfsg-10_amd64.buildinfo.asc Sun Dec 28 15:08:10 UTC 2025 - build #1 for genomethreader/trixie/amd64 on infom02-amd64 done. Starting cleanup. All cleanup done. Sun Dec 28 15:08:10 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-RfoBUxW7, removing. /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 25 08:45 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 25 08:42 b2 -rw-r--r-- 1 jenkins jenkins 2236 Feb 24 2024 genomethreader_1.7.3+dfsg-10.dsc -rw------- 1 jenkins jenkins 3415 Nov 25 08:42 rbuildlog.TBT0eI9 /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/b1: total 3948 -rw-r--r-- 1 jenkins jenkins 225956 Nov 25 08:45 build.log -rw-r--r-- 1 jenkins jenkins 1675876 Nov 25 08:45 genomethreader-dbgsym_1.7.3+dfsg-10_amd64.deb -rw-r--r-- 1 jenkins jenkins 14160 Nov 25 08:45 genomethreader_1.7.3+dfsg-10.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2236 Nov 25 08:45 genomethreader_1.7.3+dfsg-10.dsc -rw-r--r-- 1 jenkins jenkins 7166 Nov 25 08:45 genomethreader_1.7.3+dfsg-10_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 8048 Nov 25 08:45 genomethreader_1.7.3+dfsg-10_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1658 Nov 25 08:45 genomethreader_1.7.3+dfsg-10_amd64.changes -rw-r--r-- 1 jenkins jenkins 2085136 Nov 25 08:45 genomethreader_1.7.3+dfsg-10_amd64.deb -rw-r--r-- 1 jenkins jenkins 1491 Nov 25 08:45 genomethreader_1.7.3+dfsg-10_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/b2: total 0 Mon Nov 25 08:45:11 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Dec 28 03:05:19 -12 2025 I: pbuilder-time-stamp: 1766934319 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [genomethreader_1.7.3+dfsg-10.dsc] I: copying [./genomethreader_1.7.3+dfsg.orig.tar.xz] I: copying [./genomethreader_1.7.3+dfsg-10.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Feb 24 19:14:33 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./genomethreader_1.7.3+dfsg-10.dsc: no acceptable signature found dpkg-source: info: extracting genomethreader in genomethreader-1.7.3+dfsg dpkg-source: info: unpacking genomethreader_1.7.3+dfsg.orig.tar.xz dpkg-source: info: unpacking genomethreader_1.7.3+dfsg-10.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-ftbfs-with-ruby-3.2.patch 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 dpkg-source: info: applying extend-clean.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2633570/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='e60271d4e60d4f26957210cd35f1f896' 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='2633570' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/pbuilderrc_tsg5 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/b1 --logfile b1/build.log genomethreader_1.7.3+dfsg-10.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom02-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2633570/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), genometools, libgenometools0-dev, 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 ... 19969 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on genometools; however: Package genometools is not installed. pbuilder-satisfydepends-dummy depends on libgenometools0-dev; 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} fonts-dejavu-mono{a} genometools{a} genometools-common{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libbz2-dev{a} libcairo2{a} libdatrie1{a} libdebhelper-perl{a} libedit2{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgenometools0-dev{a} libgenometools0t64{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libicu72{a} liblua5.1-0{a} liblua5.1-0-dev{a} libmagic-mgc{a} libmagic1t64{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} libpng16-16t64{a} libreadline-dev{a} libreadline8t64{a} libruby{a} libruby3.1t64{a} libthai-data{a} libthai0{a} libtool{a} libtre-dev{a} libtre5{a} libuchardet0{a} libvmatch-dev{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxrender1{a} libyaml-0-2{a} lua-filesystem{a} lua-lpeg{a} lua-md5{a} m4{a} man-db{a} openssl{a} po-debconf{a} rake{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl fonts-lato libarchive-cpio-perl libglib2.0-data libgpm2 libjs-jquery libltdl-dev libmail-sendmail-perl libtool-bin lynx pkg-config pkgconf shared-mime-info wget xdg-user-dirs zip 0 packages upgraded, 96 newly installed, 0 to remove and 0 not upgraded. Need to get 43.5 MB of archives. After unpacking 155 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 rubygems-integration all 1.18 [6704 B] Get: 15 http://deb.debian.org/debian trixie/main amd64 rake all 13.2.1-1 [65.2 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libruby amd64 1:3.1+nmu1 [4664 B] Get: 20 http://deb.debian.org/debian trixie/main amd64 ruby-sdbm amd64 1.0.0-5+b5 [15.6 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-1+b2 [52.7 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libruby3.1t64 amd64 3.1.2-8.4 [5411 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 ruby3.1 amd64 3.1.2-8.4 [664 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 ruby-rubygems all 3.4.20-1 [309 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 ruby amd64 1:3.1+nmu1 [5584 B] Get: 28 http://deb.debian.org/debian trixie/main amd64 ruby-asciidoctor all 2.0.23-1 [214 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 asciidoctor all 2.0.23-1 [88.7 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 41 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-2 [1501 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 liblua5.1-0 amd64 5.1.5-9+b3 [109 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [223 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [54.2 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [35.2 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libtre5 amd64 0.8.0-8 [60.5 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 lua-filesystem amd64 1.8.0-3+b2 [11.9 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 lua-lpeg amd64 1.0.2-2+b2 [37.6 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 lua-md5 amd64 1.2+git+1+8d87fee-2+b2 [13.7 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 genometools-common all 1.6.5+ds-2.2 [195 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 genometools amd64 1.6.5+ds-2.2 [1656 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libgenometools0t64 amd64 1.6.5+ds-2.2 [1420 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libgenometools0-dev amd64 1.6.5+ds-2.2 [95.2 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libncurses-dev amd64 6.5-2+b1 [351 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libreadline-dev amd64 8.2-5 [153 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 liblua5.1-0-dev amd64 5.1.5-9+b3 [132 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libtre-dev amd64 0.8.0-8 [35.4 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libvmatch-dev amd64 2.3.1+dfsg-9 [661 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 43.5 MB in 1s (33.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19969 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../02-openssl_3.3.2-2_amd64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../03-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../05-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../08-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.40.2-11_amd64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../11-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../13-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package rake. Preparing to unpack .../14-rake_13.2.1-1_all.deb ... Unpacking rake (13.2.1-1) ... Selecting previously unselected package ruby-net-telnet. 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libncurses-dev:amd64. Preparing to unpack .../90-libncurses-dev_6.5-2+b1_amd64.deb ... Unpacking libncurses-dev:amd64 (6.5-2+b1) ... Selecting previously unselected package libreadline-dev:amd64. Preparing to unpack .../91-libreadline-dev_8.2-5_amd64.deb ... Unpacking libreadline-dev:amd64 (8.2-5) ... Selecting previously unselected package liblua5.1-0-dev:amd64. 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Setting up libtre5:amd64 (0.8.0-8) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libdatrie1:amd64 (0.2.13-3+b1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1+b2) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libedit2:amd64 (3.1-20240808-1) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libvmatch-dev (2.3.1+dfsg-9) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up lua-filesystem:amd64 (1.8.0-3+b2) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:amd64 (2.82.2-2) ... No schema files found: doing nothing. Setting up lua-md5:amd64 (1.2+git+1+8d87fee-2+b2) ... Setting up libexpat1-dev:amd64 (2.6.4-1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libncurses6:amd64 (6.5-2+b1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libfribidi0:amd64 (1.0.15-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.44-2) ... Setting up autopoint (0.22.5-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up autoconf (2.72-3) ... Setting up ruby-webrick (1.8.1-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up liblua5.1-0:amd64 (5.1.5-9+b3) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up libthai-data (0.1.29-2) ... Setting up openssl (3.3.2-2) ... Setting up readline-common (8.2-5) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libtre-dev (0.8.0-8) ... Setting up libncurses-dev:amd64 (6.5-2+b1) ... Setting up gettext (0.22.5-2) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b2) ... Setting up libtool (2.4.7-8) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libharfbuzz0b:amd64 (10.0.1-1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:amd64 (1.54.0+ds-3) ... Setting up rubygems-integration (1.18) ... Setting up libreadline-dev:amd64 (8.2-5) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.2-2) ... Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... Setting up liblua5.1-0-dev:amd64 (5.1.5-9+b3) ... Setting up debhelper (13.20) ... Setting up genometools-common (1.6.5+ds-2.2) ... Setting up libgenometools0t64 (1.6.5+ds-2.2) ... Setting up genometools (1.6.5+ds-2.2) ... Setting up libgenometools0-dev (1.6.5+ds-2.2) ... Setting up libruby:amd64 (1:3.1+nmu1) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b5) ... Setting up libruby3.1t64:amd64 (3.1.2-8.4) ... Setting up ruby3.1 (3.1.2-8.4) ... Setting up ruby (1:3.1+nmu1) ... Setting up ruby-asciidoctor (2.0.23-1) ... Setting up rake (13.2.1-1) ... Setting up asciidoctor (2.0.23-1) ... Setting up ruby-rubygems (3.4.20-1) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/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-10_source.changes dpkg-buildpackage: info: source package genomethreader dpkg-buildpackage: info: source version 1.7.3+dfsg-10 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' dh_clean make licensemanager=no opt=yes 64bit=yes cleanup make[2]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' rm -rf obj lib rm -rf testsuite/stest_testsuite testsuite/stest_stest_tests rm -rf bin find gthdata -name '*.des' | xargs rm -f find gthdata -name '*.esq' | xargs rm -f find gthdata -name '*.md5' | xargs rm -f find gthdata -name '*.ois' | xargs rm -f find gthdata -name '*.sds' | xargs rm -f find gthdata -name '*.suf' | xargs rm -f find gthdata -name '*.bck' | xargs rm -f find gthdata -name '*.llv' | xargs rm -f find gthdata -name '*.bwt' | xargs rm -f find gthdata -name '*.tis' | xargs rm -f find gthdata -name '*.ssp' | xargs rm -f find gthdata -name '*.lcp' | xargs rm -f find gthdata -name '*.sti1' | xargs rm -f find testdata -name '*.des' | xargs rm -f find testdata -name '*.esq' | xargs rm -f find testdata -name '*.md5' | xargs rm -f find testdata -name '*.ois' | xargs rm -f find testdata -name '*.sds' | xargs rm -f find testdata -name '*.suf' | xargs rm -f find testdata -name '*.bck' | xargs rm -f find testdata -name '*.llv' | xargs rm -f find testdata -name '*.bwt' | xargs rm -f find testdata -name '*.tis' | xargs rm -f find testdata -name '*.ssp' | xargs rm -f find testdata -name '*.lcp' | xargs rm -f find testdata -name '*.sti1' | xargs rm -f find testdata -name '*.al1' | xargs rm -f find testdata -name '*.prj' | xargs rm -f find testdata -name '*.polya*' | xargs rm -f make[2]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' rm -rf bin/bssm debian/bssm bin/gthdata debian/gthdata rm -rf /build/reproducible-path/genomethreader-1.7.3+dfsg/debian/man rm -f debian/*substvars make[1]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' make licensemanager=no opt=yes 64bit=yes make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg' make licensemanager=no opt=yes 64bit=yes train make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg' make[1]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' make licensemanager=no 64bit=yes test make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/bin/bssm GTHDATADIR=/build/reproducible-path/genomethreader-1.7.3+dfsg/gthdata/gth \ CCACHE_DISABLE=yes HOME=/nonexistent/first-build GTHTESTDATADIR= \ ruby -I. testsuite.rb \ -testdata /build/reproducible-path/genomethreader-1.7.3+dfsg/testdata -bin /build/reproducible-path/genomethreader-1.7.3+dfsg/bin -cur /build/reproducible-path/genomethreader-1.7.3+dfsg \ -gtruby /build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg' make[1]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' mv bin/bssm debian/bssm mv bin/gthdata debian/gthdata dh_auto_install make[1]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' dh_install dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' mkdir -p /build/reproducible-path/genomethreader-1.7.3+dfsg/debian/man asciidoctor -a docdate='' -b manpage /build/reproducible-path/genomethreader-1.7.3+dfsg/debian/man_src/*.adoc cp /build/reproducible-path/genomethreader-1.7.3+dfsg/debian/man_src/*.? /build/reproducible-path/genomethreader-1.7.3+dfsg/debian/man dh_installman -- make[1]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' echo "libvmatch-dev:Version=2.3.1+dfsg-9" >> debian/genomethreader.substvars dh_gencontrol make[1]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' dh_md5sums dh_builddeb dpkg-deb: building package 'genomethreader' in '../genomethreader_1.7.3+dfsg-10_amd64.deb'. dpkg-deb: building package 'genomethreader-dbgsym' in '../genomethreader-dbgsym_1.7.3+dfsg-10_amd64.deb'. dpkg-genbuildinfo --build=binary -O../genomethreader_1.7.3+dfsg-10_amd64.buildinfo dpkg-genchanges --build=binary -O../genomethreader_1.7.3+dfsg-10_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/2633570 and its subdirectories I: Current time: Sun Dec 28 03:08:10 -12 2025 I: pbuilder-time-stamp: 1766934490 Mon Nov 25 08:45:11 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom01-amd64.debian.net. Mon Nov 25 08:45:11 UTC 2024 I: Preparing to do remote build '2' on infom01-amd64.debian.net. Mon Nov 25 08:45:11 UTC 2024 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Mon Nov 25 08:45:11 UTC 2024 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-jgdVxo' ==================================================================================== Mon Nov 25 08:45:13 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom01-amd64, called using "2 genomethreader trixie /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ 1.7.3+dfsg-10" as arguments. Mon Nov 25 08:45:13 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-IPAyWKmb" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Nov 25 08:45:13 UTC 2024 I: Downloading source for trixie/genomethreader=1.7.3+dfsg-10 Reading package lists... NOTICE: 'genomethreader' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/genomethreader.git Please use: git clone https://salsa.debian.org/med-team/genomethreader.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 40.0 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main genomethreader 1.7.3+dfsg-10 (dsc) [2236 B] Get:2 http://deb.debian.org/debian trixie/main genomethreader 1.7.3+dfsg-10 (tar) [40.0 MB] Get:3 http://deb.debian.org/debian trixie/main genomethreader 1.7.3+dfsg-10 (diff) [14.2 kB] Fetched 40.0 MB in 0s (130 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'genomethreader' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/genomethreader.git Please use: git clone https://salsa.debian.org/med-team/genomethreader.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 40.0 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main genomethreader 1.7.3+dfsg-10 (dsc) [2236 B] Get:2 http://deb.debian.org/debian trixie/main genomethreader 1.7.3+dfsg-10 (tar) [40.0 MB] Get:3 http://deb.debian.org/debian trixie/main genomethreader 1.7.3+dfsg-10 (diff) [14.2 kB] Fetched 40.0 MB in 0s (130 MB/s) Download complete and in download only mode ============================================================================= Re-Building genomethreader in trixie on amd64 on infom01-amd64 now. Date: Mon Nov 25 08:45:13 UTC 2024 Date UTC: Mon Nov 25 08:45:13 UTC 2024 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/pbuilderrc_tPwO + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' genomethreader = debian-installer -o genomethreader = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' genomethreader = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/pbuilderrc_tPwO --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/b2 --logfile b2/build.log genomethreader_1.7.3+dfsg-10.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Mon Nov 25 22:45:13 +14 2024 I: pbuilder-time-stamp: 1732524313 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [genomethreader_1.7.3+dfsg-10.dsc] I: copying [./genomethreader_1.7.3+dfsg.orig.tar.xz] I: copying [./genomethreader_1.7.3+dfsg-10.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Feb 24 19:14:33 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./genomethreader_1.7.3+dfsg-10.dsc: no acceptable signature found dpkg-source: info: extracting genomethreader in genomethreader-1.7.3+dfsg dpkg-source: info: unpacking genomethreader_1.7.3+dfsg.orig.tar.xz dpkg-source: info: unpacking genomethreader_1.7.3+dfsg-10.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-ftbfs-with-ruby-3.2.patch 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 dpkg-source: info: applying extend-clean.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2632749/tmp/hooks/D01_modify_environment starting debug: Running on infom01-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Nov 25 08:45 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2632749/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2632749/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=9f219f2d53ed45db98b454dc0b1f4b68 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2632749 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/pbuilderrc_tPwO --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/b2 --logfile b2/build.log genomethreader_1.7.3+dfsg-10.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' I: uname -a Linux i-capture-the-hostname 6.1.0-28-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2632749/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), genometools, libgenometools0-dev, 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 ... 19969 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on genometools; however: Package genometools is not installed. pbuilder-satisfydepends-dummy depends on libgenometools0-dev; 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} fonts-dejavu-mono{a} genometools{a} genometools-common{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libbz2-dev{a} libcairo2{a} libdatrie1{a} libdebhelper-perl{a} libedit2{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgenometools0-dev{a} libgenometools0t64{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libicu72{a} liblua5.1-0{a} liblua5.1-0-dev{a} libmagic-mgc{a} libmagic1t64{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} libpng16-16t64{a} libreadline-dev{a} libreadline8t64{a} libruby{a} libruby3.1t64{a} libthai-data{a} libthai0{a} libtool{a} libtre-dev{a} libtre5{a} libuchardet0{a} libvmatch-dev{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxrender1{a} libyaml-0-2{a} lua-filesystem{a} lua-lpeg{a} lua-md5{a} m4{a} man-db{a} openssl{a} po-debconf{a} rake{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl fonts-lato libarchive-cpio-perl libglib2.0-data libgpm2 libjs-jquery libltdl-dev libmail-sendmail-perl libtool-bin lynx pkg-config pkgconf shared-mime-info wget xdg-user-dirs zip 0 packages upgraded, 96 newly installed, 0 to remove and 0 not upgraded. Need to get 43.5 MB of archives. After unpacking 155 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 rubygems-integration all 1.18 [6704 B] Get: 15 http://deb.debian.org/debian trixie/main amd64 rake all 13.2.1-1 [65.2 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libruby amd64 1:3.1+nmu1 [4664 B] Get: 20 http://deb.debian.org/debian trixie/main amd64 ruby-sdbm amd64 1.0.0-5+b5 [15.6 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-1+b2 [52.7 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libruby3.1t64 amd64 3.1.2-8.4 [5411 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 ruby3.1 amd64 3.1.2-8.4 [664 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 ruby-rubygems all 3.4.20-1 [309 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 ruby amd64 1:3.1+nmu1 [5584 B] Get: 28 http://deb.debian.org/debian trixie/main amd64 ruby-asciidoctor all 2.0.23-1 [214 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 asciidoctor all 2.0.23-1 [88.7 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 41 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-2 [1501 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 liblua5.1-0 amd64 5.1.5-9+b3 [109 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [223 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [54.2 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [35.2 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libtre5 amd64 0.8.0-8 [60.5 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 lua-filesystem amd64 1.8.0-3+b2 [11.9 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 lua-lpeg amd64 1.0.2-2+b2 [37.6 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 lua-md5 amd64 1.2+git+1+8d87fee-2+b2 [13.7 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 genometools-common all 1.6.5+ds-2.2 [195 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 genometools amd64 1.6.5+ds-2.2 [1656 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libgenometools0t64 amd64 1.6.5+ds-2.2 [1420 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libgenometools0-dev amd64 1.6.5+ds-2.2 [95.2 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libncurses-dev amd64 6.5-2+b1 [351 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libreadline-dev amd64 8.2-5 [153 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 liblua5.1-0-dev amd64 5.1.5-9+b3 [132 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libtre-dev amd64 0.8.0-8 [35.4 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libvmatch-dev amd64 2.3.1+dfsg-9 [661 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 43.5 MB in 1s (82.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19969 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../02-openssl_3.3.2-2_amd64.deb ... 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Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../40-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../41-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../42-libicu72_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../43-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../44-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../45-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../46-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../47-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../48-libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../49-libbrotli1_1.1.0-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b6) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../50-libpng16-16t64_1.6.44-2_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.44-2) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../51-libfreetype6_2.13.3+dfsg-1_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../52-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../53-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../54-fontconfig-config_2.15.0-1.1+b1_amd64.deb ... Unpacking fontconfig-config (2.15.0-1.1+b1) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../55-libfontconfig1_2.15.0-1.1+b1_amd64.deb ... Unpacking libfontconfig1:amd64 (2.15.0-1.1+b1) ... Selecting previously unselected package fontconfig. Preparing to unpack .../56-fontconfig_2.15.0-1.1+b1_amd64.deb ... Unpacking fontconfig (2.15.0-1.1+b1) ... Selecting previously unselected package libpixman-1-0:amd64. Preparing to unpack .../57-libpixman-1-0_0.44.0-3_amd64.deb ... Unpacking libpixman-1-0:amd64 (0.44.0-3) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../58-libxau6_1%3a1.0.11-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../59-libxdmcp6_1%3a1.1.5-1_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.5-1) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../60-libxcb1_1.17.0-2+b1_amd64.deb ... Unpacking libxcb1:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../61-libx11-data_2%3a1.8.10-2_all.deb ... Unpacking libx11-data (2:1.8.10-2) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../62-libx11-6_2%3a1.8.10-2_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.10-2) ... Selecting previously unselected package libxcb-render0:amd64. Preparing to unpack .../63-libxcb-render0_1.17.0-2+b1_amd64.deb ... Unpacking libxcb-render0:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-shm0:amd64. Preparing to unpack .../64-libxcb-shm0_1.17.0-2+b1_amd64.deb ... Unpacking libxcb-shm0:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../65-libxext6_2%3a1.3.4-1+b2_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1+b2) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../66-libxrender1_1%3a0.9.10-1.1+b2_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.10-1.1+b2) ... Selecting previously unselected package libcairo2:amd64. Preparing to unpack .../67-libcairo2_1.18.2-2_amd64.deb ... Unpacking libcairo2:amd64 (1.18.2-2) ... Selecting previously unselected package libglib2.0-0t64:amd64. Preparing to unpack .../68-libglib2.0-0t64_2.82.2-2_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.82.2-2) ... Selecting previously unselected package liblua5.1-0:amd64. Preparing to unpack .../69-liblua5.1-0_5.1.5-9+b3_amd64.deb ... Unpacking liblua5.1-0:amd64 (5.1.5-9+b3) ... Selecting previously unselected package libfribidi0:amd64. Preparing to unpack .../70-libfribidi0_1.0.15-1_amd64.deb ... Unpacking libfribidi0:amd64 (1.0.15-1) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../71-libgraphite2-3_1.3.14-2+b1_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.14-2+b1) ... Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../72-libharfbuzz0b_10.0.1-1_amd64.deb ... Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... Selecting previously unselected package libthai-data. Preparing to unpack .../73-libthai-data_0.1.29-2_all.deb ... Unpacking libthai-data (0.1.29-2) ... Selecting previously unselected package libdatrie1:amd64. Preparing to unpack .../74-libdatrie1_0.2.13-3+b1_amd64.deb ... Unpacking libdatrie1:amd64 (0.2.13-3+b1) ... Selecting previously unselected package libthai0:amd64. Preparing to unpack .../75-libthai0_0.1.29-2+b1_amd64.deb ... Unpacking libthai0:amd64 (0.1.29-2+b1) ... Selecting previously unselected package libpango-1.0-0:amd64. Preparing to unpack .../76-libpango-1.0-0_1.54.0+ds-3_amd64.deb ... Unpacking libpango-1.0-0:amd64 (1.54.0+ds-3) ... Selecting previously unselected package libpangoft2-1.0-0:amd64. Preparing to unpack .../77-libpangoft2-1.0-0_1.54.0+ds-3_amd64.deb ... Unpacking libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... Selecting previously unselected package libpangocairo-1.0-0:amd64. Preparing to unpack .../78-libpangocairo-1.0-0_1.54.0+ds-3_amd64.deb ... Unpacking libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... Selecting previously unselected package libtre5:amd64. Preparing to unpack .../79-libtre5_0.8.0-8_amd64.deb ... Unpacking libtre5:amd64 (0.8.0-8) ... Selecting previously unselected package lua-filesystem:amd64. Preparing to unpack .../80-lua-filesystem_1.8.0-3+b2_amd64.deb ... Unpacking lua-filesystem:amd64 (1.8.0-3+b2) ... Selecting previously unselected package lua-lpeg:amd64. Preparing to unpack .../81-lua-lpeg_1.0.2-2+b2_amd64.deb ... Unpacking lua-lpeg:amd64 (1.0.2-2+b2) ... Selecting previously unselected package lua-md5:amd64. Preparing to unpack .../82-lua-md5_1.2+git+1+8d87fee-2+b2_amd64.deb ... Unpacking lua-md5:amd64 (1.2+git+1+8d87fee-2+b2) ... Selecting previously unselected package genometools-common. Preparing to unpack .../83-genometools-common_1.6.5+ds-2.2_all.deb ... Unpacking genometools-common (1.6.5+ds-2.2) ... Selecting previously unselected package genometools. Preparing to unpack .../84-genometools_1.6.5+ds-2.2_amd64.deb ... Unpacking genometools (1.6.5+ds-2.2) ... Selecting previously unselected package libbz2-dev:amd64. Preparing to unpack .../85-libbz2-dev_1.0.8-6_amd64.deb ... Unpacking libbz2-dev:amd64 (1.0.8-6) ... Selecting previously unselected package libexpat1-dev:amd64. Preparing to unpack .../86-libexpat1-dev_2.6.4-1_amd64.deb ... Unpacking libexpat1-dev:amd64 (2.6.4-1) ... Selecting previously unselected package libgenometools0t64. Preparing to unpack .../87-libgenometools0t64_1.6.5+ds-2.2_amd64.deb ... Unpacking libgenometools0t64 (1.6.5+ds-2.2) ... Selecting previously unselected package libgenometools0-dev. Preparing to unpack .../88-libgenometools0-dev_1.6.5+ds-2.2_amd64.deb ... Unpacking libgenometools0-dev (1.6.5+ds-2.2) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../89-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libncurses-dev:amd64. Preparing to unpack .../90-libncurses-dev_6.5-2+b1_amd64.deb ... Unpacking libncurses-dev:amd64 (6.5-2+b1) ... Selecting previously unselected package libreadline-dev:amd64. Preparing to unpack .../91-libreadline-dev_8.2-5_amd64.deb ... Unpacking libreadline-dev:amd64 (8.2-5) ... Selecting previously unselected package liblua5.1-0-dev:amd64. 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Setting up libtre5:amd64 (0.8.0-8) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libdatrie1:amd64 (0.2.13-3+b1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1+b2) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libedit2:amd64 (3.1-20240808-1) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libvmatch-dev (2.3.1+dfsg-9) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up lua-filesystem:amd64 (1.8.0-3+b2) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:amd64 (2.82.2-2) ... No schema files found: doing nothing. Setting up lua-md5:amd64 (1.2+git+1+8d87fee-2+b2) ... 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Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libtre-dev (0.8.0-8) ... Setting up libncurses-dev:amd64 (6.5-2+b1) ... Setting up gettext (0.22.5-2) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b2) ... Setting up libtool (2.4.7-8) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libharfbuzz0b:amd64 (10.0.1-1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:amd64 (1.54.0+ds-3) ... Setting up rubygems-integration (1.18) ... Setting up libreadline-dev:amd64 (8.2-5) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.2-2) ... Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... Setting up liblua5.1-0-dev:amd64 (5.1.5-9+b3) ... Setting up debhelper (13.20) ... Setting up genometools-common (1.6.5+ds-2.2) ... Setting up libgenometools0t64 (1.6.5+ds-2.2) ... Setting up genometools (1.6.5+ds-2.2) ... Setting up libgenometools0-dev (1.6.5+ds-2.2) ... Setting up libruby:amd64 (1:3.1+nmu1) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b5) ... Setting up libruby3.1t64:amd64 (3.1.2-8.4) ... Setting up ruby3.1 (3.1.2-8.4) ... Setting up ruby (1:3.1+nmu1) ... Setting up ruby-asciidoctor (2.0.23-1) ... Setting up rake (13.2.1-1) ... Setting up asciidoctor (2.0.23-1) ... Setting up ruby-rubygems (3.4.20-1) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2632749/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2632749/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/genomethreader-1.7.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../genomethreader_1.7.3+dfsg-10_source.changes dpkg-buildpackage: info: source package genomethreader dpkg-buildpackage: info: source version 1.7.3+dfsg-10 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' dh_clean make licensemanager=no opt=yes 64bit=yes cleanup make[2]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' rm -rf obj lib rm -rf testsuite/stest_testsuite testsuite/stest_stest_tests rm -rf bin find gthdata -name '*.des' | xargs rm -f find gthdata -name '*.esq' | xargs rm -f find gthdata -name '*.md5' | xargs rm -f find gthdata -name '*.ois' | xargs rm -f find gthdata -name '*.sds' | xargs rm -f find gthdata -name '*.suf' | xargs rm -f find gthdata -name '*.bck' | xargs rm -f find gthdata -name '*.llv' | xargs rm -f find gthdata -name '*.bwt' | xargs rm -f find gthdata -name '*.tis' | xargs rm -f find gthdata -name '*.ssp' | xargs rm -f find gthdata -name '*.lcp' | xargs rm -f find gthdata -name '*.sti1' | xargs rm -f find testdata -name '*.des' | xargs rm -f find testdata -name '*.esq' | xargs rm -f find testdata -name '*.md5' | xargs rm -f find testdata -name '*.ois' | xargs rm -f find testdata -name '*.sds' | xargs rm -f find testdata -name '*.suf' | xargs rm -f find testdata -name '*.bck' | xargs rm -f find testdata -name '*.llv' | xargs rm -f find testdata -name '*.bwt' | xargs rm -f find testdata -name '*.tis' | xargs rm -f find testdata -name '*.ssp' | xargs rm -f find testdata -name '*.lcp' | xargs rm -f find testdata -name '*.sti1' | xargs rm -f find testdata -name '*.al1' | xargs rm -f find testdata -name '*.prj' | xargs rm -f find testdata -name '*.polya*' | xargs rm -f make[2]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' rm -rf bin/bssm debian/bssm bin/gthdata debian/gthdata rm -rf /build/reproducible-path/genomethreader-1.7.3+dfsg/debian/man rm -f debian/*substvars make[1]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' make licensemanager=no opt=yes 64bit=yes make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg' make licensemanager=no opt=yes 64bit=yes train make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg' make[1]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' make licensemanager=no 64bit=yes test make[2]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' cd testsuite && env -i GTH_MEM_BOOKKEEPING=on MAKE=make PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" \ BSSMDIR=/build/reproducible-path/genomethreader-1.7.3+dfsg/bin/bssm GTHDATADIR=/build/reproducible-path/genomethreader-1.7.3+dfsg/gthdata/gth \ CCACHE_DISABLE=yes HOME=/nonexistent/second-build GTHTESTDATADIR= \ ruby -I. testsuite.rb \ -testdata /build/reproducible-path/genomethreader-1.7.3+dfsg/testdata -bin /build/reproducible-path/genomethreader-1.7.3+dfsg/bin -cur /build/reproducible-path/genomethreader-1.7.3+dfsg \ -gtruby /build/reproducible-path/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/reproducible-path/genomethreader-1.7.3+dfsg' make[1]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' mv bin/bssm debian/bssm mv bin/gthdata debian/gthdata dh_auto_install make[1]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' dh_install dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' mkdir -p /build/reproducible-path/genomethreader-1.7.3+dfsg/debian/man asciidoctor -a docdate='' -b manpage /build/reproducible-path/genomethreader-1.7.3+dfsg/debian/man_src/*.adoc cp /build/reproducible-path/genomethreader-1.7.3+dfsg/debian/man_src/*.? /build/reproducible-path/genomethreader-1.7.3+dfsg/debian/man dh_installman -- make[1]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' echo "libvmatch-dev:Version=2.3.1+dfsg-9" >> debian/genomethreader.substvars dh_gencontrol make[1]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' dh_md5sums dh_builddeb dpkg-deb: building package 'genomethreader' in '../genomethreader_1.7.3+dfsg-10_amd64.deb'. dpkg-deb: building package 'genomethreader-dbgsym' in '../genomethreader-dbgsym_1.7.3+dfsg-10_amd64.deb'. dpkg-genbuildinfo --build=binary -O../genomethreader_1.7.3+dfsg-10_amd64.buildinfo dpkg-genchanges --build=binary -O../genomethreader_1.7.3+dfsg-10_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2632749/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2632749/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2632749 and its subdirectories I: Current time: Mon Nov 25 22:47:57 +14 2024 I: pbuilder-time-stamp: 1732524477 + false + set +x Mon Nov 25 08:47:57 UTC 2024 I: Signing ./b2/genomethreader_1.7.3+dfsg-10_amd64.buildinfo as genomethreader_1.7.3+dfsg-10_amd64.buildinfo.asc Mon Nov 25 08:47:57 UTC 2024 I: Signed ./b2/genomethreader_1.7.3+dfsg-10_amd64.buildinfo as ./b2/genomethreader_1.7.3+dfsg-10_amd64.buildinfo.asc Mon Nov 25 08:47:57 UTC 2024 - build #2 for genomethreader/trixie/amd64 on infom01-amd64 done. Starting cleanup. All cleanup done. Mon Nov 25 08:47:57 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-IPAyWKmb, removing. /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ: total 244 drwxr-xr-x 2 jenkins jenkins 4096 Nov 25 08:45 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 25 08:47 b2 -rw-r--r-- 1 jenkins jenkins 2236 Feb 24 2024 genomethreader_1.7.3+dfsg-10.dsc -rw------- 1 jenkins jenkins 229660 Nov 25 08:45 rbuildlog.TBT0eI9 /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/b1: total 3960 -rw-r--r-- 1 jenkins jenkins 225956 Nov 25 08:45 build.log -rw-r--r-- 1 jenkins jenkins 1675876 Nov 25 08:45 genomethreader-dbgsym_1.7.3+dfsg-10_amd64.deb -rw-r--r-- 1 jenkins jenkins 14160 Nov 25 08:45 genomethreader_1.7.3+dfsg-10.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2236 Nov 25 08:45 genomethreader_1.7.3+dfsg-10.dsc -rw-r--r-- 1 jenkins jenkins 7166 Nov 25 08:45 genomethreader_1.7.3+dfsg-10_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 8048 Nov 25 08:45 genomethreader_1.7.3+dfsg-10_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1658 Nov 25 08:45 genomethreader_1.7.3+dfsg-10_amd64.changes -rw-r--r-- 1 jenkins jenkins 2085136 Nov 25 08:45 genomethreader_1.7.3+dfsg-10_amd64.deb -rw-r--r-- 1 jenkins jenkins 1491 Nov 25 08:45 genomethreader_1.7.3+dfsg-10_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/b2: total 3948 -rw-r--r-- 1 jenkins jenkins 227906 Nov 25 08:47 build.log -rw-r--r-- 1 jenkins jenkins 1675876 Nov 25 08:47 genomethreader-dbgsym_1.7.3+dfsg-10_amd64.deb -rw-r--r-- 1 jenkins jenkins 14160 Nov 25 08:47 genomethreader_1.7.3+dfsg-10.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2236 Nov 25 08:47 genomethreader_1.7.3+dfsg-10.dsc -rw-r--r-- 1 jenkins jenkins 7163 Nov 25 08:47 genomethreader_1.7.3+dfsg-10_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 8045 Nov 25 08:47 genomethreader_1.7.3+dfsg-10_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1658 Nov 25 08:47 genomethreader_1.7.3+dfsg-10_amd64.changes -rw-r--r-- 1 jenkins jenkins 2085136 Nov 25 08:47 genomethreader_1.7.3+dfsg-10_amd64.deb -rw-r--r-- 1 jenkins jenkins 1491 Nov 25 08:47 genomethreader_1.7.3+dfsg-10_source.changes Mon Nov 25 08:47:58 UTC 2024 I: Deleting $TMPDIR on infom01-amd64.debian.net. Mon Nov 25 08:47:58 UTC 2024 I: genomethreader_1.7.3+dfsg-10_amd64.changes: Format: 1.8 Date: Sat, 24 Feb 2024 20:05:30 +0100 Source: genomethreader Binary: genomethreader genomethreader-dbgsym Architecture: amd64 Version: 1.7.3+dfsg-10 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: genomethreader - software tool to compute gene structure predictions Closes: 1064585 Changes: genomethreader (1.7.3+dfsg-10) unstable; urgency=medium . * Team upload. . [ Aurelien Jarno ] * Make sure package gets accepted even if binNMUed in between Closes: #1064585 . [ Andreas Tille ] Use secure URI in Homepage field. Checksums-Sha1: 472464b8ff741dfd78bbeb5037a93fe4b58f38f6 1675876 genomethreader-dbgsym_1.7.3+dfsg-10_amd64.deb e6acf02fe31daa147de3b89492cc0303b381495b 7166 genomethreader_1.7.3+dfsg-10_amd64.buildinfo 3cba62a7761ccb9ea80040f074001e654f702bb5 2085136 genomethreader_1.7.3+dfsg-10_amd64.deb Checksums-Sha256: e13b9825bcaf8da280c8d01b1c4da1cbccf77adf60db56ed5a8b45bfdf3e922c 1675876 genomethreader-dbgsym_1.7.3+dfsg-10_amd64.deb 176fdd9cc6c2b1b5a96fbd5f0c4168082354bc6bc02e45932a819de4f84c2636 7166 genomethreader_1.7.3+dfsg-10_amd64.buildinfo de0493db17809aafa41bff7f063674606746d8cc979699686622e9e02526cb1b 2085136 genomethreader_1.7.3+dfsg-10_amd64.deb Files: f31800d7d7ad2d2835ba220ce8cf0dd1 1675876 debug optional genomethreader-dbgsym_1.7.3+dfsg-10_amd64.deb f6764e3bbdf3c55ebdd680eec7b9e822 7166 science optional genomethreader_1.7.3+dfsg-10_amd64.buildinfo 5d00178110160a8ea091af0adec8e36a 2085136 science optional genomethreader_1.7.3+dfsg-10_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/genomethreader_1.7.3+dfsg-10.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/genomethreader_1.7.3+dfsg-10.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/genomethreader_1.7.3+dfsg-10.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/genomethreader_1.7.3+dfsg-10.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/amd64/genomethreader_1.7.3+dfsg-10_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/genomethreader_1.7.3+dfsg-10.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-11-25 08:45:10.978374983 +0000 +++ b2/build.log 2024-11-25 08:47:58.170801420 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Dec 28 03:05:19 -12 2025 -I: pbuilder-time-stamp: 1766934319 +I: Current time: Mon Nov 25 22:45:13 +14 2024 +I: pbuilder-time-stamp: 1732524313 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -36,51 +36,83 @@ dpkg-source: info: applying extend-clean.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2633570/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2632749/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 25 08:45 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2632749/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2632749/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='e60271d4e60d4f26957210cd35f1f896' - 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='2633570' - PS1='# ' - PS2='> ' + INVOCATION_ID=9f219f2d53ed45db98b454dc0b1f4b68 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2632749 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/pbuilderrc_tsg5 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/b1 --logfile b1/build.log genomethreader_1.7.3+dfsg-10.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/pbuilderrc_tPwO --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/b2 --logfile b2/build.log genomethreader_1.7.3+dfsg-10.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2633570/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2632749/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -230,7 +262,7 @@ Get: 94 http://deb.debian.org/debian trixie/main amd64 libtre-dev amd64 0.8.0-8 [35.4 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libvmatch-dev amd64 2.3.1+dfsg-9 [661 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 43.5 MB in 1s (33.7 MB/s) +Fetched 43.5 MB in 1s (82.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19969 files and directories currently installed.) @@ -642,7 +674,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/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-10_source.changes +I: user script /srv/workspace/pbuilder/2632749/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2632749/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/genomethreader-1.7.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../genomethreader_1.7.3+dfsg-10_source.changes dpkg-buildpackage: info: source package genomethreader dpkg-buildpackage: info: source version 1.7.3+dfsg-10 dpkg-buildpackage: info: source distribution unstable @@ -1063,9 +1099,9 @@ make[1]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' make licensemanager=no 64bit=yes test make[2]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+dfsg' -cd testsuite && env -i GTH_MEM_BOOKKEEPING=on MAKE=make PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" \ +cd testsuite && env -i GTH_MEM_BOOKKEEPING=on MAKE=make PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" \ BSSMDIR=/build/reproducible-path/genomethreader-1.7.3+dfsg/bin/bssm GTHDATADIR=/build/reproducible-path/genomethreader-1.7.3+dfsg/gthdata/gth \ - CCACHE_DISABLE=yes HOME=/nonexistent/first-build GTHTESTDATADIR= \ + CCACHE_DISABLE=yes HOME=/nonexistent/second-build GTHTESTDATADIR= \ ruby -I. testsuite.rb \ -testdata /build/reproducible-path/genomethreader-1.7.3+dfsg/testdata -bin /build/reproducible-path/genomethreader-1.7.3+dfsg/bin -cur /build/reproducible-path/genomethreader-1.7.3+dfsg \ -gtruby /build/reproducible-path/genomethreader-1.7.3+dfsg/gtruby @@ -1167,12 +1203,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2632749/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2632749/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/2633570 and its subdirectories -I: Current time: Sun Dec 28 03:08:10 -12 2025 -I: pbuilder-time-stamp: 1766934490 +I: removing directory /srv/workspace/pbuilder/2632749 and its subdirectories +I: Current time: Mon Nov 25 22:47:57 +14 2024 +I: pbuilder-time-stamp: 1732524477 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/genomethreader_1.7.3+dfsg-10.diff: 67.7% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/genomethreader_1.7.3+dfsg-10.diff.gz b2/build.log: 93.3% -- replaced with stdout Compressing the 1st log... b1/build.log: 93.6% -- replaced with stdout Mon Nov 25 08:48:00 UTC 2024 I: diffoscope 283 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_genomethreader_trixie_amd64_1732524480 + touch /var/log/reproducible-builds/diffoscope_stamp_genomethreader_trixie_amd64_1732524480 + RESULT=0 + systemd-run '--description=diffoscope on genomethreader/1.7.3+dfsg-10 in trixie/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_34-36886 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ --run-session -c jenkins-reproducible-trixie-diffoscope-0c02b2cb-be44-410a-becd-a7f46cd83ddb -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/dbd-tmp-tTPykmW ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/genomethreader_1.7.3+dfsg-10.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/genomethreader_1.7.3+dfsg-10.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/genomethreader_1.7.3+dfsg-10.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/b1/genomethreader_1.7.3+dfsg-10_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/b2/genomethreader_1.7.3+dfsg-10_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_34-36886.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/genomethreader_1.7.3+dfsg-10.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/genomethreader_1.7.3+dfsg-10.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/genomethreader_1.7.3+dfsg-10.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/b1/genomethreader_1.7.3+dfsg-10_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.IbnQl0sQ/b2/genomethreader_1.7.3+dfsg-10_amd64.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: 1.549s) 1.549s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.083s) 0.083s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 1.878s CPU time consumed: 1.460s _ _ _ __ _ ___ _ __ ___ _ __ ___ ___| |_| |__ _ __ ___ __ _ __| | ___ / _` |/ _ \ '_ \ / _ \| '_ ` _ \ / _ \ __| '_ \| '__/ _ \/ _` |/ _` |/ _ \ | (_| | __/ | | | (_) | | | | | | __/ |_| | | | | | __/ (_| | (_| | __/ \__, |\___|_| |_|\___/|_| |_| |_|\___|\__|_| |_|_| \___|\__,_|\__,_|\___| |___/ _ __ | '__| | | |_| Mon Nov 25 08:48:02 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Mon Nov 25 08:48:02 UTC 2024 I: genomethreader from trixie built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-25 08:48:03] INFO: Starting at 2024-11-25 08:48:03.756004 [2024-11-25 08:48:03] INFO: Generating the pages of 1 package(s) [2024-11-25 08:48:04] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/amd64/genomethreader didn't produce a buildlog, even though it has been built. [2024-11-25 08:48:04] INFO: Finished at 2024-11-25 08:48:04.142903, took: 0:00:00.386907 Mon Nov 25 08:48:04 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/amd64/genomethreader.html Mon Nov 25 08:48:04 UTC 2024 I: Submitting .buildinfo files to external archives: Mon Nov 25 08:48:04 UTC 2024 I: Submitting 8.0K b1/genomethreader_1.7.3+dfsg-10_amd64.buildinfo.asc https://buildinfo.debian.net/e6acf02fe31daa147de3b89492cc0303b381495b/genomethreader_1.7.3+dfsg-10_amd64 Mon Nov 25 08:48:06 UTC 2024 I: Submitting 8.0K b2/genomethreader_1.7.3+dfsg-10_amd64.buildinfo.asc https://buildinfo.debian.net/df008e485b30c8177155fa81d4b4d7552e21d76f/genomethreader_1.7.3+dfsg-10_amd64 Mon Nov 25 08:48:08 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Nov 25 08:48:08 UTC 2024 I: Done submitting .buildinfo files. Mon Nov 25 08:48:08 UTC 2024 I: Removing signed genomethreader_1.7.3+dfsg-10_amd64.buildinfo.asc files: removed './b1/genomethreader_1.7.3+dfsg-10_amd64.buildinfo.asc' removed './b2/genomethreader_1.7.3+dfsg-10_amd64.buildinfo.asc' 1732524488 amd64 trixie genomethreader Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/genomethreader_1.7.3+dfsg-10.rbuild.log: 92.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/genomethreader_1.7.3+dfsg-10.rbuild.log.gz [2024-11-25 08:48:08] INFO: Starting at 2024-11-25 08:48:08.652725 [2024-11-25 08:48:08] INFO: Generating the pages of 1 package(s) [2024-11-25 08:48:09] INFO: Finished at 2024-11-25 08:48:09.173896, took: 0:00:00.521178 All cleanup done. Mon Nov 25 08:48:09 UTC 2024 - total duration: 0h 6m 8s. Mon Nov 25 08:48:09 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-lcd5ujwD, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 6min 15.361s CPU time consumed: 8.432s