Sat Sep 28 09:04:27 UTC 2024 I: starting to build genomethreader/trixie/i386 on jenkins on '2024-09-28 09:04' Sat Sep 28 09:04:27 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_10/25681/console.log Sat Sep 28 09:04:27 UTC 2024 I: Downloading source for trixie/genomethreader=1.7.3+dfsg-10 --2024-09-28 09:04:27-- 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% 191M=0s 2024-09-28 09:04:27 (191 MB/s) - ‘genomethreader_1.7.3+dfsg-10.dsc’ saved [2236/2236] Sat Sep 28 09:04:28 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----- Sat Sep 28 09:04:28 UTC 2024 I: Checking whether the package is not for us Sat Sep 28 09:04:28 UTC 2024 I: Starting 1st build on remote node ionos16-i386.debian.net. Sat Sep 28 09:04:28 UTC 2024 I: Preparing to do remote build '1' on ionos16-i386.debian.net. Sat Sep 28 09:11:03 UTC 2024 I: Deleting $TMPDIR on ionos16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Oct 31 03:27:29 -12 2025 I: pbuilder-time-stamp: 1761924449 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: using eatmydata during job 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/13552/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='551984e16f594e6881fe26e24be6c764' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='13552' 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.heOIAubg/pbuilderrc_pRdh --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.heOIAubg/b1 --logfile b1/build.log genomethreader_1.7.3+dfsg-10.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos16-i386 6.1.0-25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.106-3 (2024-08-26) 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/13552/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: i386 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 ... 19775 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 44.6 MB of archives. After unpacking 156 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-5 [69.3 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 openssl i386 3.3.2-1 [1386 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 ca-certificates all 20240203 [158 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3 [314 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3 [114 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3 [42.9 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-8 [102 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 rubygems-integration all 1.18 [6704 B] Get: 15 http://deb.debian.org/debian trixie/main i386 rake all 13.2.1-1 [65.2 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 ruby-sdbm i386 1.0.0-5+b4 [16.7 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libedit2 i386 3.1-20240808-1 [98.0 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libncurses6 i386 6.5-2 [111 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 libyaml-0-2 i386 0.2.5-1+b1 [55.2 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 libruby3.1t64 i386 3.1.2-8.4 [5470 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 ruby3.1 i386 3.1.2-8.4 [664 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libruby i386 1:3.1+nmu1 [4664 B] Get: 26 http://deb.debian.org/debian trixie/main i386 ruby-rubygems all 3.4.20-1 [309 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 ruby i386 1:3.1+nmu1 [5584 B] Get: 28 http://deb.debian.org/debian trixie/main i386 ruby-asciidoctor all 2.0.23-1 [214 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 asciidoctor all 2.0.23-1 [88.7 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-2 [723 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 41 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.191-2 [194 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5 [9550 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.1 [733 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.3-1 [107 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b4 [309 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 libpng16-16t64 i386 1.6.44-1 [288 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 libfreetype6 i386 2.13.3+dfsg-1 [464 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 fontconfig-config i386 2.15.0-1.1 [317 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 libfontconfig1 i386 2.15.0-1.1 [401 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 fontconfig i386 2.15.0-1.1 [462 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 libpixman-1-0 i386 0.42.2-1+b1 [555 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 libxau6 i386 1:1.0.9-1+b1 [18.5 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 libxdmcp6 i386 1:1.1.2-3+b1 [24.8 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 libxcb1 i386 1.17.0-2 [148 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 libx11-data all 2:1.8.7-1 [328 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 libx11-6 i386 2:1.8.7-1+b1 [822 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 libxcb-render0 i386 1.17.0-2 [116 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 libxcb-shm0 i386 1.17.0-2 [105 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 67 http://deb.debian.org/debian trixie/main i386 libxrender1 i386 1:0.9.10-1.1+b1 [28.8 kB] Get: 68 http://deb.debian.org/debian trixie/main i386 libcairo2 i386 1.18.2-2 [591 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 libglib2.0-0t64 i386 2.82.1-1 [1570 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 liblua5.1-0 i386 5.1.5-9+b2 [118 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 libfribidi0 i386 1.0.15-1 [72.4 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 libgraphite2-3 i386 1.3.14-2 [77.7 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 libharfbuzz0b i386 9.0.0-1 [500 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 libthai-data all 0.1.29-2 [168 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 libdatrie1 i386 0.2.13-3 [39.5 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 libthai0 i386 0.1.29-2 [50.1 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 libpango-1.0-0 i386 1.54.0+ds-2 [230 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 libpangoft2-1.0-0 i386 1.54.0+ds-2 [57.9 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 libpangocairo-1.0-0 i386 1.54.0+ds-2 [36.0 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 libtre5 i386 0.8.0-8 [60.7 kB] Get: 81 http://deb.debian.org/debian trixie/main i386 lua-filesystem i386 1.8.0-3+b1 [13.1 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 lua-lpeg i386 1.0.2-2+b1 [41.6 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 lua-md5 i386 1.2+git+1+8d87fee-2+b1 [13.7 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 genometools-common all 1.6.5+ds-2.2 [195 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 genometools i386 1.6.5+ds-2.2 [1708 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 libbz2-dev i386 1.0.8-6 [32.1 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 libexpat1-dev i386 2.6.3-1 [164 kB] Get: 88 http://deb.debian.org/debian trixie/main i386 libgenometools0t64 i386 1.6.5+ds-2.2 [1456 kB] Get: 89 http://deb.debian.org/debian trixie/main i386 libgenometools0-dev i386 1.6.5+ds-2.2 [95.2 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-5 [173 kB] Get: 91 http://deb.debian.org/debian trixie/main i386 libncurses-dev i386 6.5-2 [380 kB] Get: 92 http://deb.debian.org/debian trixie/main i386 libreadline-dev i386 8.2-5 [166 kB] Get: 93 http://deb.debian.org/debian trixie/main i386 liblua5.1-0-dev i386 5.1.5-9+b2 [150 kB] Get: 94 http://deb.debian.org/debian trixie/main i386 libtre-dev i386 0.8.0-8 [35.7 kB] Get: 95 http://deb.debian.org/debian trixie/main i386 libvmatch-dev i386 2.3.1+dfsg-9 [701 kB] Get: 96 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1 [915 kB] Fetched 44.6 MB in 3s (15.1 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 ... 19775 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_3.3.2-1_i386.deb ... 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Selecting previously unselected package libelf1t64:i386. Preparing to unpack .../40-libelf1t64_0.191-2_i386.deb ... Unpacking libelf1t64:i386 (0.191-2) ... Selecting previously unselected package dwz. Preparing to unpack .../41-dwz_0.15-1+b1_i386.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../42-libicu72_72.1-5_i386.deb ... Unpacking libicu72:i386 (72.1-5) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../43-libxml2_2.12.7+dfsg+really2.9.14-0.1_i386.deb ... Unpacking libxml2:i386 (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../44-gettext_0.22.5-2_i386.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. 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Preparing to unpack .../70-libfribidi0_1.0.15-1_i386.deb ... Unpacking libfribidi0:i386 (1.0.15-1) ... Selecting previously unselected package libgraphite2-3:i386. Preparing to unpack .../71-libgraphite2-3_1.3.14-2_i386.deb ... Unpacking libgraphite2-3:i386 (1.3.14-2) ... Selecting previously unselected package libharfbuzz0b:i386. Preparing to unpack .../72-libharfbuzz0b_9.0.0-1_i386.deb ... Unpacking libharfbuzz0b:i386 (9.0.0-1) ... 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:i386. Preparing to unpack .../74-libdatrie1_0.2.13-3_i386.deb ... Unpacking libdatrie1:i386 (0.2.13-3) ... Selecting previously unselected package libthai0:i386. Preparing to unpack .../75-libthai0_0.1.29-2_i386.deb ... Unpacking libthai0:i386 (0.1.29-2) ... Selecting previously unselected package libpango-1.0-0:i386. Preparing to unpack .../76-libpango-1.0-0_1.54.0+ds-2_i386.deb ... Unpacking libpango-1.0-0:i386 (1.54.0+ds-2) ... Selecting previously unselected package libpangoft2-1.0-0:i386. Preparing to unpack .../77-libpangoft2-1.0-0_1.54.0+ds-2_i386.deb ... Unpacking libpangoft2-1.0-0:i386 (1.54.0+ds-2) ... Selecting previously unselected package libpangocairo-1.0-0:i386. Preparing to unpack .../78-libpangocairo-1.0-0_1.54.0+ds-2_i386.deb ... Unpacking libpangocairo-1.0-0:i386 (1.54.0+ds-2) ... Selecting previously unselected package libtre5:i386. Preparing to unpack .../79-libtre5_0.8.0-8_i386.deb ... Unpacking libtre5:i386 (0.8.0-8) ... Selecting previously unselected package lua-filesystem:i386. Preparing to unpack .../80-lua-filesystem_1.8.0-3+b1_i386.deb ... Unpacking lua-filesystem:i386 (1.8.0-3+b1) ... Selecting previously unselected package lua-lpeg:i386. Preparing to unpack .../81-lua-lpeg_1.0.2-2+b1_i386.deb ... Unpacking lua-lpeg:i386 (1.0.2-2+b1) ... Selecting previously unselected package lua-md5:i386. Preparing to unpack .../82-lua-md5_1.2+git+1+8d87fee-2+b1_i386.deb ... Unpacking lua-md5:i386 (1.2+git+1+8d87fee-2+b1) ... 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_i386.deb ... Unpacking genometools (1.6.5+ds-2.2) ... Selecting previously unselected package libbz2-dev:i386. Preparing to unpack .../85-libbz2-dev_1.0.8-6_i386.deb ... Unpacking libbz2-dev:i386 (1.0.8-6) ... Selecting previously unselected package libexpat1-dev:i386. Preparing to unpack .../86-libexpat1-dev_2.6.3-1_i386.deb ... Unpacking libexpat1-dev:i386 (2.6.3-1) ... Selecting previously unselected package libgenometools0t64. Preparing to unpack .../87-libgenometools0t64_1.6.5+ds-2.2_i386.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_i386.deb ... Unpacking libgenometools0-dev (1.6.5+ds-2.2) ... Selecting previously unselected package libreadline8t64:i386. Preparing to unpack .../89-libreadline8t64_8.2-5_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-5) ... Selecting previously unselected package libncurses-dev:i386. Preparing to unpack .../90-libncurses-dev_6.5-2_i386.deb ... Unpacking libncurses-dev:i386 (6.5-2) ... Selecting previously unselected package libreadline-dev:i386. Preparing to unpack .../91-libreadline-dev_8.2-5_i386.deb ... Unpacking libreadline-dev:i386 (8.2-5) ... Selecting previously unselected package liblua5.1-0-dev:i386. Preparing to unpack .../92-liblua5.1-0-dev_5.1.5-9+b2_i386.deb ... Unpacking liblua5.1-0-dev:i386 (5.1.5-9+b2) ... Selecting previously unselected package libtre-dev. Preparing to unpack .../93-libtre-dev_0.8.0-8_i386.deb ... Unpacking libtre-dev (0.8.0-8) ... Selecting previously unselected package libvmatch-dev. Preparing to unpack .../94-libvmatch-dev_2.3.1+dfsg-9_i386.deb ... Unpacking libvmatch-dev (2.3.1+dfsg-9) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../95-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1_i386.deb ... Unpacking zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1) ... Setting up libexpat1:i386 (2.6.3-1) ... Setting up libpipeline1:i386 (1.5.8-1) ... Setting up libgraphite2-3:i386 (1.3.14-2) ... Setting up libpixman-1-0:i386 (0.42.2-1+b1) ... Setting up libxau6:i386 (1:1.0.9-1+b1) ... Setting up libxdmcp6:i386 (1:1.1.2-3+b1) ... Setting up lua-lpeg:i386 (1.0.2-2+b1) ... Setting up libxcb1:i386 (1.17.0-2) ... Setting up libtre5:i386 (0.8.0-8) ... Setting up libicu72:i386 (72.1-5) ... Setting up bsdextrautils (2.40.2-8) ... Setting up libdatrie1:i386 (0.2.13-3) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libxcb-render0:i386 (1.17.0-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:i386 (0.2.5-1+b1) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:i386 (1.1.0-2+b4) ... Setting up libedit2:i386 (3.1-20240808-1) ... Setting up libmagic1t64:i386 (1:5.45-3) ... 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:i386 (1.17.0-2) ... Setting up file (1:5.45-3) ... 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Setting up libfreetype6:i386 (2.13.3+dfsg-1) ... Setting up libreadline8t64:i386 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libharfbuzz0b:i386 (9.0.0-1) ... Setting up libfontconfig1:i386 (2.15.0-1.1) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:i386 (1.54.0+ds-2) ... Setting up rubygems-integration (1.18) ... Setting up libreadline-dev:i386 (8.2-5) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:i386 (1.18.2-2) ... Setting up libpangoft2-1.0-0:i386 (1.54.0+ds-2) ... Setting up libpangocairo-1.0-0:i386 (1.54.0+ds-2) ... Setting up liblua5.1-0-dev:i386 (5.1.5-9+b2) ... 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) ... 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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 i386 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=no 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=no 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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/findfile.c -o obj/src/libgenomethreader/findfile.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gt_align_dna.c -o obj/src/libgenomethreader/gt_align_dna.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gt_gthgetseq.c -o obj/src/libgenomethreader/gt_gthgetseq.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gthmkvtree.c -o obj/src/libgenomethreader/gthmkvtree.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gthpolyafunc.c -o obj/src/libgenomethreader/gthpolyafunc.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gthpre.c -o obj/src/libgenomethreader/gthpre.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gthversionfunc.c -o obj/src/libgenomethreader/gthversionfunc.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gthvmatch.c -o obj/src/libgenomethreader/gthvmatch.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/jt.c -o obj/src/libgenomethreader/jt.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/jt_align_dna.c -o obj/src/libgenomethreader/jt_align_dna.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/jt_align_protein.c -o obj/src/libgenomethreader/jt_align_protein.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/seq_con_multiseq.c -o obj/src/libgenomethreader/seq_con_multiseq.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/ags.c -o obj/src/gth/ags.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/ags_build.c -o obj/src/gth/ags_build.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/align_dna.c -o obj/src/gth/align_dna.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/align_protein.c -o obj/src/gth/align_protein.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/backtrace_path.c -o obj/src/gth/backtrace_path.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_helper.c -o obj/src/gth/bssm_helper.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_param.c -o obj/src/gth/bssm_param.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_param_rmsd.c -o obj/src/gth/bssm_param_rmsd.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_seq_processor.c -o obj/src/gth/bssm_seq_processor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_train_stream.c -o obj/src/gth/bssm_train_stream.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_train_visitor.c -o obj/src/gth/bssm_train_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/call_info.c -o obj/src/gth/call_info.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/chain_collection.c -o obj/src/gth/chain_collection.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/chaining.c -o obj/src/gth/chaining.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/compute_scores.c -o obj/src/gth/compute_scores.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/desc_cache.c -o obj/src/gth/desc_cache.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/dp_options_core.c -o obj/src/gth/dp_options_core.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/dp_options_est.c -o obj/src/gth/dp_options_est.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/dp_options_postpro.c -o obj/src/gth/dp_options_postpro.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/dp_param.c -o obj/src/gth/dp_param.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/dp_scores_protein.c -o obj/src/gth/dp_scores_protein.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/editoperation.c -o obj/src/gth/editoperation.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gff3_pgl_visitor.c -o obj/src/gth/gff3_pgl_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gff3_sa_visitor.c -o obj/src/gth/gff3_sa_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gth.c -o obj/src/gth/gt_gth.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthbssmbuild.c -o obj/src/gth/gt_gthbssmbuild.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthbssmfileinfo.c -o obj/src/gth/gt_gthbssmfileinfo.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthbssmprint.c -o obj/src/gth/gt_gthbssmprint.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthbssmrmsd.c -o obj/src/gth/gt_gthbssmrmsd.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthbssmtrain.c -o obj/src/gth/gt_gthbssmtrain.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthconsensus.c -o obj/src/gth/gt_gthconsensus.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthfilestat.c -o obj/src/gth/gt_gthfilestat.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthmkbssmfiles.c -o obj/src/gth/gt_gthmkbssmfiles.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthsplit.c -o obj/src/gth/gt_gthsplit.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthalignment.c -o obj/src/gth/gthalignment.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthchain.c -o obj/src/gth/gthchain.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthcluster.c -o obj/src/gth/gthcluster.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthcutoffsminimal.c -o obj/src/gth/gthcutoffsminimal.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthcutoffsrelaxed.c -o obj/src/gth/gthcutoffsrelaxed.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthcutoffsstrict.c -o obj/src/gth/gthcutoffsstrict.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthmatch.c -o obj/src/gth/gthmatch.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthorf.c -o obj/src/gth/gthorf.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthoutput.c -o obj/src/gth/gthoutput.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthsadistri.c -o obj/src/gth/gthsadistri.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthsortags.c -o obj/src/gth/gthsortags.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthsplicesitescr.c -o obj/src/gth/gthsplicesitescr.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthtrans.c -o obj/src/gth/gthtrans.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthtravalign.c -o obj/src/gth/gthtravalign.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthverbosefunc.c -o obj/src/gth/gthverbosefunc.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthverbosefuncvm.c -o obj/src/gth/gthverbosefuncvm.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthxml.c -o obj/src/gth/gthxml.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/indent.c -o obj/src/gth/indent.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/input.c -o obj/src/gth/input.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/intermediate.c -o obj/src/gth/intermediate.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/md5_cache.c -o obj/src/gth/md5_cache.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/parse_options.c -o obj/src/gth/parse_options.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/path_matrix.c -o obj/src/gth/path_matrix.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/path_walker.c -o obj/src/gth/path_walker.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/pgl.c -o obj/src/gth/pgl.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/pgl_collection.c -o obj/src/gth/pgl_collection.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/pgl_visitor.c -o obj/src/gth/pgl_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/proc_sa_collection.c -o obj/src/gth/proc_sa_collection.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/region_factory.c -o obj/src/gth/region_factory.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/run_header.c -o obj/src/gth/run_header.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/sa.c -o obj/src/gth/sa.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/sa_cmp.c -o obj/src/gth/sa_cmp.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/sa_collection.c -o obj/src/gth/sa_collection.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/sa_filter.c -o obj/src/gth/sa_filter.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/sa_visitor.c -o obj/src/gth/sa_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/seq_con.c -o obj/src/gth/seq_con.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/similarity_filter.c -o obj/src/gth/similarity_filter.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/splice_site_model.c -o obj/src/gth/splice_site_model.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/spliced_seq.c -o obj/src/gth/spliced_seq.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/stat.c -o obj/src/gth/stat.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/time.c -o obj/src/gth/time.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/txt_pgl_visitor.c -o obj/src/gth/txt_pgl_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/txt_sa_visitor.c -o obj/src/gth/txt_sa_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/xml_final_sa_visitor.c -o obj/src/gth/xml_final_sa_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/xml_inter_sa_visitor.c -o obj/src/gth/xml_inter_sa_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/xml_pgl_visitor.c -o obj/src/gth/xml_pgl_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth.c -o obj/src/gth.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthconsensus.c -o obj/src/gthconsensus.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthbssmfileinfo.c -o obj/src/gthbssmfileinfo.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthbssmbuild.c -o obj/src/gthbssmbuild.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthbssmprint.c -o obj/src/gthbssmprint.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthbssmrmsd.c -o obj/src/gthbssmrmsd.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthbssmtrain.c -o obj/src/gthbssmtrain.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthfilestat.c -o obj/src/gthfilestat.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthmkbssmfiles.c -o obj/src/gthmkbssmfiles.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthsplit.c -o obj/src/gthsplit.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthunit.c -o obj/src/gthunit.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthgetseq.c -o obj/src/gthgetseq.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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 -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/align_dna.c -o obj/src/align_dna.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+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=no 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=no nofastdp=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 -keywords not fastdp 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 8: gth regression test (-gff3out -skipalignmentout) : 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 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-dbgsym' in '../genomethreader-dbgsym_1.7.3+dfsg-10_i386.deb'. dpkg-deb: building package 'genomethreader' in '../genomethreader_1.7.3+dfsg-10_i386.deb'. dpkg-genbuildinfo --build=binary -O../genomethreader_1.7.3+dfsg-10_i386.buildinfo dpkg-genchanges --build=binary -O../genomethreader_1.7.3+dfsg-10_i386.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/13552 and its subdirectories I: Current time: Fri Oct 31 03:34:00 -12 2025 I: pbuilder-time-stamp: 1761924840 Sat Sep 28 09:11:04 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos12-i386.debian.net. Sat Sep 28 09:11:04 UTC 2024 I: Preparing to do remote build '2' on ionos12-i386.debian.net. Sat Sep 28 09:13:44 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. Sat Sep 28 09:13:44 UTC 2024 I: genomethreader_1.7.3+dfsg-10_i386.changes: Format: 1.8 Date: Sat, 24 Feb 2024 20:05:30 +0100 Source: genomethreader Binary: genomethreader genomethreader-dbgsym Architecture: i386 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: 04499b893baf7fe8ef9992f7aad2749d634b8bb7 1331784 genomethreader-dbgsym_1.7.3+dfsg-10_i386.deb 235b0ede9700611c39667699e77b673e255a97d8 7010 genomethreader_1.7.3+dfsg-10_i386.buildinfo 9e9810a2f847e4d5c57db2c6a86a91257cc07404 2102204 genomethreader_1.7.3+dfsg-10_i386.deb Checksums-Sha256: 39f21e239b05a9679a52a4d9a92a03c78345ff7e3ddf7624979be65f01a2f10c 1331784 genomethreader-dbgsym_1.7.3+dfsg-10_i386.deb 5226d68ad1ab8dabfc5241afd02d20b04e552fd9814e533f93fa0946b6535754 7010 genomethreader_1.7.3+dfsg-10_i386.buildinfo 464b7101f3c3e82c85b87168c23d92c9a75ae57099a67cc124001145214c8217 2102204 genomethreader_1.7.3+dfsg-10_i386.deb Files: eae7b9c0f27780c6b23ca9b9b362db41 1331784 debug optional genomethreader-dbgsym_1.7.3+dfsg-10_i386.deb 979b11dbb0a8433784cc1c7d6544371e 7010 science optional genomethreader_1.7.3+dfsg-10_i386.buildinfo 2863aa67ab1627bd8c35a2f8d1195004 2102204 science optional genomethreader_1.7.3+dfsg-10_i386.deb Sat Sep 28 09:13:45 UTC 2024 I: diffoscope 278 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_10-25681.service Warning: program compiled against libxml 212 using older 209 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.heOIAubg/genomethreader_1.7.3+dfsg-10.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.heOIAubg/genomethreader_1.7.3+dfsg-10.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.heOIAubg/genomethreader_1.7.3+dfsg-10.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.heOIAubg/b1/genomethreader_1.7.3+dfsg-10_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.heOIAubg/b2/genomethreader_1.7.3+dfsg-10_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.422s) 0.422s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.055s) 0.055s 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: 771ms CPU time consumed: 765ms Sat Sep 28 09:13:46 UTC 2024 I: diffoscope 278 found no differences in the changes files, and a .buildinfo file also exists. Sat Sep 28 09:13:46 UTC 2024 I: genomethreader from trixie built successfully and reproducibly on i386. Sat Sep 28 09:13:47 UTC 2024 I: Submitting .buildinfo files to external archives: Sat Sep 28 09:13:47 UTC 2024 I: Submitting 8.0K b1/genomethreader_1.7.3+dfsg-10_i386.buildinfo.asc Sat Sep 28 09:13:48 UTC 2024 I: Submitting 8.0K b2/genomethreader_1.7.3+dfsg-10_i386.buildinfo.asc Sat Sep 28 09:13:49 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Sep 28 09:13:49 UTC 2024 I: Done submitting .buildinfo files. Sat Sep 28 09:13:49 UTC 2024 I: Removing signed genomethreader_1.7.3+dfsg-10_i386.buildinfo.asc files: removed './b1/genomethreader_1.7.3+dfsg-10_i386.buildinfo.asc' removed './b2/genomethreader_1.7.3+dfsg-10_i386.buildinfo.asc'