Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/g/genomethreader/genomethreader_1.7.3+dfsg-6+b1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/genomethreader-1.7.3+dfsg-6+b1tuuaqvln/genomethreader_1.7.3+dfsg-6+b1_amd64.buildinfo Get source package info: genomethreader=1.7.3+dfsg-6 Source URL: http://snapshot.notset.fr/mr/package/genomethreader/1.7.3+dfsg-6/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=asciidoctor=2.0.16-2 autoconf=2.71-2 automake=1:1.16.5-1.3 autopoint=0.21-6 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6 binutils=2.38-3 binutils-common=2.38-3 binutils-x86-64-linux-gnu=2.38-3 bsdextrautils=2.38-4 bsdutils=1:2.38-4 build-essential=12.9 bzip2=1.0.8-5 ca-certificates=20211016 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.3.0-1 dash=0.5.11+git20210903+057cd650a4ed-8 debconf=1.5.79 debhelper=13.7.1 debianutils=5.7-0.1 dh-autoreconf=20 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 dpkg=1.21.7 dpkg-dev=1.21.7 dwz=0.14-1 file=1:5.41-4 findutils=4.9.0-3 fontconfig=2.13.1-4.4 fontconfig-config=2.13.1-4.4 fonts-dejavu-core=2.37-2 g++=4:11.2.0-2 g++-11=11.3.0-1 gcc=4:11.2.0-2 gcc-11=11.3.0-1 gcc-11-base=11.3.0-1 gcc-12-base=12-20220319-1 genometools=1.6.2+ds-2 genometools-common=1.6.2+ds-2 gettext=0.21-6 gettext-base=0.21-6 grep=3.7-1 groff-base=1.22.4-8 gzip=1.12-1 hostname=3.23 init-system-helpers=1.62 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libasan6=11.3.0-1 libatomic1=12-20220319-1 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1+b1 libbinutils=2.38-3 libblkid1=2.38-4 libbrotli1=1.0.9-2+b3 libbsd0=0.11.6-1 libbz2-1.0=1.0.8-5 libbz2-dev=1.0.8-5 libc-bin=2.33-7 libc-dev-bin=2.33-7 libc6=2.33-7 libc6-dev=2.33-7 libcairo2=1.16.0-5 libcap-ng0=0.7.9-2.2+b2 libcap2=1:2.44-1 libcc1-0=12-20220319-1 libcom-err2=1.46.5-2 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.38-3 libctf0=2.38-3 libdatrie1=0.2.13-2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.262 libdebhelper-perl=13.7.1 libdpkg-perl=1.21.7 libedit2=3.1-20210910-1 libelf1=0.186-1 libexpat1=2.4.8-1 libexpat1-dev=2.4.8-1 libffi8=3.4.2-4 libfile-stripnondeterminism-perl=1.13.0-1 libfontconfig1=2.13.1-4.4 libfreetype6=2.11.1+dfsg-2 libfribidi0=1.0.8-2.1 libgcc-11-dev=11.3.0-1 libgcc-s1=12-20220319-1 libgcrypt20=1.10.1-2 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libgenometools0=1.6.2+ds-2 libgenometools0-dev=1.6.2+ds-2 libglib2.0-0=2.72.1-1 libgmp10=2:6.2.1+dfsg-3 libgomp1=12-20220319-1 libgpg-error0=1.43-3 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.19.2-2+b1 libharfbuzz0b=2.7.4-1+b1 libicu71=71.1-2 libisl23=0.24-2 libitm1=12-20220319-1 libk5crypto3=1.19.2-2+b1 libkeyutils1=1.6.1-3 libkrb5-3=1.19.2-2+b1 libkrb5support0=1.19.2-2+b1 liblsan0=12-20220319-1 liblua5.1-0=5.1.5-9 liblua5.1-0-dev=5.1.5-9 liblz4-1=1.9.3-2 liblzma5=5.2.5-2.1 libmagic-mgc=1:5.41-4 libmagic1=1:5.41-4 libmd0=1.0.4-1 libmount1=2.38-4 libmpc3=1.2.1-2 libmpfr6=4.1.0-3 libncurses-dev=6.3+20220423-1 libncurses6=6.3+20220423-1 libncursesw6=6.3+20220423-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-13 libpam-modules-bin=1.4.0-13 libpam-runtime=1.4.0-13 libpam0g=1.4.0-13 libpango-1.0-0=1.50.6+ds-2 libpangocairo-1.0-0=1.50.6+ds-2 libpangoft2-1.0-0=1.50.6+ds-2 libpcre2-8-0=10.40-1 libpcre3=2:8.39-14 libperl5.34=5.34.0-4 libpipeline1=1.5.6-1 libpixman-1-0=0.40.0-1 libpng16-16=1.6.37-5 libquadmath0=12-20220319-1 libreadline-dev=8.1.2-1.2 libreadline8=8.1.2-1.2 libruby3.0=3.0.4-7 libseccomp2=2.5.4-1 libselinux1=3.3-1+b2 libsigsegv2=2.14-1 libsmartcols1=2.38-4 libsqlite3-0=3.38.3-1 libssl1.1=1.1.1n-1 libstdc++-11-dev=11.3.0-1 libstdc++6=12-20220319-1 libsub-override-perl=0.09-2 libsystemd0=250.4-1 libthai-data=0.1.29-1 libthai0=0.1.29-1 libtinfo6=6.3+20220423-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.7-3 libtre-dev=0.8.0-6+b1 libtre5=0.8.0-6+b1 libtsan0=11.3.0-1 libubsan1=12-20220319-1 libuchardet0=0.0.7-1 libudev1=250.4-1 libunistring2=1.0-1 libuuid1=2.38-4 libvmatch-dev=2.3.1+dfsg-7 libx11-6=2:1.7.5-1 libx11-data=2:1.7.5-1 libxau6=1:1.0.9-1 libxcb-render0=1.14-3 libxcb-shm0=1.14-3 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.4-1 libxml2=2.9.13+dfsg-1+b1 libxrender1=1:0.9.10-1 libyaml-0-2=0.2.2-1 libzstd1=1.5.2+dfsg-1 linux-libc-dev=5.17.3-1 login=1:4.11.1+dfsg1-2 lsb-base=11.1.0 lua-filesystem=1.8.0-2 lua-lpeg=1.0.2-1 lua-md5=1.2+git+1+8d87fee-1.1 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.2-1 mawk=1.3.4.20200120-3+b1 ncurses-base=6.3+20220423-1 ncurses-bin=6.3+20220423-1 openssl=1.1.1n-1 patch=2.7.6-7 perl=5.34.0-4 perl-base=5.34.0-4 perl-modules-5.34=5.34.0-4 po-debconf=1.0.21+nmu1 rake=13.0.6-3 readline-common=8.1.2-1.2 rpcsvc-proto=1.4.2-4 ruby=1:3.0+1 ruby-asciidoctor=2.0.16-2 ruby-net-telnet=0.1.1-2 ruby-rubygems=3.3.5-2 ruby-xmlrpc=0.3.2-1 ruby3.0=3.0.4-7 rubygems-integration=1.18 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.03-1 tar=1.34+dfsg-1 ucf=3.0043 util-linux=2.38-4 util-linux-extra=2.38-4 xz-utils=5.2.5-2.1 zlib1g=1:1.2.11.dfsg-4 zlib1g-dev=1:1.2.11.dfsg-4 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211001T033837Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211001T033837Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220507T085652Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220428T025707Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d genomethreader=1.7.3+dfsg-6 && mkdir -p /build/genomethreader-9PoLMs && dpkg-source --no-check -x /*.dsc /build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg && cd /build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg && { printf '%s' 'genomethreader (1.7.3+dfsg-6+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild for outdated Built-Using -- amd64 / i386 Build Daemon (x86-csail-01) Sun, 01 May 2022 20:12:33 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/genomethreader-9PoLMs" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1651435953" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/genomethreader-9PoLMs /tmp/genomethreader-1.7.3+dfsg-6+b1tuuaqvln bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220428T025707Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.JywRVRtlsB as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.JywRVRtlsB Reading package lists... Building dependency tree... util-linux is already the newest version (2.38-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 135 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220428T025707Z unstable/main amd64 libfakeroot amd64 1.28-1 [48.2 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220428T025707Z unstable/main amd64 fakeroot amd64 1.28-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 135 kB in 0s (982 kB/s) Selecting previously unselected package libfakeroot:amd64. (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 ... 4627 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.28-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.28-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.28-1_amd64.deb ... Unpacking fakeroot (1.28-1) ... Setting up libfakeroot:amd64 (1.28-1) ... Setting up fakeroot (1.28-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-7) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211001T033837Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211001T033837Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220507T085652Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220428T025707Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.JywRVRtlsB Get:1 http://snapshot.notset.fr/archive/debian/20211001T033837Z bookworm InRelease [128 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220507T085652Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20220428T025707Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20211001T033837Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211001T033837Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211001T033837Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211001T033837Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211001T033837Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211001T033837Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20211001T033837Z bookworm/main Sources [11.6 MB] Get:5 http://snapshot.notset.fr/archive/debian/20211001T033837Z bookworm/main amd64 Packages [11.2 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20220507T085652Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20220507T085652Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20220507T085652Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20220507T085652Z unstable/main amd64 Packages [12.4 MB] Fetched 35.6 MB in 29s (1242 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.JywRVRtlsB I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d genomethreader=1.7.3+dfsg-6 && mkdir -p /build/genomethreader-9PoLMs && dpkg-source --no-check -x /*.dsc /build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg && cd /build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg && { printf '%s' 'genomethreader (1.7.3+dfsg-6+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild for outdated Built-Using -- amd64 / i386 Build Daemon (x86-csail-01) Sun, 01 May 2022 20:12:33 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/genomethreader-9PoLMs"' exec /tmp/mmdebstrap.JywRVRtlsB Reading package lists... NOTICE: 'genomethreader' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/genomethreader.git Please use: git clone https://salsa.debian.org/med-team/genomethreader.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 40.0 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211001T033837Z bookworm/main genomethreader 1.7.3+dfsg-6 (dsc) [2228 B] Get:2 http://snapshot.notset.fr/archive/debian/20211001T033837Z bookworm/main genomethreader 1.7.3+dfsg-6 (tar) [40.0 MB] Get:3 http://snapshot.notset.fr/archive/debian/20211001T033837Z bookworm/main genomethreader 1.7.3+dfsg-6 (diff) [13.5 kB] Fetched 40.0 MB in 31s (1293 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'genomethreader_1.7.3+dfsg-6.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting genomethreader in /build/genomethreader-9PoLMs/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-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying debian-gt-libs.patch dpkg-source: info: applying gt-path-fix.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying search-paths.patch dpkg-source: info: applying m32-m64-ignore.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying disable-fastdp-tests.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1651435953" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.JywRVRtlsB dpkg-buildpackage: info: source package genomethreader dpkg-buildpackage: info: source version 1.7.3+dfsg-6+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by amd64 / i386 Build Daemon (x86-csail-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg' dh_clean rm -rf bin/bssm debian/bssm bin/gthdata debian/gthdata rm -rf /build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/debian/man rm -f debian/*substvars make[1]: Leaving directory '/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg' make licensemanager=no opt=yes 64bit=yes make[2]: Entering directory '/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg' [create obj/gth_config.h] [compile findfile.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/findfile.c -o obj/src/libgenomethreader/findfile.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/findfile.c -o obj/src/libgenomethreader/findfile.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/findfile.o [compile gt_align_dna.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/gt_align_dna.c -o obj/src/libgenomethreader/gt_align_dna.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gt_align_dna.c -o obj/src/libgenomethreader/gt_align_dna.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gt_align_dna.o [compile gt_gthgetseq.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/gt_gthgetseq.c -o obj/src/libgenomethreader/gt_gthgetseq.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gt_gthgetseq.c -o obj/src/libgenomethreader/gt_gthgetseq.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gt_gthgetseq.o [compile gthmkvtree.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/gthmkvtree.c -o obj/src/libgenomethreader/gthmkvtree.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gthmkvtree.c -o obj/src/libgenomethreader/gthmkvtree.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gthmkvtree.o [compile gthpolyafunc.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/gthpolyafunc.c -o obj/src/libgenomethreader/gthpolyafunc.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gthpolyafunc.c -o obj/src/libgenomethreader/gthpolyafunc.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gthpolyafunc.o [compile gthpre.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/gthpre.c -o obj/src/libgenomethreader/gthpre.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gthpre.c -o obj/src/libgenomethreader/gthpre.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gthpre.o [compile gthversionfunc.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/gthversionfunc.c -o obj/src/libgenomethreader/gthversionfunc.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gthversionfunc.c -o obj/src/libgenomethreader/gthversionfunc.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gthversionfunc.o [compile gthvmatch.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/gthvmatch.c -o obj/src/libgenomethreader/gthvmatch.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gthvmatch.c -o obj/src/libgenomethreader/gthvmatch.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gthvmatch.o [compile jt.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/jt.c -o obj/src/libgenomethreader/jt.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/jt.c -o obj/src/libgenomethreader/jt.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/jt.o [compile jt_align_dna.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/jt_align_dna.c -o obj/src/libgenomethreader/jt_align_dna.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/jt_align_dna.c -o obj/src/libgenomethreader/jt_align_dna.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/jt_align_dna.o [compile jt_align_protein.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/jt_align_protein.c -o obj/src/libgenomethreader/jt_align_protein.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/jt_align_protein.c -o obj/src/libgenomethreader/jt_align_protein.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/jt_align_protein.o [compile seq_con_multiseq.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/libgenomethreader/seq_con_multiseq.c -o obj/src/libgenomethreader/seq_con_multiseq.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/seq_con_multiseq.c -o obj/src/libgenomethreader/seq_con_multiseq.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/seq_con_multiseq.o [compile ags.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/ags.c -o obj/src/gth/ags.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/ags.c -o obj/src/gth/ags.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/ags.o [compile ags_build.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/ags_build.c -o obj/src/gth/ags_build.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/ags_build.c -o obj/src/gth/ags_build.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/ags_build.o [compile align_dna.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/align_dna.c -o obj/src/gth/align_dna.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/align_dna.c -o obj/src/gth/align_dna.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/align_dna.o [compile align_protein.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/align_protein.c -o obj/src/gth/align_protein.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/align_protein.c -o obj/src/gth/align_protein.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/align_protein.o [compile backtrace_path.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/backtrace_path.c -o obj/src/gth/backtrace_path.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/backtrace_path.c -o obj/src/gth/backtrace_path.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/backtrace_path.o [compile bssm_helper.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/bssm_helper.c -o obj/src/gth/bssm_helper.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_helper.c -o obj/src/gth/bssm_helper.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/bssm_helper.o [compile bssm_param.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/bssm_param.c -o obj/src/gth/bssm_param.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_param.c -o obj/src/gth/bssm_param.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/bssm_param.o [compile bssm_param_rmsd.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/bssm_param_rmsd.c -o obj/src/gth/bssm_param_rmsd.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_param_rmsd.c -o obj/src/gth/bssm_param_rmsd.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/bssm_param_rmsd.o [compile bssm_seq_processor.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/bssm_seq_processor.c -o obj/src/gth/bssm_seq_processor.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_seq_processor.c -o obj/src/gth/bssm_seq_processor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/bssm_seq_processor.o [compile bssm_train_stream.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/bssm_train_stream.c -o obj/src/gth/bssm_train_stream.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_train_stream.c -o obj/src/gth/bssm_train_stream.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/bssm_train_stream.o [compile bssm_train_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/bssm_train_visitor.c -o obj/src/gth/bssm_train_visitor.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_train_visitor.c -o obj/src/gth/bssm_train_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/bssm_train_visitor.o [compile call_info.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/call_info.c -o obj/src/gth/call_info.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/call_info.c -o obj/src/gth/call_info.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/call_info.o [compile chain_collection.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/chain_collection.c -o obj/src/gth/chain_collection.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/chain_collection.c -o obj/src/gth/chain_collection.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/chain_collection.o [compile chaining.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/chaining.c -o obj/src/gth/chaining.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/chaining.c -o obj/src/gth/chaining.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/chaining.o [compile compute_scores.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/compute_scores.c -o obj/src/gth/compute_scores.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/compute_scores.c -o obj/src/gth/compute_scores.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/compute_scores.o [compile desc_cache.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/desc_cache.c -o obj/src/gth/desc_cache.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/desc_cache.c -o obj/src/gth/desc_cache.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/desc_cache.o [compile dp_options_core.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/dp_options_core.c -o obj/src/gth/dp_options_core.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/dp_options_core.c -o obj/src/gth/dp_options_core.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/dp_options_core.o [compile dp_options_est.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/dp_options_est.c -o obj/src/gth/dp_options_est.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/dp_options_est.c -o obj/src/gth/dp_options_est.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/dp_options_est.o [compile dp_options_postpro.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/dp_options_postpro.c -o obj/src/gth/dp_options_postpro.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/dp_options_postpro.c -o obj/src/gth/dp_options_postpro.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/dp_options_postpro.o [compile dp_param.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/dp_param.c -o obj/src/gth/dp_param.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/dp_param.c -o obj/src/gth/dp_param.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/dp_param.o [compile dp_scores_protein.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/dp_scores_protein.c -o obj/src/gth/dp_scores_protein.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/dp_scores_protein.c -o obj/src/gth/dp_scores_protein.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/dp_scores_protein.o [compile editoperation.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/editoperation.c -o obj/src/gth/editoperation.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/editoperation.c -o obj/src/gth/editoperation.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/editoperation.o [compile gff3_pgl_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gff3_pgl_visitor.c -o obj/src/gth/gff3_pgl_visitor.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gff3_pgl_visitor.c -o obj/src/gth/gff3_pgl_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gff3_pgl_visitor.o [compile gff3_sa_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gff3_sa_visitor.c -o obj/src/gth/gff3_sa_visitor.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gff3_sa_visitor.c -o obj/src/gth/gff3_sa_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gff3_sa_visitor.o [compile gt_gth.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gt_gth.c -o obj/src/gth/gt_gth.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gth.c -o obj/src/gth/gt_gth.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gth.o [compile gt_gthbssmbuild.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gt_gthbssmbuild.c -o obj/src/gth/gt_gthbssmbuild.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthbssmbuild.c -o obj/src/gth/gt_gthbssmbuild.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthbssmbuild.o [compile gt_gthbssmfileinfo.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gt_gthbssmfileinfo.c -o obj/src/gth/gt_gthbssmfileinfo.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthbssmfileinfo.c -o obj/src/gth/gt_gthbssmfileinfo.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthbssmfileinfo.o [compile gt_gthbssmprint.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gt_gthbssmprint.c -o obj/src/gth/gt_gthbssmprint.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthbssmprint.c -o obj/src/gth/gt_gthbssmprint.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthbssmprint.o [compile gt_gthbssmrmsd.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gt_gthbssmrmsd.c -o obj/src/gth/gt_gthbssmrmsd.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthbssmrmsd.c -o obj/src/gth/gt_gthbssmrmsd.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthbssmrmsd.o [compile gt_gthbssmtrain.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gt_gthbssmtrain.c -o obj/src/gth/gt_gthbssmtrain.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthbssmtrain.c -o obj/src/gth/gt_gthbssmtrain.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthbssmtrain.o [compile gt_gthconsensus.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gt_gthconsensus.c -o obj/src/gth/gt_gthconsensus.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthconsensus.c -o obj/src/gth/gt_gthconsensus.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthconsensus.o [compile gt_gthfilestat.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gt_gthfilestat.c -o obj/src/gth/gt_gthfilestat.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthfilestat.c -o obj/src/gth/gt_gthfilestat.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthfilestat.o [compile gt_gthmkbssmfiles.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gt_gthmkbssmfiles.c -o obj/src/gth/gt_gthmkbssmfiles.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthmkbssmfiles.c -o obj/src/gth/gt_gthmkbssmfiles.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthmkbssmfiles.o [compile gt_gthsplit.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gt_gthsplit.c -o obj/src/gth/gt_gthsplit.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthsplit.c -o obj/src/gth/gt_gthsplit.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthsplit.o [compile gthalignment.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthalignment.c -o obj/src/gth/gthalignment.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthalignment.c -o obj/src/gth/gthalignment.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthalignment.o [compile gthchain.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthchain.c -o obj/src/gth/gthchain.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthchain.c -o obj/src/gth/gthchain.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthchain.o [compile gthcluster.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthcluster.c -o obj/src/gth/gthcluster.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthcluster.c -o obj/src/gth/gthcluster.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthcluster.o [compile gthcutoffsminimal.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthcutoffsminimal.c -o obj/src/gth/gthcutoffsminimal.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthcutoffsminimal.c -o obj/src/gth/gthcutoffsminimal.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthcutoffsminimal.o [compile gthcutoffsrelaxed.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthcutoffsrelaxed.c -o obj/src/gth/gthcutoffsrelaxed.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthcutoffsrelaxed.c -o obj/src/gth/gthcutoffsrelaxed.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthcutoffsrelaxed.o [compile gthcutoffsstrict.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthcutoffsstrict.c -o obj/src/gth/gthcutoffsstrict.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthcutoffsstrict.c -o obj/src/gth/gthcutoffsstrict.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthcutoffsstrict.o [compile gthmatch.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthmatch.c -o obj/src/gth/gthmatch.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthmatch.c -o obj/src/gth/gthmatch.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthmatch.o [compile gthorf.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthorf.c -o obj/src/gth/gthorf.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthorf.c -o obj/src/gth/gthorf.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthorf.o [compile gthoutput.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthoutput.c -o obj/src/gth/gthoutput.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthoutput.c -o obj/src/gth/gthoutput.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthoutput.o [compile gthsadistri.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthsadistri.c -o obj/src/gth/gthsadistri.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthsadistri.c -o obj/src/gth/gthsadistri.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthsadistri.o [compile gthsortags.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthsortags.c -o obj/src/gth/gthsortags.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthsortags.c -o obj/src/gth/gthsortags.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthsortags.o [compile gthsplicesitescr.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthsplicesitescr.c -o obj/src/gth/gthsplicesitescr.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthsplicesitescr.c -o obj/src/gth/gthsplicesitescr.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthsplicesitescr.o [compile gthtrans.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthtrans.c -o obj/src/gth/gthtrans.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthtrans.c -o obj/src/gth/gthtrans.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthtrans.o [compile gthtravalign.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthtravalign.c -o obj/src/gth/gthtravalign.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthtravalign.c -o obj/src/gth/gthtravalign.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthtravalign.o [compile gthverbosefunc.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthverbosefunc.c -o obj/src/gth/gthverbosefunc.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthverbosefunc.c -o obj/src/gth/gthverbosefunc.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthverbosefunc.o [compile gthverbosefuncvm.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthverbosefuncvm.c -o obj/src/gth/gthverbosefuncvm.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthverbosefuncvm.c -o obj/src/gth/gthverbosefuncvm.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthverbosefuncvm.o [compile gthxml.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/gthxml.c -o obj/src/gth/gthxml.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthxml.c -o obj/src/gth/gthxml.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthxml.o [compile indent.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/indent.c -o obj/src/gth/indent.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/indent.c -o obj/src/gth/indent.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/indent.o [compile input.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/input.c -o obj/src/gth/input.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/input.c -o obj/src/gth/input.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/input.o [compile intermediate.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/intermediate.c -o obj/src/gth/intermediate.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/intermediate.c -o obj/src/gth/intermediate.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/intermediate.o [compile md5_cache.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/md5_cache.c -o obj/src/gth/md5_cache.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/md5_cache.c -o obj/src/gth/md5_cache.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/md5_cache.o [compile parse_options.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/parse_options.c -o obj/src/gth/parse_options.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/parse_options.c -o obj/src/gth/parse_options.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/parse_options.o [compile path_matrix.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/path_matrix.c -o obj/src/gth/path_matrix.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/path_matrix.c -o obj/src/gth/path_matrix.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/path_matrix.o [compile path_walker.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/path_walker.c -o obj/src/gth/path_walker.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/path_walker.c -o obj/src/gth/path_walker.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/path_walker.o [compile pgl.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/pgl.c -o obj/src/gth/pgl.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/pgl.c -o obj/src/gth/pgl.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/pgl.o [compile pgl_collection.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/pgl_collection.c -o obj/src/gth/pgl_collection.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/pgl_collection.c -o obj/src/gth/pgl_collection.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/pgl_collection.o [compile pgl_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/pgl_visitor.c -o obj/src/gth/pgl_visitor.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/pgl_visitor.c -o obj/src/gth/pgl_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/pgl_visitor.o [compile proc_sa_collection.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/proc_sa_collection.c -o obj/src/gth/proc_sa_collection.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/proc_sa_collection.c -o obj/src/gth/proc_sa_collection.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/proc_sa_collection.o [compile region_factory.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/region_factory.c -o obj/src/gth/region_factory.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/region_factory.c -o obj/src/gth/region_factory.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/region_factory.o [compile run_header.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/run_header.c -o obj/src/gth/run_header.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/run_header.c -o obj/src/gth/run_header.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/run_header.o [compile sa.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/sa.c -o obj/src/gth/sa.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/sa.c -o obj/src/gth/sa.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/sa.o [compile sa_cmp.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/sa_cmp.c -o obj/src/gth/sa_cmp.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/sa_cmp.c -o obj/src/gth/sa_cmp.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/sa_cmp.o [compile sa_collection.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/sa_collection.c -o obj/src/gth/sa_collection.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/sa_collection.c -o obj/src/gth/sa_collection.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/sa_collection.o [compile sa_filter.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/sa_filter.c -o obj/src/gth/sa_filter.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/sa_filter.c -o obj/src/gth/sa_filter.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/sa_filter.o [compile sa_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/sa_visitor.c -o obj/src/gth/sa_visitor.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/sa_visitor.c -o obj/src/gth/sa_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/sa_visitor.o [compile seq_con.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/seq_con.c -o obj/src/gth/seq_con.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/seq_con.c -o obj/src/gth/seq_con.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/seq_con.o [compile similarity_filter.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/similarity_filter.c -o obj/src/gth/similarity_filter.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/similarity_filter.c -o obj/src/gth/similarity_filter.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/similarity_filter.o [compile splice_site_model.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/splice_site_model.c -o obj/src/gth/splice_site_model.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/splice_site_model.c -o obj/src/gth/splice_site_model.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/splice_site_model.o [compile spliced_seq.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/spliced_seq.c -o obj/src/gth/spliced_seq.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/spliced_seq.c -o obj/src/gth/spliced_seq.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/spliced_seq.o [compile stat.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/stat.c -o obj/src/gth/stat.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/stat.c -o obj/src/gth/stat.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/stat.o [compile time.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/time.c -o obj/src/gth/time.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/time.c -o obj/src/gth/time.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/time.o [compile txt_pgl_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/txt_pgl_visitor.c -o obj/src/gth/txt_pgl_visitor.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/txt_pgl_visitor.c -o obj/src/gth/txt_pgl_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/txt_pgl_visitor.o [compile txt_sa_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/txt_sa_visitor.c -o obj/src/gth/txt_sa_visitor.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/txt_sa_visitor.c -o obj/src/gth/txt_sa_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/txt_sa_visitor.o [compile xml_final_sa_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/xml_final_sa_visitor.c -o obj/src/gth/xml_final_sa_visitor.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/xml_final_sa_visitor.c -o obj/src/gth/xml_final_sa_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/xml_final_sa_visitor.o [compile xml_inter_sa_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/xml_inter_sa_visitor.c -o obj/src/gth/xml_inter_sa_visitor.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/xml_inter_sa_visitor.c -o obj/src/gth/xml_inter_sa_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/xml_inter_sa_visitor.o [compile xml_pgl_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth/xml_pgl_visitor.c -o obj/src/gth/xml_pgl_visitor.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/xml_pgl_visitor.c -o obj/src/gth/xml_pgl_visitor.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/xml_pgl_visitor.o [link libgenomethreader.a] ar: `u' modifier ignored since `D' is the default (see `U') ar: creating lib/libgenomethreader.a [compile gth.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gth.c -o obj/src/gth.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth.c -o obj/src/gth.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth.o [link gth] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gth.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gth [compile gthconsensus.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gthconsensus.c -o obj/src/gthconsensus.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthconsensus.c -o obj/src/gthconsensus.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthconsensus.o [link gthconsensus] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthconsensus.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthconsensus [compile gthbssmfileinfo.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gthbssmfileinfo.c -o obj/src/gthbssmfileinfo.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthbssmfileinfo.c -o obj/src/gthbssmfileinfo.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthbssmfileinfo.o [link gthbssmfileinfo] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthbssmfileinfo.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthbssmfileinfo [compile gthbssmbuild.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gthbssmbuild.c -o obj/src/gthbssmbuild.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthbssmbuild.c -o obj/src/gthbssmbuild.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthbssmbuild.o [link gthbssmbuild] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthbssmbuild.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthbssmbuild [compile gthbssmprint.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gthbssmprint.c -o obj/src/gthbssmprint.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthbssmprint.c -o obj/src/gthbssmprint.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthbssmprint.o [link gthbssmprint] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthbssmprint.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthbssmprint [compile gthbssmrmsd.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gthbssmrmsd.c -o obj/src/gthbssmrmsd.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthbssmrmsd.c -o obj/src/gthbssmrmsd.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthbssmrmsd.o [link gthbssmrmsd] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthbssmrmsd.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthbssmrmsd [compile gthbssmtrain.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gthbssmtrain.c -o obj/src/gthbssmtrain.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthbssmtrain.c -o obj/src/gthbssmtrain.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthbssmtrain.o [link gthbssmtrain] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthbssmtrain.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthbssmtrain [compile gthfilestat.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gthfilestat.c -o obj/src/gthfilestat.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthfilestat.c -o obj/src/gthfilestat.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthfilestat.o [link gthfilestat] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthfilestat.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthfilestat [compile gthmkbssmfiles.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gthmkbssmfiles.c -o obj/src/gthmkbssmfiles.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthmkbssmfiles.c -o obj/src/gthmkbssmfiles.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthmkbssmfiles.o [link gthmkbssmfiles] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthmkbssmfiles.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthmkbssmfiles [compile gthsplit.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gthsplit.c -o obj/src/gthsplit.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthsplit.c -o obj/src/gthsplit.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthsplit.o [link gthsplit] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthsplit.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthsplit [compile gthunit.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gthunit.c -o obj/src/gthunit.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthunit.c -o obj/src/gthunit.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthunit.o [link gthunit] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthunit.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthunit [compile gthgetseq.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gthgetseq.c -o obj/src/gthgetseq.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthgetseq.c -o obj/src/gthgetseq.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthgetseq.o [link gthgetseq] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthgetseq.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthgetseq [compile align_dna.o] cc -Wdate-time -D_FORTIFY_SOURCE=2 -c src/align_dna.c -o obj/src/align_dna.o -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/align_dna.c -o obj/src/align_dna.d -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/align_dna.o [link align_dna] cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Llib obj/src/align_dna.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/align_dna make[2]: Leaving directory '/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg' make licensemanager=no opt=yes 64bit=yes train make[2]: Entering directory '/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg' [train arabidopsis.bssm] [train rice.bssm] [train maize.bssm] [train medicago.bssm] [write old BSSMs] [copy gthdata stuff to bin] make[2]: Leaving directory '/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg' make[1]: Leaving directory '/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg' mv bin/bssm debian/bssm mv bin/gthdata debian/gthdata dh_auto_install make[1]: Leaving directory '/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg' dh_install -a dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installman make[1]: Entering directory '/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg' mkdir -p /build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/debian/man asciidoctor -a docdate='' -b manpage /build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/debian/man_src/*.adoc cp /build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/debian/man_src/*.? /build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg/debian/man dh_installman -- make[1]: Leaving directory '/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a debian/rules override_dh_gencontrol make[1]: Entering directory '/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg' echo "libvmatch-dev:Version=2.3.1+dfsg-7" >> debian/genomethreader.substvars dh_gencontrol make[1]: Leaving directory '/build/genomethreader-9PoLMs/genomethreader-1.7.3+dfsg' dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'genomethreader-dbgsym' in '../genomethreader-dbgsym_1.7.3+dfsg-6+b1_amd64.deb'. dpkg-deb: building package 'genomethreader' in '../genomethreader_1.7.3+dfsg-6+b1_amd64.deb'. dpkg-genbuildinfo --build=any -O../genomethreader_1.7.3+dfsg-6+b1_amd64.buildinfo dpkg-genchanges --build=any -O../genomethreader_1.7.3+dfsg-6+b1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/genomethreader-9PoLMs /tmp/genomethreader-1.7.3+dfsg-6+b1tuuaqvln I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.JywRVRtlsB... I: success in 398.8130 seconds md5: genomethreader-dbgsym_1.7.3+dfsg-6+b1_amd64.deb: OK md5: genomethreader_1.7.3+dfsg-6+b1_amd64.deb: OK sha1: genomethreader-dbgsym_1.7.3+dfsg-6+b1_amd64.deb: OK sha1: genomethreader_1.7.3+dfsg-6+b1_amd64.deb: OK sha256: genomethreader-dbgsym_1.7.3+dfsg-6+b1_amd64.deb: OK sha256: genomethreader_1.7.3+dfsg-6+b1_amd64.deb: OK Checksums: OK