Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/g/genomethreader/genomethreader_1.7.3+dfsg-5+b1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/genomethreader-1.7.3+dfsg-5+b1hg8ga410/genomethreader_1.7.3+dfsg-5+b1_amd64.buildinfo Get source package info: genomethreader=1.7.3+dfsg-5 Source URL: http://snapshot.notset.fr/mr/package/genomethreader/1.7.3+dfsg-5/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=asciidoctor=2.0.12-2 autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-3 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.48 bash=5.1-2 binutils=2.35.1-7 binutils-common=2.35.1-7 binutils-x86-64-linux-gnu=2.35.1-7 bsdextrautils=2.36.1-6 bsdutils=1:2.36.1-5 build-essential=12.9 bzip2=1.0.8-4 ca-certificates=20200601 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 dash=0.5.11+git20200708+dd9ef66-5 debconf=1.5.74 debhelper=13.3.1 debianutils=4.11.2 dh-autoreconf=19 dh-strip-nondeterminism=1.10.0-1 diffutils=1:3.7-5 dpkg=1.20.7.1 dpkg-dev=1.20.7.1 dwz=0.13+20201015-2 file=1:5.39-3 findutils=4.8.0-1 fontconfig=2.13.1-4.2 fontconfig-config=2.13.1-4.2 fonts-dejavu-core=2.37-2 g++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 genometools=1.6.1+ds-3 genometools-common=1.6.1+ds-3 gettext=0.21-3 gettext-base=0.21-3 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-9 libarchive-zip-perl=1.68-1 libasan6=10.2.1-6 libatomic1=10.2.1-6 libattr1=1:2.4.48-6 libaudit-common=1:3.0-2 libaudit1=1:3.0-2 libbinutils=2.35.1-7 libblkid1=2.36.1-5 libbrotli1=1.0.9-2+b2 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-4 libbz2-dev=1.0.8-4 libc-bin=2.31-9 libc-dev-bin=2.31-9 libc6=2.31-9 libc6-dev=2.31-9 libcairo2=1.16.0-5 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-6 libcom-err2=1.45.6-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-7 libctf0=2.35.1-7 libdatrie1=0.2.12-3 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.256 libdebhelper-perl=13.3.1 libdpkg-perl=1.20.7.1 libelf1=0.182-3 libexpat1=2.2.10-1 libexpat1-dev=2.2.10-1 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.10.0-1 libfontconfig1=2.13.1-4.2 libfreetype6=2.10.4+dfsg-1 libfribidi0=1.0.8-2 libgcc-10-dev=10.2.1-6 libgcc-s1=10.2.1-6 libgcrypt20=1.8.7-2 libgdbm-compat4=1.19-1 libgdbm6=1.19-1 libgenometools0=1.6.1+ds-3 libgenometools0-dev=1.6.1+ds-3 libglib2.0-0=2.66.4-1 libgmp10=2:6.2.1+dfsg-1 libgomp1=10.2.1-6 libgpg-error0=1.38-2 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.18.3-4 libharfbuzz0b=2.7.4-1 libicu67=67.1-6 libisl23=0.23-1 libitm1=10.2.1-6 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblsan0=10.2.1-6 liblua5.1-0=5.1.5-8.1+b3 liblua5.1-0-dev=5.1.5-8.1+b3 liblz4-1=1.9.3-1 liblzma5=5.2.5-1.0 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-5 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libncurses-dev=6.2+20201114-2 libncurses6=6.2+20201114-2 libncursesw6=6.2+20201114-2 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-2 libpam-modules-bin=1.4.0-2 libpam-runtime=1.4.0-2 libpam0g=1.4.0-2 libpango-1.0-0=1.46.2-3 libpangocairo-1.0-0=1.46.2-3 libpangoft2-1.0-0=1.46.2-3 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.0-6 libpipeline1=1.5.3-1 libpixman-1-0=0.40.0-1 libpng16-16=1.6.37-3 libpth20=2.0.7-22 libquadmath0=10.2.1-6 libreadline-dev=8.1-1 libreadline8=8.1-1 libruby2.7=2.7.2-3 libseccomp2=2.5.1-1 libselinux1=3.1-2+b2 libsigsegv2=2.12-3 libsmartcols1=2.36.1-5 libsqlite3-0=3.34.0-1 libssl1.1=1.1.1i-1 libstdc++-10-dev=10.2.1-6 libstdc++6=10.2.1-6 libsub-override-perl=0.09-2 libsystemd0=247.2-4 libthai-data=0.1.28-3 libthai0=0.1.28-3 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtool=2.4.6-15 libtre-dev=0.8.0-6+b1 libtre5=0.8.0-6+b1 libtsan0=10.2.1-6 libubsan1=10.2.1-6 libuchardet0=0.0.7-1 libudev1=247.2-4 libunistring2=0.9.10-4 libuuid1=2.36.1-5 libvmatch-dev=2.3.1+dfsg-6 libx11-6=2:1.7.0-2 libx11-data=2:1.7.0-2 libxau6=1:1.0.8-1+b2 libxcb-render0=1.14-2.1 libxcb-shm0=1.14-2.1 libxcb1=1.14-2.1 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.3-1.1 libxml2=2.9.10+dfsg-6.3+b1 libxrender1=1:0.9.10-1 libyaml-0-2=0.2.2-1 libzstd1=1.4.8+dfsg-1 linux-libc-dev=5.10.5-1 login=1:4.8.1-1 lsb-base=11.1.0 lua-filesystem=1.8.0-1 lua-lpeg=1.0.2-1 lua-md5=1.2+git+1+8d87fee-1.1 m4=1.4.18-5 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 openssl=1.1.1i-1 patch=2.7.6-7 perl=5.32.0-6 perl-base=5.32.0-6 perl-modules-5.32=5.32.0-6 po-debconf=1.0.21+nmu1 rake=13.0.1-4 readline-common=8.1-1 ruby=1:2.7+2 ruby-asciidoctor=2.0.12-2 ruby-minitest=5.13.0-1 ruby-net-telnet=0.1.1-2 ruby-power-assert=1.1.7-1 ruby-rubygems=3.2.5-2 ruby-test-unit=3.3.9-1 ruby-xmlrpc=0.3.0-2 ruby2.7=2.7.2-3 rubygems-integration=1.18 sed=4.7-1 sensible-utils=0.0.14 sysvinit-utils=2.96-5 tar=1.32+dfsg-1 ucf=3.0043 util-linux=2.36.1-5 xz-utils=5.2.5-1.0 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210205T091048Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210117T204310Z/ 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-5 && mkdir -p /build/genomethreader-bhb15k && dpkg-source --no-check -x /*.dsc /build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg && cd /build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg && { printf '%s' 'genomethreader (1.7.3+dfsg-5+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) Mon, 18 Jan 2021 23:03:42 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/genomethreader-bhb15k" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1611011022" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/genomethreader-bhb15k /tmp/genomethreader-1.7.3+dfsg-5+b1hg8ga410 bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210117T204310Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.5hiW4eKBgh 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.5hiW4eKBgh Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-5). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210117T204310Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210117T204310Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1071 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 ... 4661 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-9) ... 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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210205T091048Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210117T204310Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.5hiW4eKBgh Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210205T091048Z unstable InRelease [153 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20210117T204310Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20210205T091048Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20210205T091048Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20210205T091048Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20210205T091048Z unstable/main amd64 Packages [11.7 MB] Fetched 34.4 MB in 29s (1174 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.5hiW4eKBgh I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d genomethreader=1.7.3+dfsg-5 && mkdir -p /build/genomethreader-bhb15k && dpkg-source --no-check -x /*.dsc /build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg && cd /build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg && { printf '%s' 'genomethreader (1.7.3+dfsg-5+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) Mon, 18 Jan 2021 23:03:42 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/genomethreader-bhb15k"' exec /tmp/mmdebstrap.5hiW4eKBgh 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/20210814T212851Z bookworm/main genomethreader 1.7.3+dfsg-5 (dsc) [1902 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main genomethreader 1.7.3+dfsg-5 (tar) [40.0 MB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main genomethreader 1.7.3+dfsg-5 (diff) [13.4 kB] Fetched 40.0 MB in 32s (1269 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'genomethreader_1.7.3+dfsg-5.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting genomethreader in /build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg dpkg-source: info: unpacking genomethreader_1.7.3+dfsg.orig.tar.xz dpkg-source: info: unpacking genomethreader_1.7.3+dfsg-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying debian-gt-libs.patch dpkg-source: info: applying gt-path-fix.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying search-paths.patch dpkg-source: info: applying m32-m64-ignore.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying disable-fastdp-tests.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1611011022" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.5hiW4eKBgh dpkg-buildpackage: info: source package genomethreader dpkg-buildpackage: info: source version 1.7.3+dfsg-5+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 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg' dh_clean rm -rf bin/bssm debian/bssm bin/gthdata debian/gthdata rm -rf /build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/debian/man rm -f debian/*substvars make[1]: Leaving directory '/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg' dh_clean debian/rules build-arch dh build-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-bhb15k/genomethreader-1.7.3+dfsg' make licensemanager=no opt=yes 64bit=yes make[2]: Entering directory '/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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-bhb15k/genomethreader-1.7.3+dfsg/src -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg' make licensemanager=no opt=yes 64bit=yes train make[2]: Entering directory '/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg' make[1]: Leaving directory '/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg' make licensemanager=no 64bit=yes test make[2]: Entering directory '/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg' cd testsuite && env -i GTH_MEM_BOOKKEEPING=on MAKE=make PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin" \ BSSMDIR=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/bin/bssm GTHDATADIR=/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/gthdata/gth \ CCACHE_DISABLE=yes HOME=/nonexistent GTHTESTDATADIR= \ ruby -I. testsuite.rb \ -testdata /build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/testdata -bin /build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/bin -cur /build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg \ -gtruby /build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/gtruby 1: gth : ok 2: gth -help : ok 3: gth -help+ : ok 4: gth -version : ok 5: gth regression test (assertion in gthsafilter) : ok 6: gth regression test (-gff3out -intermediate) : ok 7: gth regression test (-gff3out -intermediate -fastdp) : ok 8: gth regression test (-gff3out -skipalignmentout) : ok 9: gth regression test (-gff3out -skipalignmentout -fastdp) : ok 10: gth regression test (-gff3out -intermediate -o) : ok 11: gth regression test (-gff3out -skipalignmentout -o) : ok 12: gthconsensus regression test (-gff3out -intermediate) : ok 13: gthconsensus regression test (-gff3out -skipalignmentout) : ok 14: gthconsensus regression test (-gff3out -intermediate -o) : ok 15: gthconsensus regression test (-gff3out -skipalignmentout -o): ok 16: gth regression test (-exondistri) : ok 17: gth regression test (-introndistri) : ok 18: gth regression test (-refseqcovdistri) : ok 19: gth regression test (all distributions) : ok 20: gth regression test (-skipindexcheck) : ok 21: gth regression test (index reconstruction) : ok 22: gth regression test (-createindicesonly & -noautoindex) : ok 23: gth regression test (coverage assertion) : ok 24: gth -gff3out -intermediate (long intron files) : ok 25: gth -gff3out -skipalignmentout (long intron files) : ok 26: gth -gff3out -frompos (correct positions in sequence region): ok 27: gth -gff3out -intermediate (correct reverse positions) : ok 28: gth arabidopsis : ok 29: gth illegal character in protein file : ok 30: align_dna : ok 31: gth -gff3descranges (single exon) : ok 32: gthconsensus -help : ok 33: gthconsensus -help+ : ok 34: gthconsensus empty_file : ok 35: gthconsensus empty_file.gz : ok 36: gthconsensus empty_file.bz2 : ok 37: gthbssmfileinfo (arabidopsis) : ok 38: gthbssmfileinfo (human) : ok 39: gthbssmprint (arabidopsis) : ok 40: gthbssmprint (human) : ok 41: gthbssmrmsd (arabidopsis) : ok 42: gthbssmtrain (examples from manual) : ok 43: gthbssmtrain (file, no introns) : ok 44: gthbssmtrain (file, introns) : ok 45: gthbssmtrain (stdin, no introns) : ok 46: gthbssmtrain (stdin, introns) : ok 47: gthbssmtrain (short intron) : ok 48: gthunit : ok 49: fastdp 01 : ok 50: fastdp (U89959) : ok 51: fastdp (U89959, introncutout) : ok make[2]: Leaving directory '/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg' make[1]: Leaving directory '/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg' mv bin/bssm debian/bssm mv bin/gthdata debian/gthdata dh_auto_install make[1]: Leaving directory '/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg' mkdir -p /build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/debian/man asciidoctor -a docdate='' -b manpage /build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/debian/man_src/*.adoc cp /build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/debian/man_src/*.? /build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg/debian/man dh_installman -- make[1]: Leaving directory '/build/genomethreader-bhb15k/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-bhb15k/genomethreader-1.7.3+dfsg' echo "libvmatch-dev:Version=2.3.1+dfsg-6" >> debian/genomethreader.substvars dh_gencontrol make[1]: Leaving directory '/build/genomethreader-bhb15k/genomethreader-1.7.3+dfsg' dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'genomethreader' in '../genomethreader_1.7.3+dfsg-5+b1_amd64.deb'. dpkg-deb: building package 'genomethreader-dbgsym' in '../genomethreader-dbgsym_1.7.3+dfsg-5+b1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../genomethreader_1.7.3+dfsg-5+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-bhb15k /tmp/genomethreader-1.7.3+dfsg-5+b1hg8ga410 I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.5hiW4eKBgh... I: success in 542.9541 seconds md5: genomethreader-dbgsym_1.7.3+dfsg-5+b1_amd64.deb: OK md5: genomethreader_1.7.3+dfsg-5+b1_amd64.deb: OK sha1: genomethreader-dbgsym_1.7.3+dfsg-5+b1_amd64.deb: OK sha1: genomethreader_1.7.3+dfsg-5+b1_amd64.deb: OK sha256: genomethreader-dbgsym_1.7.3+dfsg-5+b1_amd64.deb: OK sha256: genomethreader_1.7.3+dfsg-5+b1_amd64.deb: OK Checksums: OK