genomethreader →
1.7.3+dfsg-7 →
armhf → 2022-10-11 10:07:45
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| genomethreader 1.7.3+dfsg-7 (armhf) Tue, 11 Oct 2022 09:58:09 +0000 |
+==============================================================================+
Package: genomethreader
Version: 1.7.3+dfsg-7
Source Version: 1.7.3+dfsg-7
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-49895dbe-6675-4032-92ad-b02414370b8e' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.4 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.2 MB]
Fetched 27.6 MB in 10s (2877 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
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://172.17.4.1/private bookworm-staging/main genomethreader 1.7.3+dfsg-7 (dsc) [2228 B]
Get:2 http://172.17.4.1/private bookworm-staging/main genomethreader 1.7.3+dfsg-7 (tar) [40.0 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main genomethreader 1.7.3+dfsg-7 (diff) [13.6 kB]
Fetched 40.0 MB in 4s (10.4 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/genomethreader-bszLMl/genomethreader-1.7.3+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/genomethreader-bszLMl' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-rY1XoU/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-rY1XoU/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-rY1XoU/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-rY1XoU/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-rY1XoU/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-rY1XoU/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-rY1XoU/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-rY1XoU/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (9565 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libpam-cap netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 6 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-rY1XoU/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (70.0 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12808 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), genometools (>= 1.6.1), libgenometools0-dev (>= 1.6.1), libvmatch-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, liblua5.1-0-dev, libtre-dev, asciidoctor
Filtered Build-Depends: debhelper-compat (= 13), genometools (>= 1.6.1), libgenometools0-dev (>= 1.6.1), libvmatch-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, liblua5.1-0-dev, libtre-dev, asciidoctor
dpkg-deb: building package 'sbuild-build-depends-genomethreader-dummy' in '/<<BUILDDIR>>/resolver-rY1XoU/apt_archive/sbuild-build-depends-genomethreader-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-genomethreader-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-rY1XoU/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-rY1XoU/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-rY1XoU/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-rY1XoU/apt_archive ./ Sources [566 B]
Get:5 copy:/<<BUILDDIR>>/resolver-rY1XoU/apt_archive ./ Packages [645 B]
Fetched 2544 B in 0s (12.1 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install genomethreader build dependencies (apt-based resolver)
--------------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev bsdextrautils
ca-certificates debhelper dh-autoreconf dh-strip-nondeterminism dwz file
fontconfig fontconfig-config fonts-dejavu-core genometools
genometools-common gettext gettext-base groff-base intltool-debian
libarchive-zip-perl libbrotli1 libbsd0 libbz2-dev libcairo2 libdatrie1
libdebhelper-perl libedit2 libelf1 libexpat1 libexpat1-dev
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0
libgenometools0 libgenometools0-dev libglib2.0-0 libgraphite2-3
libharfbuzz0b libicu71 liblua5.1-0 liblua5.1-0-dev libmagic-mgc libmagic1
libmd0 libncurses-dev libncurses6 libpango-1.0-0 libpangocairo-1.0-0
libpangoft2-1.0-0 libpipeline1 libpixman-1-0 libpng16-16 libreadline-dev
libruby libruby3.0 libsub-override-perl libthai-data libthai0 libtool
libtre-dev libtre5 libuchardet0 libvmatch-dev libx11-6 libx11-data libxau6
libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxrender1
libyaml-0-2 lua-filesystem lua-lpeg lua-md5 m4 man-db openssl po-debconf
rake ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems ruby-sdbm
ruby-webrick ruby-xmlrpc ruby3.0 rubygems-integration ucf zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff ncurses-doc readline-doc libtool-doc
gfortran | fortran95-compiler gcj-jdk tre-agrep m4-doc apparmor less
www-browser libmail-box-perl ri ruby-dev bundler
Recommended packages:
curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs pkg-config libtool-bin libgpm2 libltdl-dev
libmail-sendmail-perl zip fonts-lato libjs-jquery
The following NEW packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev bsdextrautils
ca-certificates debhelper dh-autoreconf dh-strip-nondeterminism dwz file
fontconfig fontconfig-config fonts-dejavu-core genometools
genometools-common gettext gettext-base groff-base intltool-debian
libarchive-zip-perl libbrotli1 libbsd0 libbz2-dev libcairo2 libdatrie1
libdebhelper-perl libedit2 libelf1 libexpat1 libexpat1-dev
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0
libgenometools0 libgenometools0-dev libglib2.0-0 libgraphite2-3
libharfbuzz0b libicu71 liblua5.1-0 liblua5.1-0-dev libmagic-mgc libmagic1
libmd0 libncurses-dev libncurses6 libpango-1.0-0 libpangocairo-1.0-0
libpangoft2-1.0-0 libpipeline1 libpixman-1-0 libpng16-16 libreadline-dev
libruby libruby3.0 libsub-override-perl libthai-data libthai0 libtool
libtre-dev libtre5 libuchardet0 libvmatch-dev libx11-6 libx11-data libxau6
libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxrender1
libyaml-0-2 lua-filesystem lua-lpeg lua-md5 m4 man-db openssl po-debconf
rake ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems ruby-sdbm
ruby-webrick ruby-xmlrpc ruby3.0 rubygems-integration
sbuild-build-depends-genomethreader-dummy ucf zlib1g-dev
0 upgraded, 97 newly installed, 0 to remove and 6 not upgraded.
Need to get 40.5 MB of archives.
After this operation, 146 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-rY1XoU/apt_archive ./ sbuild-build-depends-genomethreader-dummy 0.invalid.0 [936 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-1 [137 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.6-3 [34.3 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.10.2-3 [1364 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf openssl armhf 3.0.5-2 [1372 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf ca-certificates all 20211016 [156 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-9 [171 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf rubygems-integration all 1.18 [6704 B]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf rake all 13.0.6-3 [83.9 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf ruby-net-telnet all 0.1.1-2.1 [12.7 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf ruby-webrick all 1.7.0-4 [50.9 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf ruby-xmlrpc all 0.3.2-2 [24.4 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf ruby-sdbm armhf 1.0.0-5 [13.4 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-2 [28.6 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.7-1 [112 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libedit2 armhf 3.1-20210910-1 [81.2 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3+20220423-2 [79.6 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libyaml-0-2 armhf 0.2.5-1 [44.6 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf libruby3.0 armhf 3.0.4-8 [5136 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf ruby3.0 armhf 3.0.4-8 [683 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libruby armhf 1:3.0+3.1 [11.3 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf ruby-rubygems all 3.3.15-1 [293 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf ruby armhf 1:3.0+3.1 [12.2 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf ruby-asciidoctor all 2.0.16-2 [210 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf asciidoctor all 2.0.16-2 [87.6 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-9 [510 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.10 [79.8 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-3 [10.4 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14+20220924-2 [93.1 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-3 [8855 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1 [591 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-9 [1220 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.10 [940 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.9-1 [83.3 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.38-2 [273 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libfreetype6 armhf 2.12.1+dfsg-3 [352 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf fontconfig-config armhf 2.13.1-4.5 [281 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf libfontconfig1 armhf 2.13.1-4.5 [330 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf fontconfig armhf 2.13.1-4.5 [416 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libpixman-1-0 armhf 0.40.0-1 [463 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libx11-data all 2:1.8.1-2 [308 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.8.1-2 [704 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libxcb-render0 armhf 1.15-1 [114 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libxcb-shm0 armhf 1.15-1 [106 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.0 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libcairo2 armhf 1.16.0-6 [496 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.74.0-2 [1265 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf liblua5.1-0 armhf 5.1.5-9 [86.7 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libfribidi0 armhf 1.0.8-2.1 [63.7 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libharfbuzz0b armhf 5.2.0-2 [1835 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libthai-data all 0.1.29-1 [176 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libdatrie1 armhf 0.2.13-2+b2 [39.9 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libthai0 armhf 0.1.29-1 [54.5 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf libpango-1.0-0 armhf 1.50.10+ds-1 [214 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libpangoft2-1.0-0 armhf 1.50.10+ds-1 [68.6 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf libpangocairo-1.0-0 armhf 1.50.10+ds-1 [58.3 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf libtre5 armhf 0.8.0-6 [52.0 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf lua-filesystem armhf 1.8.0-2 [11.9 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf lua-lpeg armhf 1.0.2-2 [32.3 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf lua-md5 armhf 1.2+git+1+8d87fee-1.1 [12.3 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf genometools-common all 1.6.2+ds-2 [197 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf genometools armhf 1.6.2+ds-2 [1445 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf libbz2-dev armhf 1.0.8-5+b2 [26.8 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf libexpat1-dev armhf 2.4.9-1 [136 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libgenometools0 armhf 1.6.2+ds-2 [1214 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf libgenometools0-dev armhf 1.6.2+ds-2 [97.4 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf libncurses-dev armhf 6.3+20220423-2 [289 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf libreadline-dev armhf 8.2-1 [123 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf liblua5.1-0-dev armhf 5.1.5-9 [116 kB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf libtre-dev armhf 0.8.0-6 [27.4 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf libvmatch-dev armhf 2.3.1+dfsg-8 [521 kB]
Get:97 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4.1 [183 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up rubygems-integration (1.18) ...
Setting up man-db (2.10.2-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.10) ...
Setting up rake (13.0.6-3) ...
Setting up libruby3.0:armhf (3.0.4-8) ...
Setting up ruby3.0 (3.0.4-8) ...
Setting up libruby:armhf (1:3.0+3.1) ...
Setting up ruby (1:3.0+3.1) ...
Setting up ruby-asciidoctor (2.0.16-2) ...
Setting up asciidoctor (2.0.16-2) ...
Setting up ruby-sdbm:armhf (1.0.0-5) ...
Setting up ruby-rubygems (3.3.15-1) ...
Processing triggers for sgml-base (1.30) ...
Setting up libfontconfig1:armhf (2.13.1-4.5) ...
Setting up fontconfig (2.13.1-4.5) ...
Regenerating fonts cache... done.
Processing triggers for libc-bin (2.35-1+rpi2) ...
Setting up libpango-1.0-0:armhf (1.50.10+ds-1) ...
Setting up libcairo2:armhf (1.16.0-6) ...
Setting up libpangoft2-1.0-0:armhf (1.50.10+ds-1) ...
Setting up libpangocairo-1.0-0:armhf (1.50.10+ds-1) ...
Setting up genometools-common (1.6.2+ds-2) ...
Setting up libgenometools0 (1.6.2+ds-2) ...
Setting up libgenometools0-dev (1.6.2+ds-2) ...
Setting up genometools (1.6.2+ds-2) ...
Setting up sbuild-build-depends-genomethreader-dummy (0.invalid.0) ...
Processing triggers for ca-certificates (20211016) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Processing triggers for libc-bin (2.35-1+rpi2) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-187-generic armhf (armv8l)
Toolchain package versions: binutils_2.39-6+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-3+rpi1 gcc-12_12.2.0-3+rpi1 libc6-dev_2.35-1+rpi2 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 linux-libc-dev_5.19.6-1+rpi1
Package versions: adduser_3.129 apt_2.5.3 asciidoctor_2.0.16-2 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-9 autotools-dev_20220109.1 base-files_12.2+rpi1 base-passwd_3.6.1 bash_5.2~rc2-2 binutils_2.39-6+rpi1 binutils-arm-linux-gnueabihf_2.39-6+rpi1 binutils-common_2.39-6+rpi1 bsdextrautils_2.38.1-1 bsdutils_1:2.38.1-1 build-essential_12.9 bzip2_1.0.8-5+b2 ca-certificates_20211016 coreutils_9.1-1 cpp_4:12.2.0-1+rpi1 cpp-12_12.2.0-3+rpi1 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.79 debhelper_13.10 debianutils_5.7-0.3 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dirmngr_2.2.39-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 fontconfig_2.13.1-4.5 fontconfig-config_2.13.1-4.5 fonts-dejavu-core_2.37-2 g++_4:12.2.0-1+rpi1 g++-12_12.2.0-3+rpi1 gcc_4:12.2.0-1+rpi1 gcc-12_12.2.0-3+rpi1 gcc-12-base_12.2.0-3+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 genometools_1.6.2+ds-2 genometools-common_1.6.2+ds-2 gettext_0.21-9 gettext-base_0.21-9 gnupg_2.2.39-1 gnupg-l10n_2.2.39-1 gnupg-utils_2.2.39-1 gpg_2.2.39-1 gpg-agent_2.2.39-1 gpg-wks-client_2.2.39-1 gpg-wks-server_2.2.39-1 gpgconf_2.2.39-1 gpgsm_2.2.39-1 gpgv_2.2.39-1 grep_3.7-1 groff-base_1.22.4-8 gzip_1.12-1 hostname_3.23 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20211215-1 krb5-locales_1.20-1 libacl1_2.3.1-1 libapt-pkg6.0_2.5.3 libarchive-zip-perl_1.68-1 libasan8_12.2.0-3+rpi1 libassuan0_2.5.5-4 libatomic1_12.2.0-3+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libbinutils_2.39-6+rpi1 libblkid1_2.38.1-1 libbrotli1_1.0.9-2+b2 libbsd0_0.11.7-1 libbz2-1.0_1.0.8-5+b2 libbz2-dev_1.0.8-5+b2 libc-bin_2.35-1+rpi2 libc-dev-bin_2.35-1+rpi2 libc6_2.35-1+rpi2 libc6-dev_2.35-1+rpi2 libcairo2_1.16.0-6 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_12.2.0-3+rpi1 libcom-err2_1.46.6~rc1-1 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 libctf-nobfd0_2.39-6+rpi1 libctf0_2.39-6+rpi1 libdatrie1_0.2.13-2+b2 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.264 libdebhelper-perl_13.10 libdpkg-perl_1.21.9+rpi1 libedit2_3.1-20210910-1 libelf1_0.187-2+rpi2 libexpat1_2.4.9-1 libexpat1-dev_2.4.9-1 libext2fs2_1.46.6~rc1-1 libfakeroot_1.29-1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libfontconfig1_2.13.1-4.5 libfreetype6_2.12.1+dfsg-3 libfribidi0_1.0.8-2.1 libgcc-12-dev_12.2.0-3+rpi1 libgcc-s1_12.2.0-3+rpi1 libgcrypt20_1.10.1-2+b2 libgdbm-compat4_1.23-2 libgdbm6_1.23-2 libgenometools0_1.6.2+ds-2 libgenometools0-dev_1.6.2+ds-2 libglib2.0-0_2.74.0-2 libgmp10_2:6.2.1+dfsg1-1 libgnutls30_3.7.7-2 libgomp1_12.2.0-3+rpi1 libgpg-error0_1.45-2 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.20-1 libharfbuzz0b_5.2.0-2 libhogweed6_3.8.1-2 libicu71_71.1-3 libidn2-0_2.3.3-1 libisl23_0.25-1 libk5crypto3_1.20-1 libkeyutils1_1.6.3-1 libkrb5-3_1.20-1 libkrb5support0_1.20-1 libksba8_1.6.0-3 libldap-2.5-0_2.5.13+dfsg-2+rpi1 liblua5.1-0_5.1.5-9 liblua5.1-0-dev_5.1.5-9 liblz4-1_1.9.4-1+rpi1 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmd0_1.0.4-2 libmount1_2.38.1-1 libmpc3_1.2.1-2 libmpfr6_4.1.0-3 libncurses-dev_6.3+20220423-2 libncurses6_6.3+20220423-2 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.1-1 libpam-cap_1:2.44-1 libpam-modules_1.5.2-2 libpam-modules-bin_1.5.2-2 libpam-runtime_1.5.2-2 libpam0g_1.5.2-2 libpango-1.0-0_1.50.10+ds-1 libpangocairo-1.0-0_1.50.10+ds-1 libpangoft2-1.0-0_1.50.10+ds-1 libpcre2-8-0_10.40-1+b2 libpcre3_2:8.39-14 libperl5.34_5.34.0-5 libpipeline1_1.5.6-3 libpixman-1-0_0.40.0-1 libpng16-16_1.6.38-2 libreadline-dev_8.2-1 libreadline8_8.2-1 libruby_1:3.0+3.1 libruby3.0_3.0.4-8 libsasl2-2_2.1.28+dfsg-8 libsasl2-modules-db_2.1.28+dfsg-8 libseccomp2_2.5.4-1+rpi1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsepol1_3.1-1 libsepol2_3.4-2 libsmartcols1_2.38.1-1 libsqlite3-0_3.39.4-1 libss2_1.46.6~rc1-1 libssl1.1_1.1.1o-1 libssl3_3.0.5-2 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 libsub-override-perl_0.09-3 libsystemd0_251.4-3+rpi1 libtasn1-6_4.19.0-2 libthai-data_0.1.29-1 libthai0_0.1.29-1 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-4 libtre-dev_0.8.0-6 libtre5_0.8.0-6 libubsan1_12.2.0-3+rpi1 libuchardet0_0.0.7-1 libudev1_251.4-3+rpi1 libunistring2_1.0-1 libuuid1_2.38.1-1 libvmatch-dev_2.3.1+dfsg-8 libx11-6_2:1.8.1-2 libx11-data_2:1.8.1-2 libxau6_1:1.0.9-1 libxcb-render0_1.15-1 libxcb-shm0_1.15-1 libxcb1_1.15-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1 libxml2_2.9.14+dfsg-1 libxrender1_1:0.9.10-1.1 libxxhash0_0.8.1-1 libyaml-0-2_0.2.5-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.19.6-1+rpi1 login_1:4.11.1+dfsg1-2 logsave_1.46.6~rc1-1 lsb-base_11.4+rpi1 lua-filesystem_1.8.0-2 lua-lpeg_1.0.2-2 lua-md5_1.2+git+1+8d87fee-1.1 m4_1.4.19-1 make_4.3-4.1 man-db_2.10.2-3 mawk_1.3.4.20200120-3.1 mount_2.38.1-1 nano_6.4-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 netbase_6.3 openssl_3.0.5-2 passwd_1:4.11.1+dfsg1-2 patch_2.7.6-7 perl_5.34.0-5 perl-base_5.34.0-5 perl-modules-5.34_5.34.0-5 pinentry-curses_1.2.0-2 po-debconf_1.0.21+nmu1 rake_13.0.6-3 raspbian-archive-keyring_20120528.2 readline-common_8.2-1 rpcsvc-proto_1.4.2-4 ruby_1:3.0+3.1 ruby-asciidoctor_2.0.16-2 ruby-net-telnet_0.1.1-2.1 ruby-rubygems_3.3.15-1 ruby-sdbm_1.0.0-5 ruby-webrick_1.7.0-4 ruby-xmlrpc_0.3.2-2 ruby3.0_3.0.4-8 rubygems-integration_1.18 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-genomethreader-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.30 sysvinit-utils_3.05-6 tar_1.34+dfsg-1 tzdata_2022d-1 ucf_3.0043 util-linux_2.38.1-1 util-linux-extra_2.38.1-1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4.1 zlib1g-dev_1:1.2.11.dfsg-4.1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.2PqtPIfg/trustedkeys.kbx': General error
gpgv: Signature made Sat Oct 8 14:02:29 2022 UTC
gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./genomethreader_1.7.3+dfsg-7.dsc
dpkg-source: info: extracting genomethreader in /<<BUILDDIR>>/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-7.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
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-49895dbe-6675-4032-92ad-b02414370b8e
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package genomethreader
dpkg-buildpackage: info: source version 1.7.3+dfsg-7
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/genomethreader-1.7.3+dfsg'
dh_clean
rm -rf bin/bssm debian/bssm bin/gthdata debian/gthdata
rm -rf /<<BUILDDIR>>/genomethreader-1.7.3+dfsg/debian/man
rm -f debian/*substvars
make[1]: Leaving directory '/<<BUILDDIR>>/genomethreader-1.7.3+dfsg'
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/genomethreader-1.7.3+dfsg'
make licensemanager=no opt=yes 64bit=no
make[2]: Entering directory '/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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="<unistd.h>" -DEXPAT_H="<expat.h>" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/src -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/../vstree/src/include -I/<<BUILDDIR>>/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 '/<<BUILDDIR>>/genomethreader-1.7.3+dfsg'
make licensemanager=no opt=yes 64bit=no train
make[2]: Entering directory '/<<BUILDDIR>>/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 '/<<BUILDDIR>>/genomethreader-1.7.3+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/genomethreader-1.7.3+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/genomethreader-1.7.3+dfsg'
make licensemanager=no 64bit=no test
make[2]: Entering directory '/<<BUILDDIR>>/genomethreader-1.7.3+dfsg'
cd testsuite && env -i GTH_MEM_BOOKKEEPING=on MAKE=make PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" \
BSSMDIR=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/bin/bssm GTHDATADIR=/<<BUILDDIR>>/genomethreader-1.7.3+dfsg/gthdata/gth \
CCACHE_DISABLE=yes HOME=/sbuild-nonexistent GTHTESTDATADIR= \
ruby -I. testsuite.rb \
-testdata /<<BUILDDIR>>/genomethreader-1.7.3+dfsg/testdata -bin /<<BUILDDIR>>/genomethreader-1.7.3+dfsg/bin -cur /<<BUILDDIR>>/genomethreader-1.7.3+dfsg \
-gtruby /<<BUILDDIR>>/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 '/<<BUILDDIR>>/genomethreader-1.7.3+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/genomethreader-1.7.3+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/genomethreader-1.7.3+dfsg'
mv bin/bssm debian/bssm
mv bin/gthdata debian/gthdata
dh_auto_install
make[1]: Leaving directory '/<<BUILDDIR>>/genomethreader-1.7.3+dfsg'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installman
make[1]: Entering directory '/<<BUILDDIR>>/genomethreader-1.7.3+dfsg'
mkdir -p /<<BUILDDIR>>/genomethreader-1.7.3+dfsg/debian/man
asciidoctor -a docdate='' -b manpage /<<BUILDDIR>>/genomethreader-1.7.3+dfsg/debian/man_src/*.adoc
cp /<<BUILDDIR>>/genomethreader-1.7.3+dfsg/debian/man_src/*.? /<<BUILDDIR>>/genomethreader-1.7.3+dfsg/debian/man
dh_installman --
make[1]: Leaving directory '/<<BUILDDIR>>/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 '/<<BUILDDIR>>/genomethreader-1.7.3+dfsg'
echo "libvmatch-dev:Version=2.3.1+dfsg-8" >> debian/genomethreader.substvars
dh_gencontrol
make[1]: Leaving directory '/<<BUILDDIR>>/genomethreader-1.7.3+dfsg'
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'genomethreader' in '../genomethreader_1.7.3+dfsg-7_armhf.deb'.
dpkg-deb: building package 'genomethreader-dbgsym' in '../genomethreader-dbgsym_1.7.3+dfsg-7_armhf.deb'.
dpkg-genbuildinfo --build=any -O../genomethreader_1.7.3+dfsg-7_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../genomethreader_1.7.3+dfsg-7_armhf.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)
--------------------------------------------------------------------------------
Build finished at 2022-10-11T10:07:42Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
genomethreader_1.7.3+dfsg-7_armhf.changes:
------------------------------------------
Format: 1.8
Date: Sat, 08 Oct 2022 13:52:00 +0000
Source: genomethreader
Binary: genomethreader genomethreader-dbgsym
Architecture: armhf
Version: 1.7.3+dfsg-7
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Sascha Steinbiss <satta@debian.org>
Description:
genomethreader - software tool to compute gene structure predictions
Changes:
genomethreader (1.7.3+dfsg-7) unstable; urgency=medium
.
* Fix watchfile to detect new versions on github
* Bump Standards-Version.
Checksums-Sha1:
910cec588c821110693de1dab73b59ada3d55dce 1544712 genomethreader-dbgsym_1.7.3+dfsg-7_armhf.deb
b5333c36f128b584f777d2ef31749b8a7c3a6fd4 7004 genomethreader_1.7.3+dfsg-7_armhf.buildinfo
742cfcbd34bd011f6b85710236eba07a55d0c059 1863616 genomethreader_1.7.3+dfsg-7_armhf.deb
Checksums-Sha256:
4b7ccc0718d24754a84cac0caf50a4d9a941fa2a9d5a66d94b71c2cb64061fb7 1544712 genomethreader-dbgsym_1.7.3+dfsg-7_armhf.deb
49bbfb8d214890a531c877053e6e92b26372586207b590684a507c23826687f5 7004 genomethreader_1.7.3+dfsg-7_armhf.buildinfo
84eee4e2b4ec29295b98825344ae10b76fdf96537bd52aaab6024ecfb718f55a 1863616 genomethreader_1.7.3+dfsg-7_armhf.deb
Files:
e912862b1d754156a445d5bb25b046c3 1544712 debug optional genomethreader-dbgsym_1.7.3+dfsg-7_armhf.deb
ee65c0e539d57523abed6ead24fc7120 7004 science optional genomethreader_1.7.3+dfsg-7_armhf.buildinfo
624643c99bf01bbd8aad1755a35afd28 1863616 science optional genomethreader_1.7.3+dfsg-7_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
genomethreader-dbgsym_1.7.3+dfsg-7_armhf.deb
--------------------------------------------
new Debian package, version 2.0.
size 1544712 bytes: control archive=1148 bytes.
860 bytes, 12 lines control
1366 bytes, 13 lines md5sums
Package: genomethreader-dbgsym
Source: genomethreader
Version: 1.7.3+dfsg-7
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2147
Depends: genomethreader (= 1.7.3+dfsg-7)
Section: debug
Priority: optional
Description: debug symbols for genomethreader
Build-Ids: 162039eb7b7ce064a2223221ed2bc9d65626dac0 2147b032dae4ec449797c3234b7f4814ae50381c 2c9142bb2464bace8a0c609ee9b7b1fccc0f194e 5273521dcd60ea00674e738cb2d0e641d7018896 582c8f0306068ee037bc86141c44b441d7d737c0 5c56083d2c32996c99159c0f7326ca0098f6bc0b 85e43a6a735a0e2c567ba47887d90703b722a431 8c9b5d067c66d669b220bad7494b2a00b58bff19 8cb3fd12ff2a76961daba534553f78ee17464885 b16357a3d6a9c636697567f941cb2ade043fc759 e8784c9ff9383fe6c00464fa14294ce4bb0920d2 fe6b3d4c54342ea8a7ef5ed6d4011b6f7ce131cf
drwxr-xr-x root/root 0 2022-10-08 13:52 ./
drwxr-xr-x root/root 0 2022-10-08 13:52 ./usr/
drwxr-xr-x root/root 0 2022-10-08 13:52 ./usr/lib/
drwxr-xr-x root/root 0 2022-10-08 13:52 ./usr/lib/debug/
drwxr-xr-x root/root 0 2022-10-08 13:52 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2022-10-08 13:52 ./usr/lib/debug/.build-id/16/
-rw-r--r-- root/root 27204 2022-10-08 13:52 ./usr/lib/debug/.build-id/16/2039eb7b7ce064a2223221ed2bc9d65626dac0.debug
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lrwxrwxrwx root/root 0 2022-10-08 13:52 ./usr/share/doc/genomethreader-dbgsym -> genomethreader
genomethreader_1.7.3+dfsg-7_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 1863616 bytes: control archive=1988 bytes.
883 bytes, 17 lines control
3091 bytes, 45 lines md5sums
Package: genomethreader
Version: 1.7.3+dfsg-7
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 22087
Depends: libc6 (>= 2.34), libexpat1 (>= 2.0.1), libgenometools0 (>= 1.6.2+ds), liblua5.1-0, zlib1g (>= 1:1.2.3.3)
Built-Using: vmatch (= 2.3.1+dfsg-8)
Section: science
Priority: optional
Homepage: http://genomethreader.org
Description: software tool to compute gene structure predictions
GenomeThreader is a software tool to compute gene structure predictions.
The gene structure predictions are calculated using a similarity-based
approach where additional cDNA/EST and/or protein sequences are used to
predict gene structures via spliced alignments. GenomeThreader was motivated
by disabling limitations in GeneSeqer, a popular gene prediction program
which is widely used for plant genome annotation.
drwxr-xr-x root/root 0 2022-10-08 13:52 ./
drwxr-xr-x root/root 0 2022-10-08 13:52 ./usr/
drwxr-xr-x root/root 0 2022-10-08 13:52 ./usr/bin/
-rwxr-xr-x root/root 2296636 2022-10-08 13:52 ./usr/bin/align_dna
-rwxr-xr-x root/root 2493276 2022-10-08 13:52 ./usr/bin/gth
-rwxr-xr-x root/root 1640052 2022-10-08 13:52 ./usr/bin/gthbssmbuild
-rwxr-xr-x root/root 1640052 2022-10-08 13:52 ./usr/bin/gthbssmfileinfo
-rwxr-xr-x root/root 1640052 2022-10-08 13:52 ./usr/bin/gthbssmprint
-rwxr-xr-x root/root 1640052 2022-10-08 13:52 ./usr/bin/gthbssmrmsd
-rwxr-xr-x root/root 67116 2022-10-08 13:52 ./usr/bin/gthbssmtrain
-rwxr-xr-x root/root 2362204 2022-10-08 13:52 ./usr/bin/gthconsensus
-rwxr-xr-x root/root 658236 2022-10-08 13:52 ./usr/bin/gthfilestat
-rwxr-xr-x root/root 658236 2022-10-08 13:52 ./usr/bin/gthgetseq
-rwxr-xr-x root/root 1640052 2022-10-08 13:52 ./usr/bin/gthmkbssmfiles
-rwxr-xr-x root/root 658236 2022-10-08 13:52 ./usr/bin/gthsplit
drwxr-xr-x root/root 0 2022-10-08 13:52 ./usr/lib/
drwxr-xr-x root/root 0 2022-10-08 13:52 ./usr/lib/genomethreader/
drwxr-xr-x root/root 0 2022-10-08 13:52 ./usr/lib/genomethreader/bssm/
-rw-r--r-- root/root 551095 2022-10-08 13:52 ./usr/lib/genomethreader/bssm/arabidopsis.bssm
-rw-r--r-- root/root 367401 2022-10-08 13:52 ./usr/lib/genomethreader/bssm/arabidopsis.old.bssm
-rw-r--r-- root/root 367401 2022-10-08 13:52 ./usr/lib/genomethreader/bssm/aspergillus.bssm
-rw-r--r-- root/root 367401 2022-10-08 13:52 ./usr/lib/genomethreader/bssm/chicken.bssm
-rw-r--r-- root/root 367401 2022-10-08 13:52 ./usr/lib/genomethreader/bssm/drosophila.bssm
-rw-r--r-- root/root 367401 2022-10-08 13:52 ./usr/lib/genomethreader/bssm/fission_yeast.bssm
-rw-r--r-- root/root 105131 2022-10-08 13:52 ./usr/lib/genomethreader/bssm/human.bssm
-rw-r--r-- root/root 551095 2022-10-08 13:52 ./usr/lib/genomethreader/bssm/maize.bssm
-rw-r--r-- root/root 367401 2022-10-08 13:52 ./usr/lib/genomethreader/bssm/maize.old.bssm
-rw-r--r-- root/root 367401 2022-10-08 13:52 ./usr/lib/genomethreader/bssm/medicago.bssm
-rw-r--r-- root/root 105131 2022-10-08 13:52 ./usr/lib/genomethreader/bssm/mouse.bssm
-rw-r--r-- root/root 367401 2022-10-08 13:52 ./usr/lib/genomethreader/bssm/nematode.bssm
-rw-r--r-- root/root 367401 2022-10-08 13:52 ./usr/lib/genomethreader/bssm/rat.bssm
-rw-r--r-- root/root 551095 2022-10-08 13:52 ./usr/lib/genomethreader/bssm/rice.bssm
drwxr-xr-x root/root 0 2022-10-08 13:52 ./usr/share/
drwxr-xr-x root/root 0 2022-10-08 13:52 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-10-08 13:52 ./usr/share/doc/genomethreader/
-rw-r--r-- root/root 632 2022-10-08 13:52 ./usr/share/doc/genomethreader/changelog.Debian.gz
-rw-r--r-- root/root 1993 2020-01-09 18:41 ./usr/share/doc/genomethreader/changelog.gz
-rw-r--r-- root/root 3339 2021-09-28 20:41 ./usr/share/doc/genomethreader/copyright
drwxr-xr-x root/root 0 2022-10-08 13:52 ./usr/share/genomethreader/
drwxr-xr-x root/root 0 2022-10-08 13:52 ./usr/share/genomethreader/gthdata/
-rw-r--r-- root/root 2122 2022-10-08 13:52 ./usr/share/genomethreader/gthdata/BLOSUM62
-rw-r--r-- root/root 39 2022-10-08 13:52 ./usr/share/genomethreader/gthdata/TransDNAX
-rw-r--r-- root/root 146 2022-10-08 13:52 ./usr/share/genomethreader/gthdata/TransProt11
-rw-r--r-- root/root 290 2022-10-08 13:52 ./usr/share/genomethreader/gthdata/polyatail.dna
drwxr-xr-x root/root 0 2022-10-08 13:52 ./usr/share/man/
drwxr-xr-x root/root 0 2022-10-08 13:52 ./usr/share/man/man1/
-rw-r--r-- root/root 510 2022-10-08 13:52 ./usr/share/man/man1/align_dna.1.gz
-rw-r--r-- root/root 3184 2022-10-08 13:52 ./usr/share/man/man1/gth.1.gz
-rw-r--r-- root/root 631 2022-10-08 13:52 ./usr/share/man/man1/gthbssmbuild.1.gz
-rw-r--r-- root/root 478 2022-10-08 13:52 ./usr/share/man/man1/gthbssmfileinfo.1.gz
-rw-r--r-- root/root 463 2022-10-08 13:52 ./usr/share/man/man1/gthbssmprint.1.gz
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-rw-r--r-- root/root 1237 2022-10-08 13:52 ./usr/share/man/man1/gthbssmtrain.1.gz
-rw-r--r-- root/root 945 2022-10-08 13:52 ./usr/share/man/man1/gthconsensus.1.gz
-rw-r--r-- root/root 624 2022-10-08 13:52 ./usr/share/man/man1/gthfilestat.1.gz
-rw-r--r-- root/root 730 2022-10-08 13:52 ./usr/share/man/man1/gthgetseq.1.gz
-rw-r--r-- root/root 460 2022-10-08 13:52 ./usr/share/man/man1/gthmkbssmfiles.1.gz
-rw-r--r-- root/root 730 2022-10-08 13:52 ./usr/share/man/man1/gthsplit.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 162116
Build-Time: 274
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 276
Job: genomethreader_1.7.3+dfsg-7
Machine Architecture: armhf
Package: genomethreader
Package-Time: 573
Source-Version: 1.7.3+dfsg-7
Space: 162116
Status: successful
Version: 1.7.3+dfsg-7
--------------------------------------------------------------------------------
Finished at 2022-10-11T10:07:42Z
Build needed 00:09:33, 162116k disk space