Raspbian Package Auto-Building

genomethreader → 1.7.3+dfsg-6 → armhf → 2021-10-01 05:13:33

sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03

+==============================================================================+
| genomethreader 1.7.3+dfsg-6 (armhf)          Fri, 01 Oct 2021 04:52:54 +0000 |
+==============================================================================+

Package: genomethreader
Version: 1.7.3+dfsg-6
Source Version: 1.7.3+dfsg-6
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-ebc828f6-7ad8-4069-b7a9-26221796b000' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.4 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.8 MB in 26s (985 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| 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://172.17.0.1/private bookworm-staging/main genomethreader 1.7.3+dfsg-6 (dsc) [2228 B]
Get:2 http://172.17.0.1/private bookworm-staging/main genomethreader 1.7.3+dfsg-6 (tar) [40.0 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main genomethreader 1.7.3+dfsg-6 (diff) [13.5 kB]
Fetched 40.0 MB in 5s (7547 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/genomethreader-Xq88Dy/genomethreader-1.7.3+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/genomethreader-Xq88Dy' 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-MKcl0G/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-MKcl0G/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-MKcl0G/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: 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-MKcl0G/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-MKcl0G/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-MKcl0G/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-MKcl0G/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-MKcl0G/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2915 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 package was automatically installed and is no longer required:
  netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 22 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-MKcl0G/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 (11.7 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12484 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-MKcl0G/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-MKcl0G/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-MKcl0G/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-MKcl0G/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-MKcl0G/apt_archive ./ Sources [566 B]
Get:5 copy:/<<BUILDDIR>>/resolver-MKcl0G/apt_archive ./ Packages [648 B]
Fetched 2547 B in 1s (3389 B/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 package was automatically installed and is no longer required:
  netbase
Use 'apt autoremove' to remove it.
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 libffi8
  libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0
  libgenometools0 libgenometools0-dev libglib2.0-0 libgraphite2-3
  libharfbuzz0b libicu67 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
  libruby2.7 libsigsegv2 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-minitest ruby-net-telnet ruby-power-assert
  ruby-rubygems ruby-test-unit ruby-xmlrpc ruby2.7 rubygems-integration
  sensible-utils 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 libffi8
  libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0
  libgenometools0 libgenometools0-dev libglib2.0-0 libgraphite2-3
  libharfbuzz0b libicu67 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
  libruby2.7 libsigsegv2 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-minitest ruby-net-telnet ruby-power-assert
  ruby-rubygems ruby-test-unit ruby-xmlrpc ruby2.7 rubygems-integration
  sbuild-build-depends-genomethreader-dummy sensible-utils ucf zlib1g-dev
0 upgraded, 100 newly installed, 0 to remove and 22 not upgraded.
Need to get 37.9 MB of archives.
After this operation, 127 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-MKcl0G/apt_archive ./ sbuild-build-depends-genomethreader-dummy 0.invalid.0 [936 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-1 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf openssl armhf 1.1.1l-1 [815 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf ca-certificates all 20210119 [158 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf rubygems-integration all 1.18 [6704 B]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf rake all 13.0.3-1 [84.7 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf ruby-minitest all 5.13.0-1 [57.3 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf ruby-net-telnet all 0.1.1-2 [12.5 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf ruby-power-assert all 1.1.7-2 [11.5 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf ruby-test-unit all 3.3.9-1 [86.1 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf ruby-xmlrpc all 0.3.0-2 [23.7 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libmd0 armhf 1.0.3-3 [27.2 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.3-1 [103 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf libedit2 armhf 3.1-20210910-1 [81.2 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf libffi8 armhf 3.4.2-2 [21.2 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf libyaml-0-2 armhf 0.2.2-1 [40.0 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libruby2.7 armhf 2.7.4-1+b1 [3902 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf ruby2.7 armhf 2.7.4-1+b1 [747 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf ruby-rubygems all 3.2.27-1 [272 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf ruby armhf 1:2.7+2 [11.7 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf ruby-asciidoctor all 2.0.16-1 [210 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf asciidoctor all 2.0.16-1 [87.5 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.4-2 [819 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:51 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:52 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:53 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.1-2 [80.3 kB]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.37-3 [276 kB]
Get:57 http://172.17.0.1/private bookworm-staging/main armhf libfreetype6 armhf 2.10.4+dfsg-1 [353 kB]
Get:58 http://172.17.0.1/private bookworm-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:59 http://172.17.0.1/private bookworm-staging/main armhf fontconfig-config all 2.13.1-4.2 [281 kB]
Get:60 http://172.17.0.1/private bookworm-staging/main armhf libfontconfig1 armhf 2.13.1-4.2 [328 kB]
Get:61 http://172.17.0.1/private bookworm-staging/main armhf fontconfig armhf 2.13.1-4.2 [416 kB]
Get:62 http://172.17.0.1/private bookworm-staging/main armhf libpixman-1-0 armhf 0.40.0-1 [463 kB]
Get:63 http://172.17.0.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:64 http://172.17.0.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:65 http://172.17.0.1/private bookworm-staging/main armhf libxcb1 armhf 1.14-3 [136 kB]
Get:66 http://172.17.0.1/private bookworm-staging/main armhf libx11-data all 2:1.7.2-2 [311 kB]
Get:67 http://172.17.0.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.7.2-2 [704 kB]
Get:68 http://172.17.0.1/private bookworm-staging/main armhf libxcb-render0 armhf 1.14-3 [110 kB]
Get:69 http://172.17.0.1/private bookworm-staging/main armhf libxcb-shm0 armhf 1.14-3 [101 kB]
Get:70 http://172.17.0.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:71 http://172.17.0.1/private bookworm-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:72 http://172.17.0.1/private bookworm-staging/main armhf libcairo2 armhf 1.16.0-5 [602 kB]
Get:73 http://172.17.0.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.70.0-1 [1208 kB]
Get:74 http://172.17.0.1/private bookworm-staging/main armhf liblua5.1-0 armhf 5.1.5-8.1+b2 [82.8 kB]
Get:75 http://172.17.0.1/private bookworm-staging/main armhf libfribidi0 armhf 1.0.8-2 [63.5 kB]
Get:76 http://172.17.0.1/private bookworm-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:77 http://172.17.0.1/private bookworm-staging/main armhf libharfbuzz0b armhf 2.7.4-1 [1422 kB]
Get:78 http://172.17.0.1/private bookworm-staging/main armhf libthai-data all 0.1.28-4.1 [171 kB]
Get:79 http://172.17.0.1/private bookworm-staging/main armhf libdatrie1 armhf 0.2.13-1+b1 [39.7 kB]
Get:80 http://172.17.0.1/private bookworm-staging/main armhf libthai0 armhf 0.1.28-4.1 [51.4 kB]
Get:81 http://172.17.0.1/private bookworm-staging/main armhf libpango-1.0-0 armhf 1.48.10+ds1-1 [184 kB]
Get:82 http://172.17.0.1/private bookworm-staging/main armhf libpangoft2-1.0-0 armhf 1.48.10+ds1-1 [66.6 kB]
Get:83 http://172.17.0.1/private bookworm-staging/main armhf libpangocairo-1.0-0 armhf 1.48.10+ds1-1 [56.8 kB]
Get:84 http://172.17.0.1/private bookworm-staging/main armhf libtre5 armhf 0.8.0-6 [52.0 kB]
Get:85 http://172.17.0.1/private bookworm-staging/main armhf lua-filesystem armhf 1.8.0-1 [11.7 kB]
Get:86 http://172.17.0.1/private bookworm-staging/main armhf lua-lpeg armhf 1.0.2-1 [28.4 kB]
Get:87 http://172.17.0.1/private bookworm-staging/main armhf lua-md5 armhf 1.2+git+1+8d87fee-1.1 [12.3 kB]
Get:88 http://172.17.0.1/private bookworm-staging/main armhf genometools-common all 1.6.2+ds-2 [197 kB]
Get:89 http://172.17.0.1/private bookworm-staging/main armhf genometools armhf 1.6.2+ds-2 [1445 kB]
Get:90 http://172.17.0.1/private bookworm-staging/main armhf libbz2-dev armhf 1.0.8-4 [28.0 kB]
Get:91 http://172.17.0.1/private bookworm-staging/main armhf libexpat1-dev armhf 2.4.1-2 [135 kB]
Get:92 http://172.17.0.1/private bookworm-staging/main armhf libgenometools0 armhf 1.6.2+ds-2 [1214 kB]
Get:93 http://172.17.0.1/private bookworm-staging/main armhf libgenometools0-dev armhf 1.6.2+ds-2 [97.4 kB]
Get:94 http://172.17.0.1/private bookworm-staging/main armhf libncurses6 armhf 6.2+20201114-4 [79.7 kB]
Get:95 http://172.17.0.1/private bookworm-staging/main armhf libncurses-dev armhf 6.2+20201114-4 [288 kB]
Get:96 http://172.17.0.1/private bookworm-staging/main armhf libreadline-dev armhf 8.1-2 [121 kB]
Get:97 http://172.17.0.1/private bookworm-staging/main armhf liblua5.1-0-dev armhf 5.1.5-8.1+b2 [115 kB]
Get:98 http://172.17.0.1/private bookworm-staging/main armhf libtre-dev armhf 0.8.0-6 [27.4 kB]
Get:99 http://172.17.0.1/private bookworm-staging/main armhf libvmatch-dev armhf 2.3.1+dfsg-6 [529 kB]
Get:100 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
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Setting up libedit2:armhf (3.1-20210910-1) ...
Setting up m4 (1.4.18-5) ...
Setting up libxcb-shm0:armhf (1.14-3) ...
Setting up libreadline-dev:armhf (8.1-2) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libthai0:armhf (0.1.28-4.1) ...
Setting up ca-certificates (20210119) ...
Updating certificates in /etc/ssl/certs...
129 added, 0 removed; done.
Setting up libfreetype6:armhf (2.10.4+dfsg-1) ...
Setting up ucf (3.0043) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.12.0-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-7) ...
Setting up libx11-6:armhf (2:1.7.2-2) ...
Setting up libharfbuzz0b:armhf (2.7.4-1) ...
Setting up automake (1:1.16.4-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up liblua5.1-0-dev:armhf (5.1.5-8.1+b2) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up fontconfig-config (2.13.1-4.2) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up rubygems-integration (1.18) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up libfontconfig1:armhf (2.13.1-4.2) ...
Setting up fontconfig (2.13.1-4.2) ...
Regenerating fonts cache... done.
Setting up libpango-1.0-0:armhf (1.48.10+ds1-1) ...
Setting up debhelper (13.5.2) ...
Setting up libcairo2:armhf (1.16.0-5) ...
Setting up libpangoft2-1.0-0:armhf (1.48.10+ds1-1) ...
Setting up libpangocairo-1.0-0:armhf (1.48.10+ds1-1) ...
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 ruby (1:2.7+2) ...
Setting up ruby-asciidoctor (2.0.16-1) ...
Setting up rake (13.0.3-1) ...
Setting up asciidoctor (2.0.16-1) ...
Setting up ruby-rubygems (3.2.27-1) ...
Setting up libruby2.7:armhf (2.7.4-1+b1) ...
Setting up sbuild-build-depends-genomethreader-dummy (0.invalid.0) ...
Setting up ruby2.7 (2.7.4-1+b1) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
Processing triggers for ca-certificates (20210119) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-9+rpi1 gcc-10_10.3.0-9+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-4+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.3.9 asciidoctor_2.0.16-1 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.51 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-1 bsdutils_1:2.37.2-1 build-essential_12.9 bzip2_1.0.8-4 ca-certificates_20210119 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-9+rpi1 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 fontconfig_2.13.1-4.2 fontconfig-config_2.13.1-4.2 fonts-dejavu-core_2.37-2 g++_4:10.2.1-1+rpi1 g++-10_10.3.0-9+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-9+rpi1 gcc-10-base_10.3.0-9+rpi1 gcc-11-base_11.2.0-4+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_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.9 libarchive-zip-perl_1.68-1 libasan6_11.2.0-4+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-4+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.5-1 libaudit1_1:3.0.5-1 libbinutils_2.37-5+rpi1 libblkid1_2.37.2-1 libbrotli1_1.0.9-2+b1 libbsd0_0.11.3-1 libbz2-1.0_1.0.8-4 libbz2-dev_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcairo2_1.16.0-5 libcap-ng0_0.7.9-2.2+b1 libcc1-0_11.2.0-4+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libdatrie1_0.2.13-1+b1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdpkg-perl_1.20.9+rpi1 libedit2_3.1-20210910-1 libelf1_0.185-2 libexpat1_2.4.1-2 libexpat1-dev_2.4.1-2 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libffi8_3.4.2-2 libfile-stripnondeterminism-perl_1.12.0-1 libfontconfig1_2.13.1-4.2 libfreetype6_2.10.4+dfsg-1 libfribidi0_1.0.8-2 libgcc-10-dev_10.3.0-9+rpi1 libgcc-s1_11.2.0-4+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.21-1 libgdbm6_1.21-1 libgenometools0_1.6.2+ds-2 libgenometools0-dev_1.6.2+ds-2 libglib2.0-0_2.70.0-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-4+rpi1 libgpg-error0_1.42-3 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.18.3-7 libharfbuzz0b_2.7.4-1 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.23-1 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblua5.1-0_5.1.5-8.1+b2 liblua5.1-0-dev_5.1.5-8.1+b2 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmd0_1.0.3-3 libmount1_2.37.2-1 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses-dev_6.2+20201114-4 libncurses6_6.2+20201114-4 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-2 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpango-1.0-0_1.48.10+ds1-1 libpangocairo-1.0-0_1.48.10+ds1-1 libpangoft2-1.0-0_1.48.10+ds1-1 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-5 libpipeline1_1.5.3-1 libpixman-1-0_0.40.0-1 libpng16-16_1.6.37-3 libreadline-dev_8.1-2 libreadline8_8.1-2 libruby2.7_2.7.4-1+b1 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-1 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-4+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.9-1+rpi1 libtasn1-6_4.17.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libthai-data_0.1.28-4.1 libthai0_0.1.28-4.1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libtre-dev_0.8.0-6 libtre5_0.8.0-6 libubsan1_11.2.0-4+rpi1 libuchardet0_0.0.7-1 libudev1_247.9-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-1 libvmatch-dev_2.3.1+dfsg-6 libx11-6_2:1.7.2-2 libx11-data_2:1.7.2-2 libxau6_1:1.0.9-1 libxcb-render0_1.14-3 libxcb-shm0_1.14-3 libxcb1_1.14-3 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1 libxml2_2.9.12+dfsg-5 libxrender1_1:0.9.10-1 libxxhash0_0.8.0-2+rpi1 libyaml-0-2_0.2.2-1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 lua-filesystem_1.8.0-1 lua-lpeg_1.0.2-1 lua-md5_1.2+git+1+8d87fee-1.1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.37.2-1 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 openssl_1.1.1l-1 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-5 perl-base_5.32.1-5 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 rake_13.0.3-1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 ruby_1:2.7+2 ruby-asciidoctor_2.0.16-1 ruby-minitest_5.13.0-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_1.1.7-2 ruby-rubygems_3.2.27-1 ruby-test-unit_3.3.9-1 ruby-xmlrpc_0.3.0-2 ruby2.7_2.7.4-1+b1 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 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021a-1 ucf_3.0043 util-linux_2.37.2-1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.Dhh5elll/trustedkeys.kbx': General error
gpgv: Signature made Tue Sep 28 21:07:38 2021 UTC
gpgv:                using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./genomethreader_1.7.3+dfsg-6.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-6.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying debian-gt-libs.patch
dpkg-source: info: applying gt-path-fix.patch
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying search-paths.patch
dpkg-source: info: applying m32-m64-ignore.patch
dpkg-source: info: applying reproducible.patch
dpkg-source: info: applying disable-fastdp-tests.patch

Check disc 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=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-ebc828f6-7ad8-4069-b7a9-26221796b000
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd

dpkg-buildpackage
-----------------

dpkg-buildpackage: info: source package genomethreader
dpkg-buildpackage: info: source version 1.7.3+dfsg-6
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-6" >> 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-6_armhf.deb'.
dpkg-deb: building package 'genomethreader-dbgsym' in '../genomethreader-dbgsym_1.7.3+dfsg-6_armhf.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../genomethreader_1.7.3+dfsg-6_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 2021-10-01T05:13:24Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Post Build Chroot                                                            |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


genomethreader_1.7.3+dfsg-6_armhf.changes:
------------------------------------------

Format: 1.8
Date: Tue, 28 Sep 2021 22:49:50 +0200
Source: genomethreader
Binary: genomethreader genomethreader-dbgsym
Architecture: armhf
Version: 1.7.3+dfsg-6
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <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-6) unstable; urgency=medium
 .
   * Fix d/watch to work with GitHub link structure.
   * Bump Standards-Version.
   * Add Rules-Requires-Root.
   * Use debhelper 13.
   * Add upstream repository metadata.
Checksums-Sha1:
 9d806b91a4117132575863348962efec0bffd06c 1519008 genomethreader-dbgsym_1.7.3+dfsg-6_armhf.deb
 579fd24f850b7db7ec9ff499c005bbde26881171 7019 genomethreader_1.7.3+dfsg-6_armhf.buildinfo
 38436a28f72cec4d94db710bee30162b4967781d 1871872 genomethreader_1.7.3+dfsg-6_armhf.deb
Checksums-Sha256:
 f05a9ce85139efedd98fab72bb2084d452068a94ec55d1005792dc4365ff0291 1519008 genomethreader-dbgsym_1.7.3+dfsg-6_armhf.deb
 294fce1ac2d8ff44abe1af3e7407c28cbe5a8af1a4ac6617cb964ec97a9018a8 7019 genomethreader_1.7.3+dfsg-6_armhf.buildinfo
 f0ef07d1828a0282d27081947621079a031ea2f2785b2ea0c117683a1311e7b7 1871872 genomethreader_1.7.3+dfsg-6_armhf.deb
Files:
 85c2b25fc7b95705ebf0ae285632478b 1519008 debug optional genomethreader-dbgsym_1.7.3+dfsg-6_armhf.deb
 ca1e13144b18934ce3e2f6b8dabfb934 7019 science optional genomethreader_1.7.3+dfsg-6_armhf.buildinfo
 49065f54281c348ad4675f6c73410f41 1871872 science optional genomethreader_1.7.3+dfsg-6_armhf.deb

+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


genomethreader-dbgsym_1.7.3+dfsg-6_armhf.deb
--------------------------------------------

 new Debian package, version 2.0.
 size 1519008 bytes: control archive=1152 bytes.
     860 bytes,    12 lines      control              
    1366 bytes,    13 lines      md5sums              
 Package: genomethreader-dbgsym
 Source: genomethreader
 Version: 1.7.3+dfsg-6
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 2128
 Depends: genomethreader (= 1.7.3+dfsg-6)
 Section: debug
 Priority: optional
 Description: debug symbols for genomethreader
 Build-Ids: 058c5d663f705da8a054cda4496fc508eda7241c 2b7b51f9525b72706a9b09fe7464bd621b07480e 38489b1bb79ced55c6182d0d6c934b63d0ab9d14 9d3e04179952de817b66b057201c986f28a2c581 abc09913732ced3d8f33c64d1910d9ab0b1c2a72 c24010215853b7ff1b990f7e9026ddef74e21e5d cd2df3a5fa303fe8f77af9968b3ca2b0c7c0df0f ce5aa1eaeb4cdc3cfe6124e18310107badbc7d70 d05494886c405ef5c43573b20a28900424bf588c d67bfad120b733d14ce034ad43fb583ce1b0461b ede368e5c6d225f92892a51b4db6325e8ff24a95 f0a845491598393b54710f549ad3fb0566b04e95

drwxr-xr-x root/root         0 2021-09-28 20:49 ./
drwxr-xr-x root/root         0 2021-09-28 20:49 ./usr/
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drwxr-xr-x root/root         0 2021-09-28 20:49 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root         0 2021-09-28 20:49 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root     40084 2021-09-28 20:49 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/genomethreader.debug
drwxr-xr-x root/root         0 2021-09-28 20:49 ./usr/share/
drwxr-xr-x root/root         0 2021-09-28 20:49 ./usr/share/doc/
lrwxrwxrwx root/root         0 2021-09-28 20:49 ./usr/share/doc/genomethreader-dbgsym -> genomethreader


genomethreader_1.7.3+dfsg-6_armhf.deb
-------------------------------------

 new Debian package, version 2.0.
 size 1871872 bytes: control archive=1984 bytes.
     883 bytes,    17 lines      control              
    3091 bytes,    45 lines      md5sums              
 Package: genomethreader
 Version: 1.7.3+dfsg-6
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 21679
 Depends: libc6 (>= 2.29), 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-6)
 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 2021-09-28 20:49 ./
drwxr-xr-x root/root         0 2021-09-28 20:49 ./usr/
drwxr-xr-x root/root         0 2021-09-28 20:49 ./usr/bin/
-rwxr-xr-x root/root   2251580 2021-09-28 20:49 ./usr/bin/align_dna
-rwxr-xr-x root/root   2448220 2021-09-28 20:49 ./usr/bin/gth
-rwxr-xr-x root/root   1594996 2021-09-28 20:49 ./usr/bin/gthbssmbuild
-rwxr-xr-x root/root   1594996 2021-09-28 20:49 ./usr/bin/gthbssmfileinfo
-rwxr-xr-x root/root   1594996 2021-09-28 20:49 ./usr/bin/gthbssmprint
-rwxr-xr-x root/root   1594996 2021-09-28 20:49 ./usr/bin/gthbssmrmsd
-rwxr-xr-x root/root     50732 2021-09-28 20:49 ./usr/bin/gthbssmtrain
-rwxr-xr-x root/root   2308956 2021-09-28 20:49 ./usr/bin/gthconsensus
-rwxr-xr-x root/root    654140 2021-09-28 20:49 ./usr/bin/gthfilestat
-rwxr-xr-x root/root    641852 2021-09-28 20:49 ./usr/bin/gthgetseq
-rwxr-xr-x root/root   1594996 2021-09-28 20:49 ./usr/bin/gthmkbssmfiles
-rwxr-xr-x root/root    645948 2021-09-28 20:49 ./usr/bin/gthsplit
drwxr-xr-x root/root         0 2021-09-28 20:49 ./usr/lib/
drwxr-xr-x root/root         0 2021-09-28 20:49 ./usr/lib/genomethreader/
drwxr-xr-x root/root         0 2021-09-28 20:49 ./usr/lib/genomethreader/bssm/
-rw-r--r-- root/root    551095 2021-09-28 20:49 ./usr/lib/genomethreader/bssm/arabidopsis.bssm
-rw-r--r-- root/root    367401 2021-09-28 20:49 ./usr/lib/genomethreader/bssm/arabidopsis.old.bssm
-rw-r--r-- root/root    367401 2021-09-28 20:49 ./usr/lib/genomethreader/bssm/aspergillus.bssm
-rw-r--r-- root/root    367401 2021-09-28 20:49 ./usr/lib/genomethreader/bssm/chicken.bssm
-rw-r--r-- root/root    367401 2021-09-28 20:49 ./usr/lib/genomethreader/bssm/drosophila.bssm
-rw-r--r-- root/root    367401 2021-09-28 20:49 ./usr/lib/genomethreader/bssm/fission_yeast.bssm
-rw-r--r-- root/root    105131 2021-09-28 20:49 ./usr/lib/genomethreader/bssm/human.bssm
-rw-r--r-- root/root    551095 2021-09-28 20:49 ./usr/lib/genomethreader/bssm/maize.bssm
-rw-r--r-- root/root    367401 2021-09-28 20:49 ./usr/lib/genomethreader/bssm/maize.old.bssm
-rw-r--r-- root/root    367401 2021-09-28 20:49 ./usr/lib/genomethreader/bssm/medicago.bssm
-rw-r--r-- root/root    105131 2021-09-28 20:49 ./usr/lib/genomethreader/bssm/mouse.bssm
-rw-r--r-- root/root    367401 2021-09-28 20:49 ./usr/lib/genomethreader/bssm/nematode.bssm
-rw-r--r-- root/root    367401 2021-09-28 20:49 ./usr/lib/genomethreader/bssm/rat.bssm
-rw-r--r-- root/root    551095 2021-09-28 20:49 ./usr/lib/genomethreader/bssm/rice.bssm
drwxr-xr-x root/root         0 2021-09-28 20:49 ./usr/share/
drwxr-xr-x root/root         0 2021-09-28 20:49 ./usr/share/doc/
drwxr-xr-x root/root         0 2021-09-28 20:49 ./usr/share/doc/genomethreader/
-rw-r--r-- root/root       589 2021-09-28 20:49 ./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 2021-09-28 20:49 ./usr/share/genomethreader/
drwxr-xr-x root/root         0 2021-09-28 20:49 ./usr/share/genomethreader/gthdata/
-rw-r--r-- root/root      2122 2021-09-28 20:49 ./usr/share/genomethreader/gthdata/BLOSUM62
-rw-r--r-- root/root        39 2021-09-28 20:49 ./usr/share/genomethreader/gthdata/TransDNAX
-rw-r--r-- root/root       146 2021-09-28 20:49 ./usr/share/genomethreader/gthdata/TransProt11
-rw-r--r-- root/root       290 2021-09-28 20:49 ./usr/share/genomethreader/gthdata/polyatail.dna
drwxr-xr-x root/root         0 2021-09-28 20:49 ./usr/share/man/
drwxr-xr-x root/root         0 2021-09-28 20:49 ./usr/share/man/man1/
-rw-r--r-- root/root       510 2021-09-28 20:49 ./usr/share/man/man1/align_dna.1.gz
-rw-r--r-- root/root      3184 2021-09-28 20:49 ./usr/share/man/man1/gth.1.gz
-rw-r--r-- root/root       631 2021-09-28 20:49 ./usr/share/man/man1/gthbssmbuild.1.gz
-rw-r--r-- root/root       478 2021-09-28 20:49 ./usr/share/man/man1/gthbssmfileinfo.1.gz
-rw-r--r-- root/root       463 2021-09-28 20:49 ./usr/share/man/man1/gthbssmprint.1.gz
-rw-r--r-- root/root       484 2021-09-28 20:49 ./usr/share/man/man1/gthbssmrmsd.1.gz
-rw-r--r-- root/root      1237 2021-09-28 20:49 ./usr/share/man/man1/gthbssmtrain.1.gz
-rw-r--r-- root/root       945 2021-09-28 20:49 ./usr/share/man/man1/gthconsensus.1.gz
-rw-r--r-- root/root       624 2021-09-28 20:49 ./usr/share/man/man1/gthfilestat.1.gz
-rw-r--r-- root/root       730 2021-09-28 20:49 ./usr/share/man/man1/gthgetseq.1.gz
-rw-r--r-- root/root       460 2021-09-28 20:49 ./usr/share/man/man1/gthmkbssmfiles.1.gz
-rw-r--r-- root/root       730 2021-09-28 20:49 ./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: 162196
Build-Time: 731
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 439
Job: genomethreader_1.7.3+dfsg-6
Machine Architecture: armhf
Package: genomethreader
Package-Time: 1230
Source-Version: 1.7.3+dfsg-6
Space: 162196
Status: successful
Version: 1.7.3+dfsg-6
--------------------------------------------------------------------------------
Finished at 2021-10-01T05:13:24Z
Build needed 00:20:30, 162196k disc space

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