[med-svn] r21381 - trunk/packages/genometools/trunk/debian
Sascha Steinbiss
sascha-guest at moszumanska.debian.org
Sat Feb 6 14:08:46 UTC 2016
Author: sascha-guest
Date: 2016-02-06 14:08:46 +0000 (Sat, 06 Feb 2016)
New Revision: 21381
Added:
trunk/packages/genometools/trunk/debian/README.status
Removed:
trunk/packages/genometools/trunk/debian/README.status
trunk/packages/genometools/trunk/debian/changelog
trunk/packages/genometools/trunk/debian/compat
trunk/packages/genometools/trunk/debian/control
trunk/packages/genometools/trunk/debian/copyright
trunk/packages/genometools/trunk/debian/genometools-common.install
trunk/packages/genometools/trunk/debian/genometools-doc.doc-base
trunk/packages/genometools/trunk/debian/genometools-doc.docs
trunk/packages/genometools/trunk/debian/genometools.docs
trunk/packages/genometools/trunk/debian/genometools.install
trunk/packages/genometools/trunk/debian/genometools.manpages
trunk/packages/genometools/trunk/debian/libgenometools0-dev.install
trunk/packages/genometools/trunk/debian/libgenometools0-dev.links
trunk/packages/genometools/trunk/debian/libgenometools0.install
trunk/packages/genometools/trunk/debian/libgenometools0.postinst
trunk/packages/genometools/trunk/debian/libgenometools0.postrm
trunk/packages/genometools/trunk/debian/patches/
trunk/packages/genometools/trunk/debian/rules
trunk/packages/genometools/trunk/debian/source/
trunk/packages/genometools/trunk/debian/strip-nondeterminism/
trunk/packages/genometools/trunk/debian/tests/
trunk/packages/genometools/trunk/debian/upstream/
trunk/packages/genometools/trunk/debian/watch
Log:
clean up svn repo
Deleted: trunk/packages/genometools/trunk/debian/README.status
===================================================================
--- trunk/packages/genometools/trunk/debian/README.status 2016-02-06 13:58:07 UTC (rev 21380)
+++ trunk/packages/genometools/trunk/debian/README.status 2016-02-06 14:08:46 UTC (rev 21381)
@@ -1 +0,0 @@
-This package has been migrated to Git: https://anonscm.debian.org/git/debian-med/genometools.git
Added: trunk/packages/genometools/trunk/debian/README.status
===================================================================
--- trunk/packages/genometools/trunk/debian/README.status (rev 0)
+++ trunk/packages/genometools/trunk/debian/README.status 2016-02-06 14:08:46 UTC (rev 21381)
@@ -0,0 +1 @@
+This package has been migrated to Git: https://anonscm.debian.org/git/debian-med/genometools.git
Deleted: trunk/packages/genometools/trunk/debian/changelog
===================================================================
--- trunk/packages/genometools/trunk/debian/changelog 2016-02-06 13:58:07 UTC (rev 21380)
+++ trunk/packages/genometools/trunk/debian/changelog 2016-02-06 14:08:46 UTC (rev 21381)
@@ -1,233 +0,0 @@
-genometools (1.5.8-1) unstable; urgency=medium
-
- * New upstream release.
- * Ensure that /usr/share/genometools/* is complete.
- * Fix spelling.
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Thu, 07 Jan 2016 22:18:31 +0000
-
-genometools (1.5.7-7) unstable; urgency=medium
-
- * build API documentation reproducibly
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Sat, 12 Dec 2015 19:13:40 +0000
-
-genometools (1.5.7-6) unstable; urgency=medium
-
- * Reintroduce mips64el which was removed my mistake.
- * Fix detection of x32 build
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Wed, 09 Dec 2015 22:20:47 +0000
-
-genometools (1.5.7-5) unstable; urgency=medium
-
- * Try to load correct renamed .so file in Python bindings
- * Refresh patches
- * Use DEB_TARGET_ARCH to determine build archs
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Tue, 08 Dec 2015 00:42:49 +0000
-
-genometools (1.5.7-4) unstable; urgency=medium
-
- * Fix builds on less popular platforms
- - Check if faketime works
- - Do no use -m32/-m64 on x32
- * Improve reproducibility
- - sort files to compile by name
- * Add autopkgtests
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Fri, 04 Dec 2015 22:18:11 +0000
-
-genometools (1.5.7-3) unstable; urgency=low
-
- * d/control: remove obsolete dependency on libncurses5
- Closes: #804576
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Mon, 09 Nov 2015 19:15:29 +0000
-
-genometools (1.5.7-2) unstable; urgency=low
-
- * disable parallel building
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Sat, 10 Oct 2015 12:04:37 +0000
-
-genometools (1.5.7-1) unstable; urgency=low
-
- * New upstream release.
- * d/rules: try ro improve reproducibility
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Sun, 13 Sep 2015 08:22:39 +0000
-
-genometools (1.5.6-1) unstable; urgency=low
-
- * New upstream release.
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Mon, 22 Jun 2015 19:26:35 +0000
-
-genometools (1.5.5-2) unstable; urgency=low
-
- * Disable faketime on hurd-i386 to fix FTBFS on that arch.
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Wed, 10 Jun 2015 10:03:22 +0000
-
-genometools (1.5.5-1) unstable; urgency=low
-
- * New upstream release.
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Sat, 06 Jun 2015 09:49:49 +0000
-
-genometools (1.5.4-2) experimental; urgency=low
-
- * Work towards reproducibility.
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Sun, 22 Mar 2015 08:09:07 +0000
-
-genometools (1.5.4-1) experimental; urgency=low
-
- * New upstream release.
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Fri, 12 Dec 2014 12:06:42 +0000
-
-genometools (1.5.3-2) unstable; urgency=low
-
- * Reactivate missing patch.
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Fri, 05 Sep 2014 14:23:31 +0100
-
-genometools (1.5.3-1) unstable; urgency=low
-
- * New upstream release.
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Wed, 16 Jul 2014 20:32:19 +0100
-
-genometools (1.5.2-4) unstable; urgency=low
-
- * Incorporate patches addressing type conversion errors (thanks to
- Michael Tautschnig).
- Closes: #748305
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Sat, 24 May 2014 18:57:45 +0000
-
-genometools (1.5.2-3) unstable; urgency=low
-
- * Address building issues on s390x, powerpc and armhf
- * Don't use -m64 for arm64 (thanks to Logan Rosen)
- Closes: #748708
- * Build-depend on docbook-xsl to fix FTBFS while offline (thanks to
- Logan Rosen)
- Closes: #748709
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Mon, 19 May 2014 23:06:34 +0000
-
-genometools (1.5.2-2) unstable; urgency=low
-
- * Split manuals into separate documents to avoid strange LaTeX build issues.
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Thu, 15 May 2014 23:23:20 +0000
-
-genometools (1.5.2-1) unstable; urgency=low
-
- * New upstream release.
- * Remove symbols file because private symbols are exported (next upstream
- version will properly control exported symbols and a new symbols file
- will be created and maintained)
- * Remove manpages from debian directory as they are now autogenerated on
- build
- * Fix some missing symbols problems
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Thu, 15 May 2014 10:51:41 +0000
-
-genometools (1.5.1-3) unstable; urgency=low
-
- * debian/rules
- - Add basic tests to check whether cairo/pango linking works
- - Clean up indices created by tests to make repeated builds possible
- - Make sure bin/examples/sketch_parsed_with_* are built
- - Enable compiler optimization
- * debian/control
- - Move libgenometools0 package into libs section
- - Switch pango deps to new package
- - Add ruby builddep, required for the testsuite
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Wed, 06 Nov 2013 14:28:41 +0100
-
-genometools (1.5.1-2) unstable; urgency=low
-
- * debian/control
- - Add myself to Uploaders
- - cme fix dpkg-control
- - Follow liblua package name transition
- Closes: #728017
- - Remove depends from virtual package python-ctypes which is provided
- by python
- * provide symbols file
-
- -- Andreas Tille <tille at debian.org> Mon, 28 Oct 2013 08:17:04 +0100
-
-genometools (1.5.1-1) unstable; urgency=low
-
- * New upstream release.
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Thu, 07 Mar 2013 14:08:05 +0100
-
-genometools (1.5.0-2) unstable; urgency=low
-
- * Patch manuals not to use includecomment/excludecomment
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Sat, 16 Feb 2013 16:58:11 +0100
-
-genometools (1.5.0-1) unstable; urgency=low
-
- * New upstream release
- * bugfixes and cleanups
- * development tool `gt sain' added to run an induced suffix array sorting
- algorithm
- * the -typecheck option in the `gt gff3` and `gt gff3validator` tools
- now also validates parent (part-of) relationships, see -help output for
- details
- * new option -encseq besides -seqfile(s) and -regionmapping to select a
- encseq index as a sequence source
- * GtBioseq backend switched to GtEncseq
- * GtSeqCol is now an interface, GtEncseqCol added
- * GtRankedList added
- * GtSNPAnnotatorStream and `gt snpper' tool added
- * node sorting code is now aware of MD5 hash presence
- * compatibility with old Pango versions inproved
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Tue, 05 Feb 2013 18:52:22 +0100
-
-genometools (1.4.2-4) unstable; urgency=low
-
- * Remove shlibs.local file
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Tue, 09 Oct 2012 12:24:17 +0200
-
-genometools (1.4.2-3) unstable; urgency=low
-
- * Build with pbuilder to obtain reasonable libc dependency (>= 2.13)
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Tue, 09 Oct 2012 10:04:34 +0200
-
-genometools (1.4.2-2) unstable; urgency=low
-
- * Fixed libpango-dev dependency
- * Updated manpages
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Mon, 08 Oct 2012 07:51:52 +0200
-
-genometools (1.4.2-1) unstable; urgency=low
-
- * New upstream release
- [ Sponsor Steffen Moeller ]
- * Update of policy to 3.9.4
- * Added DMUA flag
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Fri, 05 Oct 2012 15:47:56 +0200
-
-genometools (1.4.1-1) unstable; urgency=low
-
- * Initial release (Closes: #657923)
- * the GFF3 parser now handles children which are defined before their parents
- * many small improvements to the GFF3 parser
-
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Mon, 09 Jul 2012 14:10:23 +0100
Deleted: trunk/packages/genometools/trunk/debian/compat
===================================================================
--- trunk/packages/genometools/trunk/debian/compat 2016-02-06 13:58:07 UTC (rev 21380)
+++ trunk/packages/genometools/trunk/debian/compat 2016-02-06 14:08:46 UTC (rev 21381)
@@ -1 +0,0 @@
-9
Deleted: trunk/packages/genometools/trunk/debian/control
===================================================================
--- trunk/packages/genometools/trunk/debian/control 2016-02-06 13:58:07 UTC (rev 21380)
+++ trunk/packages/genometools/trunk/debian/control 2016-02-06 14:08:46 UTC (rev 21381)
@@ -1,134 +0,0 @@
-Source: genometools
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Sascha Steinbiss <sascha at steinbiss.name>,
- Andreas Tille <tille at debian.org>
-Section: science
-Priority: optional
-Build-Depends: debhelper (>= 9),
- liblua5.1-0-dev,
- lua-md5-dev,
- lua-filesystem-dev,
- lua-lpeg-dev,
- libcairo2-dev,
- zlib1g-dev,
- libbz2-dev,
- libexpat1-dev,
- libsqlite3-dev,
- libbam-dev,
- libpango1.0-dev,
- libtre-dev,
- texlive-latex-base,
- texlive-latex-extra,
- texlive-fonts-extra,
- latex-xcolor,
- texlive-fonts-recommended,
- python,
- asciidoc,
- libxml2-utils,
- xsltproc,
- ruby,
- docbook-xsl,
- faketime,
- imagemagick
-Standards-Version: 3.9.6
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/genometools/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/genometools/trunk/
-Homepage: http://genometools.org
-
-Package: genometools
-Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x alpha hppa hurd-i386 kfreebsd-amd64 m68k mips64el kfreebsd-i386 ppc64 sh4 x32
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- genometools-common
-Description: versatile genome analysis toolkit
- The GenomeTools contains a collection of useful tools for biological
- sequence analysis and -presentation combined into a single binary.
- .
- The toolkit contains binaries for sequence and annotation handling, sequence
- compression, index structure generation and access, annotation visualization,
- and much more.
-
-Package: genometools-common
-Architecture: all
-Depends: ${misc:Depends},
- liblua5.1-0,
- libcairo2,
- zlib1g,
- libbz2-1.0,
- libexpat1,
- libpth20,
- libsqlite3-0,
- libpango-1.0-0,
- libpangocairo-1.0-0,
- libtre5
-Description: shared data files for GenomeTools
- This package contains configuration files such as alphabet
- transformations, style files, etc. required to use the GenomeTools
- executable and/or library.
-
-Package: libgenometools0
-Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x alpha hppa hurd-i386 kfreebsd-amd64 m68k mips64el kfreebsd-i386 ppc64 sh4 x32
-Section: libs
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- genometools-common
-Description: versatile genome analysis library
- This package contains the GenomeTools shared library and header
- files. It offers efficient sequence analysis components, available
- via an object-oriented interface.
- .
- Besides basic bioinformatics data structures, the library contains components
- for sequence and annotation handling, sequence compression, index structure
- generation and access, efficient matching, annotation visualization and much
- more.
-
-Package: libgenometools0-dev
-Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x alpha hppa hurd-i386 kfreebsd-amd64 m68k mips64el kfreebsd-i386 ppc64 sh4 x32
-Section: libdevel
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- libgenometools0 (= ${binary:Version})
-Description: development files for GenomeTools
- This package contains the GenomeTools static library and necessary
- header files.
- .
- Besides basic bioinformatics data structures, the library contains components
- for sequence and annotation handling, sequence compression, index structure
- generation and access, efficient matching, annotation visualization and much
- more.
-
-Package: genometools-doc
-Architecture: all
-Section: doc
-Depends: ${misc:Depends}
-Description: documentation for GenomeTools
- This package contains API documentation and tool documentation for
- GenomeTools. The GenomeTools toolkit contains binaries for sequence and
- annotation handling, sequence compression, index structure generation and
- access, annotation visualization, and much more.
-
-Package: genometools-dbg
-Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x alpha hppa hurd-i386 kfreebsd-amd64 m68k mips64el kfreebsd-i386 ppc64 sh4 x32
-Section: debug
-Priority: extra
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- genometools (= ${binary:Version}) | libgenometools0 (= ${binary:Version})
-Description: versatile genome analysis toolkit, with debug symbols
- This package contains debug information stripped from the GenomeTools.
- You may decide to install it to help identifying issues, typically
- to help communication with upstream developers.
-
-Package: python-genometools
-Architecture: all
-Section: python
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- ${python:Depends},
- python-ctypes,
- libgenometools0
-Description: Python bindings for genometools
- Partial Python2 bindings for the GenomeTools library. Besides basic
- bioinformatics data structures, the library contains components for sequence
- and annotation handling, sequence compression, index structure generation and
- access, efficient matching, annotation visualization and much more.
Deleted: trunk/packages/genometools/trunk/debian/copyright
===================================================================
--- trunk/packages/genometools/trunk/debian/copyright 2016-02-06 13:58:07 UTC (rev 21380)
+++ trunk/packages/genometools/trunk/debian/copyright 2016-02-06 14:08:46 UTC (rev 21381)
@@ -1,112 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: genometools
-Source: http://genometools.org
-
-Files:
- *
-Copyright:
- 2001-2014 Stefan Kurtz
- 2003-2014 Gordon Gremme
- 2007-2014 Sascha Steinbiss
- 2004-2012 Stefan Bienert
- 2010-2011 Joachim Bonnet
- 2007 David Ellinghaus
- 2008 Johannes Fischer
- 2009-2014 Giorgio Gonnella
- 2007-2008 Thomas Jahns
- 2007 Malte Mader
- 2009 Brent Pedersen
- 2007 Christin Schaerfer
- 2007 David Schmitz-Huebsch
- 2003-2005 Michael E Sparks
- 2009 Zhihao Tang
- 2010-2014 Dirk Willrodt
- 2004-2014 Center for Bioinformatics, University of Hamburg
- 2014 Genome Research Ltd
-License: ISC
- Permission to use, copy, modify, and distribute this software for any
- purpose with or without fee is hereby granted, provided that the above
- copyright notice and this permission notice appear in all copies.
- .
- THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
- WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
- MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
- ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
- WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
- ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
- OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
-
-Files:
- src/core/yarandom.*
-Copyright:
- 1997,1998,2003 Jamie Zawinski
-License: yarandom
- Permission to use, copy, modify, distribute, and sell this software and its
- documentation for any purpose is hereby granted without fee, provided that
- the above copyright notice appear in all copies and that both that
- copyright notice and this permission notice appear in supporting
- documentation. No representations are made about the suitability of this
- software for any purpose. It is provided "as is" without express or
- implied warranty.
-
-Files:
- src/core/msort.*
-Copyright:
- 1992, 1993 The Regents of the University of California
- This code is derived from software contributed
- to Berkeley by Peter McIlroy.
-License: BSD-3-clause
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions
- are met:
- 1. Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
- 2. Redistributions in binary form must reproduce the above copyright
- notice, this list of conditions and the following disclaimer in the
- documentation and/or other materials provided with the distribution.
- 3. Neither the name of the University nor the names of its contributors
- may be used to endorse or promote products derived from this software
- without specific prior written permission.
- .
- THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND
- ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE
- FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
- DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
- OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
- HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
- OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
- SUCH DAMAGE.
-
-Files:
- src/extended/rbtree.*
-Copyright:
- Copyright (c) 2009 Charles Wilson
-License: Expat
- Derived from code released into the public domain by Julienne Walker:
- http://eternallyconfuzzled.com/tuts/datastructures/jsw_tut_rbtree.aspx
- > Created (Julienne Walker): August 23, 2003
- > Modified (Julienne Walker): March 14, 2008
- .
- Permission is hereby granted, free of charge, to any person
- obtaining a copy of this software and associated documentation
- files (the "Software"), to deal in the Software without
- restriction, including without limitation the rights to use,
- copy, modify, merge, publish, distribute, sublicense, and/or sell
- copies of the Software, and to permit persons to whom the
- Software is furnished to do so, subject to the following
- conditions:
- .
- The above copyright notice and this permission notice shall be
- included in all copies or substantial portions of the Software.
- .
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- OTHER DEALINGS IN THE SOFTWARE.
Deleted: trunk/packages/genometools/trunk/debian/genometools-common.install
===================================================================
--- trunk/packages/genometools/trunk/debian/genometools-common.install 2016-02-06 13:58:07 UTC (rev 21380)
+++ trunk/packages/genometools/trunk/debian/genometools-common.install 2016-02-06 14:08:46 UTC (rev 21381)
@@ -1,18 +0,0 @@
-usr/bin/gtdata/doc usr/share/genometools/gtdata
-usr/bin/gtdata/obo_files usr/share/genometools/gtdata
-usr/bin/gtdata/sketch usr/share/genometools/gtdata
-usr/bin/gtdata/spec usr/share/genometools/gtdata
-usr/bin/gtdata/trans usr/share/genometools/gtdata
-usr/bin/gtdata/xrf_abbr usr/share/genometools/gtdata
-usr/bin/gtdata/modules/fileutils.lua usr/share/genometools/gtdata/modules
-usr/bin/gtdata/modules/gtdoclib.lua usr/share/genometools/gtdata/modules
-usr/bin/gtdata/modules/gtdoclib usr/share/genometools/gtdata/modules
-usr/bin/gtdata/modules/gtlua.lua usr/share/genometools/gtdata/modules
-usr/bin/gtdata/modules/gtlua usr/share/genometools/gtdata/modules
-usr/bin/gtdata/modules/gtmodulehelper.lua usr/share/genometools/gtdata/modules
-usr/bin/gtdata/modules/stringext.lua usr/share/genometools/gtdata/modules
-usr/bin/gtdata/modules/warning.lua usr/share/genometools/gtdata/modules
-usr/bin/gtdata/modules/gtlua.lua usr/share/genometools/gtdata/modules
-usr/bin/gtdata/modules/external/md5.lua usr/share/genometools/gtdata/modules/external
-usr/bin/gtdata/modules/external/re.lua usr/share/genometools/gtdata/modules/external
-
Deleted: trunk/packages/genometools/trunk/debian/genometools-doc.doc-base
===================================================================
--- trunk/packages/genometools/trunk/debian/genometools-doc.doc-base 2016-02-06 13:58:07 UTC (rev 21380)
+++ trunk/packages/genometools/trunk/debian/genometools-doc.doc-base 2016-02-06 14:08:46 UTC (rev 21381)
@@ -1,14 +0,0 @@
-Document: genometools-doc
-Title: GenomeTools manuals
-Author: GenomeTools Team
-Abstract: User manuals for GenomeTools
- The GenomeTools contains a collection of useful tools for biological
- sequence analysis and -presentation combined into a single binary.
- .
- The toolkit contains binaries for sequence and annotation handling, sequence
- compression, index structure generation and access, annotation visualization,
- and much more.
-Section: Science/Biology
-
-Format: PDF
-Files: /usr/share/doc/genometools-doc/*.pdf.gz
Deleted: trunk/packages/genometools/trunk/debian/genometools-doc.docs
===================================================================
--- trunk/packages/genometools/trunk/debian/genometools-doc.docs 2016-02-06 13:58:07 UTC (rev 21380)
+++ trunk/packages/genometools/trunk/debian/genometools-doc.docs 2016-02-06 14:08:46 UTC (rev 21381)
@@ -1,2 +0,0 @@
-doc/manuals/*.pdf
-doc/devguide/devguide.pdf
Deleted: trunk/packages/genometools/trunk/debian/genometools.docs
===================================================================
--- trunk/packages/genometools/trunk/debian/genometools.docs 2016-02-06 13:58:07 UTC (rev 21380)
+++ trunk/packages/genometools/trunk/debian/genometools.docs 2016-02-06 14:08:46 UTC (rev 21381)
@@ -1,3 +0,0 @@
-README
-CONTRIBUTORS
-VERSION
Deleted: trunk/packages/genometools/trunk/debian/genometools.install
===================================================================
--- trunk/packages/genometools/trunk/debian/genometools.install 2016-02-06 13:58:07 UTC (rev 21380)
+++ trunk/packages/genometools/trunk/debian/genometools.install 2016-02-06 14:08:46 UTC (rev 21381)
@@ -1,3 +0,0 @@
-usr/bin/gt
-usr/bin/gt
-
Deleted: trunk/packages/genometools/trunk/debian/genometools.manpages
===================================================================
--- trunk/packages/genometools/trunk/debian/genometools.manpages 2016-02-06 13:58:07 UTC (rev 21380)
+++ trunk/packages/genometools/trunk/debian/genometools.manpages 2016-02-06 14:08:46 UTC (rev 21381)
@@ -1 +0,0 @@
-debian/tmp/usr/share/man/man1/*
Deleted: trunk/packages/genometools/trunk/debian/libgenometools0-dev.install
===================================================================
--- trunk/packages/genometools/trunk/debian/libgenometools0-dev.install 2016-02-06 13:58:07 UTC (rev 21380)
+++ trunk/packages/genometools/trunk/debian/libgenometools0-dev.install 2016-02-06 14:08:46 UTC (rev 21381)
@@ -1 +0,0 @@
-usr/include
Deleted: trunk/packages/genometools/trunk/debian/libgenometools0-dev.links
===================================================================
--- trunk/packages/genometools/trunk/debian/libgenometools0-dev.links 2016-02-06 13:58:07 UTC (rev 21380)
+++ trunk/packages/genometools/trunk/debian/libgenometools0-dev.links 2016-02-06 14:08:46 UTC (rev 21381)
@@ -1 +0,0 @@
-usr/lib/libgenometools.so.0 usr/lib/libgenometools.so
Deleted: trunk/packages/genometools/trunk/debian/libgenometools0.install
===================================================================
--- trunk/packages/genometools/trunk/debian/libgenometools0.install 2016-02-06 13:58:07 UTC (rev 21380)
+++ trunk/packages/genometools/trunk/debian/libgenometools0.install 2016-02-06 14:08:46 UTC (rev 21381)
@@ -1 +0,0 @@
-lib/libgenometools.so.0 usr/lib
Deleted: trunk/packages/genometools/trunk/debian/libgenometools0.postinst
===================================================================
--- trunk/packages/genometools/trunk/debian/libgenometools0.postinst 2016-02-06 13:58:07 UTC (rev 21380)
+++ trunk/packages/genometools/trunk/debian/libgenometools0.postinst 2016-02-06 14:08:46 UTC (rev 21381)
@@ -1,37 +0,0 @@
-#!/bin/sh
-# postinst script for #PACKAGE#
-#
-# see: dh_installdeb(1)
-
-set -e
-
-# summary of how this script can be called:
-# * <postinst> `configure' <most-recently-configured-version>
-# * <old-postinst> `abort-upgrade' <new version>
-# * <conflictor's-postinst> `abort-remove' `in-favour' <package>
-# <new-version>
-# * <postinst> `abort-remove'
-# * <deconfigured's-postinst> `abort-deconfigure' `in-favour'
-# <failed-install-package> <version> `removing'
-# <conflicting-package> <version>
-# for details, see http://www.debian.org/doc/debian-policy/ or
-# the debian-policy package
-
-
-case "$1" in
- configure)
- ldconfig
- ;;
-
- abort-upgrade|abort-remove|abort-deconfigure)
- ;;
-
- *)
- echo "postinst called with unknown argument \`$1'" >&2
- exit 1
- ;;
-esac
-
-#DEBHELPER#
-
-exit 0
Deleted: trunk/packages/genometools/trunk/debian/libgenometools0.postrm
===================================================================
--- trunk/packages/genometools/trunk/debian/libgenometools0.postrm 2016-02-06 13:58:07 UTC (rev 21380)
+++ trunk/packages/genometools/trunk/debian/libgenometools0.postrm 2016-02-06 14:08:46 UTC (rev 21381)
@@ -1,38 +0,0 @@
-#!/bin/sh
-# postrm script for #PACKAGE#
-#
-# see: dh_installdeb(1)
-
-set -e
-
-# summary of how this script can be called:
-# * <postrm> `remove'
-# * <postrm> `purge'
-# * <old-postrm> `upgrade' <new-version>
-# * <new-postrm> `failed-upgrade' <old-version>
-# * <new-postrm> `abort-install'
-# * <new-postrm> `abort-install' <old-version>
-# * <new-postrm> `abort-upgrade' <old-version>
-# * <disappearer's-postrm> `disappear' <overwriter>
-# <overwriter-version>
-# for details, see http://www.debian.org/doc/debian-policy/ or
-# the debian-policy package
-
-
-case "$1" in
- purge|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear)
- ;;
-
- remove)
- ldconfig
- ;;
-
- *)
- echo "postrm called with unknown argument \`$1'" >&2
- exit 1
- ;;
-esac
-
-#DEBHELPER#
-
-exit 0
Deleted: trunk/packages/genometools/trunk/debian/rules
===================================================================
--- trunk/packages/genometools/trunk/debian/rules 2016-02-06 13:58:07 UTC (rev 21380)
+++ trunk/packages/genometools/trunk/debian/rules 2016-02-06 14:08:46 UTC (rev 21381)
@@ -1,68 +0,0 @@
-#!/usr/bin/make -f
-# -*- makefile -*-
-
-#export DH_VERBOSE=1
-export DESTDIR=$(CURDIR)/debian/tmp
-export DH_ALWAYS_EXCLUDE=.gitignore
-export PATH := $(CURDIR)/debian/strip-nondeterminism:$(PATH)
-export SOURCE_DATE_EPOCH = $(shell date -d "$$(dpkg-parsechangelog -SDate)" +%s)
-
-DARCH:=$(shell dpkg-architecture | fgrep DEB_TARGET_ARCH= | cut -f 2 -d'=')
-BITS:=$(shell dpkg-architecture | fgrep DEB_TARGET_ARCH_BITS= | cut -f 2 -d'=')
-
-ifeq ($(DARCH),x32)
- X32:=yes
-else
- X32:=no
-endif
-
-ifeq ($(BITS),64)
- 64BIT:=yes
-else
- 64BIT:=no
-endif
-
-# check whether faketime can be used
-ifeq ($(shell faketime 'last friday' date > /dev/null 2> /dev/null; echo $$?),0)
- FAKETIME:=faketime -f "`TZ=UTC date -d @$(SOURCE_DATE_EPOCH) +'%Y-%m-%d %H:%M:%S'`"
-endif
-
-%:
- dh $@ --with python2
-
-override_dh_auto_clean:
- $(MAKE) cleanup
- cd doc/manuals; $(MAKE) cleanup
- # should be deleted inside doc/manuals/Makefile
- rm -f doc/manuals/annotationsketch.out \
- doc/manuals/api_reference.tex \
- doc/manuals/gtscript_reference.tex
- find doc . -name "*.toc" -delete
- find testdata \( -name '*.ois' -or -name '*.sds' -or -name '*.esq' -or \
- -name '*.ssp' -or -name '*.des' -or -name "*.md5" \) -and \( -not \
- -name '*foo.32.*' -not -name '*foo.64.*' \) -delete
- rm -f www/genometools.org/htdocs/images/callbacks.png \
- www/genometools.org/htdocs/images/parsed.png \
- www/genometools.org/htdocs/images/constructed.png \
- doc/manuals/annotationsketch.pdf
- rm -f www/genometools.org/htdocs/docs.html \
- www/genometools.org/htdocs/examples.html \
- www/genometools.org/htdocs/libgenometools.html \
- www/genometools.org/htdocs/tools/gt.html
- rm -rf gtpython/build
-
-override_dh_auto_build:
- $(FAKETIME) dh_auto_build -- useshared=yes x32=$(X32) 64bit=$(64BIT) errorcheck=no all docs manuals
-
-override_dh_auto_test:
- bin/gt -test
- cd testsuite; ./testsuite.rb -keywords 'gt_sketch and not gt_python and not gt_ruby' -threads 3
-
-override_dh_auto_install:
- dh_auto_install -- installmanpages useshared=yes \
- x32=$(X32) 64bit=$(64BIT) errorcheck=no prefix=$(DESTDIR)/usr
- dh_auto_install --sourcedirectory=gtpython \
- --destdir=$(CURDIR)/debian/python-genometools
-
-override_dh_strip:
- dh_strip --dbg-package=genometools-dbg
Deleted: trunk/packages/genometools/trunk/debian/watch
===================================================================
--- trunk/packages/genometools/trunk/debian/watch 2016-02-06 13:58:07 UTC (rev 21380)
+++ trunk/packages/genometools/trunk/debian/watch 2016-02-06 14:08:46 UTC (rev 21381)
@@ -1,2 +0,0 @@
-version=3
-http://genometools.org/pub/genometools-([0-9.]+)\.tar\.gz
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