libbio-graphics-perl (2.11-1) debian-dir only changes

Summary

 debian/README.Debian          |   10 ++
 debian/changelog              |  144 ++++++++++++++++++++++++++++++++++
 debian/compat                 |    1 
 debian/control                |   28 ++++++
 debian/copyright              |  174 ++++++++++++++++++++++++++++++++++++++++++
 debian/docs                   |    1 
 debian/examples               |    1 
 debian/rules                  |    7 +
 debian/upstream-metadata.yaml |    5 +
 debian/watch                  |    4 
 10 files changed, 375 insertions(+)

    
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Patch contents

--- libbio-graphics-perl-2.11.orig/debian/docs
+++ libbio-graphics-perl-2.11/debian/docs
@@ -0,0 +1 @@
+README
--- libbio-graphics-perl-2.11.orig/debian/README.Debian
+++ libbio-graphics-perl-2.11/debian/README.Debian
@@ -0,0 +1,10 @@
+Notes on how this package is tested.
+────────────────────────────────────
+
+The maintainer relies on the package's regression tests that are executed at
+build time on his computer.
+
+In the future, build logs for this package will be published in the Debian
+website so that you can inspect the results…
+
+ -- Charles Plessy <plessy@debian.org>  Mon, 29 Mar 2010 22:22:38 +0900
--- libbio-graphics-perl-2.11.orig/debian/control
+++ libbio-graphics-perl-2.11/debian/control
@@ -0,0 +1,28 @@
+Source: libbio-graphics-perl
+Section: perl
+Priority: optional
+Build-Depends: debhelper (>= 7), libmodule-build-perl
+Build-Depends-Indep:
+# Needed for the tests
+ bioperl (>= 1.6.0), libgd-gd2-perl (>= 2.3), libstatistics-descriptive-perl
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy@debian.org>
+Standards-Version: 3.9.0
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/libbio-graphics-perl/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/libbio-graphics-perl/trunk/
+Homepage: http://search.cpan.org/dist/Bio-Graphics/
+
+Package: libbio-graphics-perl
+Architecture: all
+Depends: ${perl:Depends}, ${misc:Depends}, bioperl (>= 1.6.0), libgd-gd2-perl (>= 2.3)
+Recommends: libbio-scf-perl, libfile-spec-perl, libgd-svg-perl, libstatistics-descriptive-perl
+Breaks: bioperl ( < 1.6.0)
+Description: Generate GD images of Bio::Seq objects
+ The Bio::Graphics::Panel class provides drawing and formatting
+ services for any object that implements the Bio::SeqFeatureI
+ interface, including Ace::Sequence::Feature, Das::Segment::Feature and
+ Bio::DB::Graphics objects.  It can be used to draw sequence
+ annotations, physical (contig) maps, protein domains, or any other
+ type of map in which a set of discrete ranges need to be laid out on
+ the number line.
--- libbio-graphics-perl-2.11.orig/debian/changelog
+++ libbio-graphics-perl-2.11/debian/changelog
@@ -0,0 +1,144 @@
+libbio-graphics-perl (2.11-1) unstable; urgency=low
+
+  * New upstream release.
+  * Conformance with Policy 3.9.0:
+    - Use Breaks instead of Conflicts (debian/control).
+    - Incremented Standards-Version to reflect conformance (debian/control).
+  * Mention the download directory instead of the full URL as Source
+    in debian/copyright.
+
+ -- Charles Plessy <plessy@debian.org>  Tue, 13 Jul 2010 10:39:44 +0900
+
+libbio-graphics-perl (2.10-1) unstable; urgency=low
+
+  * New upstream release.
+  * Using Debhelper's ‘dh’ (debian/rules, debian/docs, debian/examples).
+  * Recommends libfile-spec-perl (debian/control).
+
+ -- Charles Plessy <plessy@debian.org>  Fri, 25 Jun 2010 20:02:53 +0900
+
+libbio-graphics-perl (2.02-1) unstable; urgency=low
+
+  * New upstream release (more support for BigWig and BigBed data,
+    and other changes).
+  * Build-depend on libstatistics-descriptive-perl, needed for the tests.
+  * Recommend libbio-scf-perl, libgd-svg-perl,
+    libstatistics-descriptive-perl, according to META.yaml.
+  * Added a few words in debian/README.Debian on how this package is tested.
+
+ -- Charles Plessy <plessy@debian.org>  Mon, 29 Mar 2010 22:23:43 +0900
+
+libbio-graphics-perl (2.01-1) unstable; urgency=low
+
+  * New upstream release.
+
+ -- Charles Plessy <plessy@debian.org>  Sat, 06 Mar 2010 19:21:41 +0900
+
+libbio-graphics-perl (2.00-1) unstable; urgency=low
+
+  * New upstream release.
+  * Incremented Standards-Version to reflect conformance
+    with Policy 3.8.4 (debian/control, no other changes needed).
+
+ -- Charles Plessy <plessy@debian.org>  Thu, 11 Feb 2010 22:45:02 +0900
+
+libbio-graphics-perl (1.995-1) unstable; urgency=low
+
+  * New upstream release.
+
+ -- Charles Plessy <plessy@debian.org>  Fri, 08 Jan 2010 13:27:40 +0900
+
+libbio-graphics-perl (1.994-1) unstable; urgency=low
+
+  * New upstream releases.
+  * debian/copyright:
+    - Updated for new upstream file.
+    - Added Artistic license version 2.0.
+
+ -- Charles Plessy <plessy@debian.org>  Fri, 11 Dec 2009 13:42:21 +0900
+
+libbio-graphics-perl (1.992-1) unstable; urgency=low
+
+  * New upstream release.
+  * Added a couple of informations in debian/upstream-metadata.yaml.
+
+ -- Charles Plessy <plessy@debian.org>  Sun, 22 Nov 2009 22:33:46 +0900
+
+libbio-graphics-perl (1.982-1) unstable; urgency=low
+
+  * New upstream release fixing DAS stylesheet support.
+  * Enhances: gbrowse (debian/control).
+
+ -- Charles Plessy <plessy@debian.org>  Fri, 02 Oct 2009 21:07:17 +0900
+
+libbio-graphics-perl (1.981-1) unstable; urgency=low
+
+  * New upstream release fixing bugs in wiggle_xyplot and improving
+    documentation.
+  * debian/control: incremented Standards-Version to reflect conformance
+    with Policy 3.8.3 (no changes needed).
+  * Removed trailing spaces in debian/changelog.
+
+ -- Charles Plessy <plessy@debian.org>  Mon, 24 Aug 2009 12:53:39 +0900
+
+libbio-graphics-perl (1.97-1) unstable; urgency=low
+
+  * New upstream release adding a “feature_limit” option.
+  * debian/control: incremented Standards-Version to reflect conformance
+    with Policy 3.8.2 (no changes needed).
+  * Format experimentations on debian/copyright.
+
+ -- Charles Plessy <plessy@debian.org>  Fri, 10 Jul 2009 19:12:27 +0900
+
+libbio-graphics-perl (1.96-1) unstable; urgency=low
+
+  * New upstream release improving DAS 1.5 support.
+  * Documented in debian/copyright files distributed under the GPL version 1 or
+    superior, or the Artistic license version 2. Ignored VCS leftovers
+    ‘lib/Bio/Graphics/Glyph/.#dna.pm.1.1’ and
+    ‘lib/Bio/Graphics/Glyph/.#hybrid_plot.pm.1.2’.
+
+ -- Charles Plessy <plessy@debian.org>  Wed, 10 Jun 2009 13:04:42 +0900
+
+libbio-graphics-perl (1.95-1) unstable; urgency=low
+
+  * New upstream release, improving SVG support.
+
+ -- Charles Plessy <plessy@debian.org>  Thu, 04 Jun 2009 19:05:06 +0900
+
+libbio-graphics-perl (1.94-1) unstable; urgency=low
+
+  * New upstream release, adding a “fast” option and fixing error in xyplot.
+
+ -- Charles Plessy <plessy@debian.org>  Sun, 03 May 2009 18:24:13 +0900
+
+libbio-graphics-perl (1.93-1) unstable; urgency=low
+
+  * New upstream release (corrections and improved documentation).
+  * debian/copyright made simpler according to current discussion
+    on machine-readable format.
+
+ -- Charles Plessy <plessy@debian.org>  Thu, 09 Apr 2009 10:40:38 +0900
+
+libbio-graphics-perl (1.91-1) unstable; urgency=low
+
+  * New upstream release with improvements on wiggle xyplots.
+  * debian/control: checked conformance with Policy 3.8.1.
+
+ -- Charles Plessy <plessy@debian.org>  Fri, 20 Mar 2009 18:49:47 +0900
+
+libbio-graphics-perl (1.85-1) unstable; urgency=low
+
+  * New upstream release:
+    - Adds including capacities in the configuration files.
+    - New object: Bio::Graphics::Glyph::hybrid_plot.
+  * debian/copyright: incremented year and added new holder.
+  * debian/rules: replaced deprecated `dh_clean -k' by `dh_prep'.
+
+ -- Charles Plessy <plessy@debian.org>  Wed, 11 Mar 2009 10:23:12 +0900
+
+libbio-graphics-perl (1.84-1) unstable; urgency=low
+
+  * Initial Release. (Closes: #511382)
+
+ -- Charles Plessy <plessy@debian.org>  Sat, 10 Jan 2009 17:49:21 +0900
--- libbio-graphics-perl-2.11.orig/debian/rules
+++ libbio-graphics-perl-2.11/debian/rules
@@ -0,0 +1,7 @@
+#!/usr/bin/make -f
+
+%:
+	dh $@
+
+override_dh_installchangelogs:
+	dh_installchangelogs Changes
--- libbio-graphics-perl-2.11.orig/debian/copyright
+++ libbio-graphics-perl-2.11/debian/copyright
@@ -0,0 +1,174 @@
+Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
+
+Name    :  Bio::Graphics
+Contact :  Lincoln Stein <lincoln.stein@oicr.on.ca>
+Source  :  http://search.cpan.org/CPAN/authors/id/L/LD/LDS/
+
+Copyright: 2001-2010, Cold Spring Harbor Laboratory
+License: Perl
+
+	This library is free software; you can redistribute it and/or modify
+	it under the same terms as Perl itself.  See the Artistic License file
+	in the main Perl distribution for specific terms and conditions of
+	use.  In addition, the following disclaimers apply:
+	
+	CSHL makes no representations whatsoever as to the SOFTWARE contained
+	herein.  It is experimental in nature and is provided WITHOUT WARRANTY
+	OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER
+	WARRANTY, EXPRESS OR IMPLIED.  CSHL MAKES NO REPRESENTATION OR
+	WARRANTY THAT THE USE OF THIS SOFTWARE WILL NOT INFRINGE ANY PATENT OR
+	OTHER PROPRIETARY RIGHT.
+	
+	By downloading this SOFTWARE, your Institution hereby indemnifies CSHL
+	against any loss, claim, damage or liability, of whatsoever kind or
+	nature, which may arise from your Institution's respective use,
+	handling or storage of the SOFTWARE.
+	
+	If publications result from research using this SOFTWARE, we ask that
+	CSHL be acknowledged and/or credit be given to CSHL scientists, as
+	scientifically appropriate.
+
+License: Perl
+	This program is free software; you can redistribute it and/or modify
+	it under the terms of either:
+	
+	a) the GNU General Public License as published by the Free Software
+	   Foundation; either version 1, or (at your option) any later
+	   version, or
+	
+	b) the "Artistic License" which comes with Perl.
+
+On Debian systems, the complete text of the Artistic License can be
+found in ‘/usr/share/common-licenses/Artistic’, and the complete text of
+the latest version of the GNU General Public License can be found in
+‘/usr/share/common-licenses/GPL’.
+
+Files: lib/Bio/Graphics/Glyph/rndrect.pm
+       lib/Bio/Graphics/Glyph/splice_site.pm
+       lib/Bio/Graphics/Glyph/extending_arrow.pm
+Copyright: © 2001 Berkeley Drosophila Genome Project
+License: Perl
+
+Files: lib/Bio/Graphics/Pictogram.pm
+Copyright: © Shawn Hoon
+License: Perl
+
+Files: lib/Bio/Graphics/RendererI.pm
+Copyright: © 2003 Institute for Systems Biology
+License: Perl
+
+Files: lib/Bio/Graphics/ConfiguratorI.pm
+Copyright: © Robert Hubley
+License: Perl
+
+Files: lib/Bio/Graphics/Glyph/hybrid_plot.pm
+Copyright: © 2008 Ontario Institute for Cancer Research
+License: Perl
+
+Files: lib/Bio/Graphics/Glyph/allele_tower.pm
+Author: Fiona Cunningham <cunningh@cshl.edu> in Lincoln Stein's lab <steinl@cshl.edu>
+Copyright: © 2003 Cold Spring Harbor Laboratory
+License: GPL-1+ or Artistic-2
+
+Files: lib/Bio/Graphics/FeatureDir.pm, lib/Bio/Graphics/Glyph/pairplot.pm, lib/Bio/Graphics/Glyph/generic.pm
+Copyright: 2008,2009,2010 Ontario Institute for Cancer Research
+           2001,2004 Cold Spring Harbor Laboratory
+License: GPL-1+ or Artistic-2
+
+License: GPL-1+ or Artistic-2
+	This package and its accompanying libraries is free software; you can
+	redistribute it and/or modify it under the terms of the GPL (either
+	version 1, or at your option, any later version) or the Artistic
+	License 2.0.  Refer to LICENSE for the full license text. In addition,
+	please see DISCLAIMER.txt for disclaimers of warranty.
+
+License: Artistic-2.0
+ Copyright (c) 2000-2006, The Perl Foundation.
+ 
+ Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
+ Preamble
+ 
+ This license establishes the terms under which a given free software Package may be copied, modified, distributed, and/or redistributed. The intent is that the Copyright Holder maintains some artistic control over the development of that Package while still keeping the Package available as open source and free software.
+ 
+ You are always permitted to make arrangements wholly outside of this license directly with the Copyright Holder of a given Package. If the terms of this license do not permit the full use that you propose to make of the Package, you should contact the Copyright Holder and seek a different licensing arrangement.
+ Definitions
+ 
+ "Copyright Holder" means the individual(s) or organization(s) named in the copyright notice for the entire Package.
+ 
+ "Contributor" means any party that has contributed code or other material to the Package, in accordance with the Copyright Holder's procedures.
+ 
+ "You" and "your" means any person who would like to copy, distribute, or modify the Package.
+ 
+ "Package" means the collection of files distributed by the Copyright Holder, and derivatives of that collection and/or of those files. A given Package may consist of either the Standard Version, or a Modified Version.
+ 
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+ 
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+ 
+ "Standard Version" refers to the Package if it has not been modified, or has been modified only in ways explicitly requested by the Copyright Holder.
+ 
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+ 
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+ 
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+ 
+ "Compiled" form means the compiled bytecode, object code, binary, or any other form resulting from mechanical transformation or translation of the Source form.
+ Permission for Use and Modification Without Distribution
+ 
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+ 
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+ 
+ (3) You may apply any bug fixes, portability changes, and other modifications made available from the Copyright Holder. The resulting Package will still be considered the Standard Version, and as such will be subject to the Original License.
+ Distribution of Modified Versions of the Package as Source
+ 
+ (4) You may Distribute your Modified Version as Source (either gratis or for a Distributor Fee, and with or without a Compiled form of the Modified Version) provided that you clearly document how it differs from the Standard Version, including, but not limited to, documenting any non-standard features, executables, or modules, and provided that you do at least ONE of the following:
+ 
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+ 
+ (5) You may Distribute Compiled forms of the Standard Version without the Source, provided that you include complete instructions on how to get the Source of the Standard Version. Such instructions must be valid at the time of your distribution. If these instructions, at any time while you are carrying out such distribution, become invalid, you must provide new instructions on demand or cease further distribution. If you provide valid instructions or cease distribution within thirty days after you become aware that the instructions are invalid, then you do not forfeit any of your rights under this license.
+ 
+ (6) You may Distribute a Modified Version in Compiled form without the Source, provided that you comply with Section 4 with respect to the Source of the Modified Version.
+ Aggregating or Linking the Package
+ 
+ (7) You may aggregate the Package (either the Standard Version or Modified Version) with other packages and Distribute the resulting aggregation provided that you do not charge a licensing fee for the Package. Distributor Fees are permitted, and licensing fees for other components in the aggregation are permitted. The terms of this license apply to the use and Distribution of the Standard or Modified Versions as included in the aggregation.
+ 
+ (8) You are permitted to link Modified and Standard Versions with other works, to embed the Package in a larger work of your own, or to build stand-alone binary or bytecode versions of applications that include the Package, and Distribute the result without restriction, provided the result does not expose a direct interface to the Package.
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+ 
+ (9) Works (including, but not limited to, modules and scripts) that merely extend or make use of the Package, do not, by themselves, cause the Package to be a Modified Version. In addition, such works are not considered parts of the Package itself, and are not subject to the terms of this license.
+ General Provisions
+ 
+ (10) Any use, modification, and distribution of the Standard or Modified Versions is governed by this Artistic License. By using, modifying or distributing the Package, you accept this license. Do not use, modify, or distribute the Package, if you do not accept this license.
+ 
+ (11) If your Modified Version has been derived from a Modified Version made by someone other than you, you are nevertheless required to ensure that your Modified Version complies with the requirements of this license.
+ 
+ (12) This license does not grant you the right to use any trademark, service mark, tradename, or logo of the Copyright Holder.
+ 
+ (13) This license includes the non-exclusive, worldwide, free-of-charge patent license to make, have made, use, offer to sell, sell, import and otherwise transfer the Package with respect to any patent claims licensable by the Copyright Holder that are necessarily infringed by the Package. If you institute patent litigation (including a cross-claim or counterclaim) against any party alleging that the Package constitutes direct or contributory patent infringement, then this Artistic License to you shall terminate on the date that such litigation is filed.
+ 
+ (14) Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES. THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT PERMITTED BY YOUR LOCAL LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER OR CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Files: debian/*
+Copyright: 2009–10, Charles Plessy <plessy@debian.org>
+License: Poetic
+	This work ‘as-is’ we provide.
+	No warranty, express or implied.
+	We’ve done our best,
+	to debug and test.
+	Liability for damages denied.
+	
+	Permission is granted hereby,
+	to copy, share, and modify.
+	Use as is fit,
+	free or for profit.
+	On this notice these rights rely.
+Comment: The text of this license is © 2005 Alexander E Genaud,
+ see `http://genaud.net/2005/10/poetic-license/'.
--- libbio-graphics-perl-2.11.orig/debian/examples
+++ libbio-graphics-perl-2.11/debian/examples
@@ -0,0 +1 @@
+eg/*
--- libbio-graphics-perl-2.11.orig/debian/upstream-metadata.yaml
+++ libbio-graphics-perl-2.11/debian/upstream-metadata.yaml
@@ -0,0 +1,5 @@
+Archive: CPAN
+Contact: Lincoln Stein <lincoln.stein@oicr.on.ca>
+Homepage: http://search.cpan.org/dist/Bio-Graphics/
+Name: Bio::Graphics
+Watch: http://search.cpan.org/dist/Bio-Graphics/   .*/Bio-Graphics-v?(\d[\d_.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$
--- libbio-graphics-perl-2.11.orig/debian/watch
+++ libbio-graphics-perl-2.11/debian/watch
@@ -0,0 +1,4 @@
+# format version number, currently 3; this line is compulsory!
+version=3
+# URL to the package page followed by a regex to search
+http://search.cpan.org/dist/Bio-Graphics/   .*/Bio-Graphics-v?(\d[\d_.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$
--- libbio-graphics-perl-2.11.orig/debian/compat
+++ libbio-graphics-perl-2.11/debian/compat
@@ -0,0 +1 @@
+7