[med-svn] [trinityrnaseq] 01/01: copyright tweak

[Michael Crusoe]

This is an automated email from the git hooks/post-receive script.

misterc-guest pushed a commit to branch master
in repository trinityrnaseq.

commit 8926f0644ef24bdb0a551ef2c8b9564803ccbe71
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Wed Feb 3 10:09:09 2016 -0800

    copyright tweak
---
 debian/control                           |  7 ++++---
 debian/copyright                         | 28 +++++++++++++++++++++++++---
 debian/patches/0001-fix_gcc5.patch.patch | 22 ----------------------
 debian/patches/series                    |  1 -
 4 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/debian/control b/debian/control
index f7b3391..b64b6ba 100644
--- a/debian/control
+++ b/debian/control
@@ -16,9 +16,9 @@ Build-Depends: debhelper (>= 9),
                libjs-jquery,
                jaligner,
                libhts-dev
-Standards-Version: 3.9.6
+Standards-Version: 3.9.7
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/trinityrnaseq.git
-Vcs-Git: https://anonscm.debian.org/debian-med/trinityrnaseq.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/trinityrnaseq.git
 Homepage: http://trinityrnaseq.github.io/
 
 Package: trinityrnaseq
@@ -44,8 +44,9 @@ Depends: ${shlibs:Depends},
          transdecoder,
          parafly,
          curl
+Recommends: ${java:Recommends},
+            trinityrnaseq-examples
 Suggests: collectl
-Recommends: ${java:Recommends}, trinityrnaseq-examples
 Description: RNA-Seq De novo Assembly
  Trinity represents a novel method for the efficient and robust de novo
  reconstruction of transcriptomes from RNA-seq data. Trinity combines three
diff --git a/debian/copyright b/debian/copyright
index 38eb0e3..8c20dd8 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -25,8 +25,8 @@ Files-Excluded: trinity-plugins/jellyfish-*.tar.gz
  Analysis/DifferentialExpression/deprecated
 
 Files: *
-Copyright: © 2011 The Broad Institute, Inc
- © 2014 trinityrnaseq
+Copyright: 2011 The Broad Institute, Inc
+           2014 trinityrnaseq
 License: BSD-3-clause
 Comment: trinity-plugins/slclust is from http://sourceforge.net/projects/slclust/
 
@@ -44,6 +44,16 @@ Copyright: (c) 2008 Genome Research Ltd (GRL).
 License: Expat
 Comment: https://github.com/fstrozzi/Fastool
 
+Files: util/misc/alexie_analyze_blast.pl
+Copyright: -
+License: GPL-3
+Comment: No copyright but the following authors are listed:
+ "Alexie Papanicolaou 1 2 with help from Paul Wilkinson 2
+ .
+ 1 Max Planck Institute for Chemical Ecology, Germany
+ 2 Centre for Ecology and Conservation, University of Exeter, UK
+  alexie at butterflybase.org"
+
 Files: debian/*
 Copyright: (c) 2015 Michigan State University
 License: BSD-3-clause
@@ -177,4 +187,16 @@ License: CC-BY-SA-3.0
  This License constitutes the entire agreement between the parties with respect to the Work licensed here. There are no understandings, agreements or representations with respect to the Work not specified here. Licensor shall not be bound by any additional provisions that may appear in any communication from You. This License may not be modified without the mutual written agreement of the Licensor and You.
  The rights granted under, and the subject matter referenced, in this License were drafted utilizing the terminology of the Berne Convention for the Protection of Literary and Artistic Works (as amended on September 28, 1979), the Rome Convention of 1961, the WIPO Copyright Treaty of 1996, the WIPO Performances and Phonograms Treaty of 1996 and the Universal Copyright Convention (as revised on July 24, 1971). These rights and subject matter take effect in the relevant jurisdiction in whi [...]
 
-
+License: GPL-3
+ This software is released under the GNU General Public License version 3
+ (GPLv3).
+ It is provided "as is" without warranty of any kind.
+ You can find the terms and conditions at
+ http://www.opensource.org/licenses/gpl-3.0.html. 
+ Please note that incorporating the whole software or parts of its code in
+ proprietary software 
+ is prohibited under the current license. .
+ .
+ On Debian systems, the full text of the GNU General Public
+ License version 3 can be found in the file
+ `/usr/share/common-licenses/GPL-3'.
diff --git a/debian/patches/0001-fix_gcc5.patch.patch b/debian/patches/0001-fix_gcc5.patch.patch
deleted file mode 100644
index 1b91c9e..0000000
--- a/debian/patches/0001-fix_gcc5.patch.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-From: Olivier Sallou <osallou at debian.org>
-Date: Thu, 20 Aug 2015 10:07:43 +0000
-Subject: fix_gcc5.patch
-
-Add code for GCC 5 Compilation
----
- Chrysalis/Makefile | 4 ++++
- 1 file changed, 4 insertions(+)
-
---- trinityrnaseq.orig/Chrysalis/Makefile
-+++ trinityrnaseq/Chrysalis/Makefile
-@@ -305,6 +305,10 @@
-   ifeq ($(GPP_MAJOR_VERSION),5)
-        SYS_INCS        = -iquote . $(XERCES_INC)
-   endif
-+  ifeq ($(GPP_MAJOR_VERSION),5)
-+       SYS_INCS = -iquote . $(XERCES_INC)
-+  endif
-+
- endif
- 
- # Linking control (e.g. to link templates):
diff --git a/debian/patches/series b/debian/patches/series
index dbcacec..7772cf5 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -6,7 +6,6 @@ noExitTester
 jellyfish-path
 update-paths
 collections15-to-4
-0001-fix_gcc5.patch.patch
 0002-fix_istream_failure_call.patch
 fix_system_paths
 hardening

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/trinityrnaseq.git