[med-svn] [rsem] 01/02: add fix for g++-6; update standards-version

[Michael Crusoe]

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

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

commit c93efa908f236fd7c5d47bae92e74a2d3ad8367e
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Sat Mar 5 05:16:36 2016 -0800

    add fix for g++-6; update standards-version
    
    and fix VCS-Git URL
---
 debian/changelog                |  7 +++++--
 debian/control                  |  6 +++---
 debian/patches/add-descriptions |  4 ++--
 debian/patches/fix-for-g++-6    | 13 +++++++++++++
 debian/patches/series           |  1 +
 5 files changed, 24 insertions(+), 7 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 97f51f2..cee7a4c 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,11 @@
-rsem (1.2.26+dfsg-1) UNRELEASED; urgency=medium
+rsem (1.2.26+dfsg-1) unstable; urgency=medium
 
   * New upstream release
+  * Now compatible with g++-6 (Closes: #811615)
+  * Section set to 'extra' due to build-dep on bowtie|bowtie2 which are both in
+    section 'extra'.
 
- -- Michael R. Crusoe <crusoe at ucdavis.edu>  Sun, 31 Jan 2016 03:20:22 -0800
+ -- Michael R. Crusoe <crusoe at ucdavis.edu>  Sat, 05 Mar 2016 05:27:01 -0800
 
 rsem (1.2.23+dfsg-1) unstable; urgency=medium
 
diff --git a/debian/control b/debian/control
index 3717946..f70895b 100644
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Michael R. Crusoe <crusoe at ucdavis.edu>,
            Andreas Tille <tille at debian.org>
 Section: science
-Priority: optional
+Priority: extra
 Build-Depends: debhelper (>= 9),
                zlib1g-dev,
                libncurses5-dev,
@@ -12,9 +12,9 @@ Build-Depends: debhelper (>= 9),
                perl,
                bowtie | bowtie2,
                help2man
-Standards-Version: 3.9.6
+Standards-Version: 3.9.7
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/rsem.git
-Vcs-Git: https://anonscm.debian.org/debian-med/rsem.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/rsem.git
 Homepage: http://deweylab.biostat.wisc.edu/rsem/
 
 Package: rsem
diff --git a/debian/patches/add-descriptions b/debian/patches/add-descriptions
index adee3cd..c6f8717 100644
--- a/debian/patches/add-descriptions
+++ b/debian/patches/add-descriptions
@@ -14,7 +14,7 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
  
 --- rsem.orig/rsem-calculate-expression
 +++ rsem/rsem-calculate-expression
-@@ -570,7 +570,7 @@
+@@ -578,7 +578,7 @@
  
  =head1 NAME
  
@@ -58,7 +58,7 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
  
 --- rsem.orig/rsem-prepare-reference
 +++ rsem/rsem-prepare-reference
-@@ -143,7 +143,7 @@
+@@ -158,7 +158,7 @@
  
  =head1 NAME
  
diff --git a/debian/patches/fix-for-g++-6 b/debian/patches/fix-for-g++-6
new file mode 100644
index 0000000..8471ec7
--- /dev/null
+++ b/debian/patches/fix-for-g++-6
@@ -0,0 +1,13 @@
+From 705099ad77f64f8d5ced8419dd066601e1cb7287 Mon Sep 17 00:00:00 2001
+From: Bo Li <bli25 at berkeley.edu>
+Date: Thu, 4 Feb 2016 09:27:03 -0800
+Subject: [PATCH] Updated Makefile to make sure the compilation works in latest
+ version of GCC
+--- rsem.orig/Makefile
++++ rsem/Makefile
+@@ -1,4 +1,4 @@
+-CC = g++
++CC = g++ -std=gnu++98
+ CFLAGS = -Wall -c -I. -I/usr/include/
+ COFLAGS = -Wall -O3 -ffast-math -c -I. -I/usr/include
+ PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads
diff --git a/debian/patches/series b/debian/patches/series
index 1c402e1..f3aad13 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -4,3 +4,4 @@ fix-sam-includes
 fix-boost
 use-flags
 add-descriptions
+fix-for-g++-6

-- 
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