[med-svn] r19379 - in trunk/packages/velvet/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2015-06-27 09:44:28 +0000 (Sat, 27 Jun 2015)
New Revision: 19379

Added:
   trunk/packages/velvet/trunk/debian/patches/0001-isCreateBinary-should-not-be-inline.patch
Modified:
   trunk/packages/velvet/trunk/debian/changelog
   trunk/packages/velvet/trunk/debian/patches/series
Log:
Fix gcc-5 build issue


Modified: trunk/packages/velvet/trunk/debian/changelog
===================================================================
--- trunk/packages/velvet/trunk/debian/changelog	2015-06-27 09:36:24 UTC (rev 19378)
+++ trunk/packages/velvet/trunk/debian/changelog	2015-06-27 09:44:28 UTC (rev 19379)
@@ -1,3 +1,10 @@
+velvet (1.2.10+dfsg1-2) UNRELEASED; urgency=medium
+
+  * Fix gcc-5 build issue by adapting upstream patch
+    Closes: #778161
+
+ -- Andreas Tille <tille at debian.org>  Sat, 27 Jun 2015 11:37:36 +0200
+
 velvet (1.2.10+dfsg1-1) unstable; urgency=medium
 
   * Drop more stuff from upstream source via Files-Excluded

Added: trunk/packages/velvet/trunk/debian/patches/0001-isCreateBinary-should-not-be-inline.patch
===================================================================
--- trunk/packages/velvet/trunk/debian/patches/0001-isCreateBinary-should-not-be-inline.patch	                        (rev 0)
+++ trunk/packages/velvet/trunk/debian/patches/0001-isCreateBinary-should-not-be-inline.patch	2015-06-27 09:44:28 UTC (rev 19379)
@@ -0,0 +1,34 @@
+From 73ff67db706f63233f4c29b1e00e960c8cb09975 Mon Sep 17 00:00:00 2001
+From: John Marshall <jm18 at sanger.ac.uk>
+Date: Thu, 17 Oct 2013 16:56:37 +0100
+Subject: [PATCH 1/4] isCreateBinary() should not be inline
+
+This function is used from several .c files; with inline here,
+compilation with clang was broken.
+---
+ src/readSet.c | 2 +-
+ src/readSet.h | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+--- a/src/readSet.c
++++ b/src/readSet.c
+@@ -72,7 +72,7 @@ static Mask * newMask(SequencesWriter *s
+ // note that createBinary is only used by velveth
+ //
+ boolean createBinary = false;
+-inline boolean isCreateBinary()
++boolean isCreateBinary()
+ {
+ 	return createBinary;
+ }
+--- a/src/readSet.h
++++ b/src/readSet.h
+@@ -61,7 +61,7 @@ void detachDubiousReads(ReadSet * reads,
+ 
+ void destroyReadSet(ReadSet * reads);
+ 
+-inline boolean isCreateBinary();
++boolean isCreateBinary();
+ void setCreateBinary(boolean val);
+ 
+ #endif

Modified: trunk/packages/velvet/trunk/debian/patches/series
===================================================================
--- trunk/packages/velvet/trunk/debian/patches/series	2015-06-27 09:36:24 UTC (rev 19378)
+++ trunk/packages/velvet/trunk/debian/patches/series	2015-06-27 09:44:28 UTC (rev 19379)
@@ -1,3 +1,4 @@
 include_debians_zlib.patch
 shuffleSequences_fasta.patch
 fix-perl-path.patch
+0001-isCreateBinary-should-not-be-inline.patch