[med-svn] [trinityrnaseq] 01/01: add GCC5 patches

[Olivier Sallou]

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osallou pushed a commit to branch master
in repository trinityrnaseq.

commit 23f11d25dd7b368c650b26df35d4a4d8e0a33f3b
Author: Olivier Sallou <osallou at debian.org>
Date:   Mon Aug 24 06:36:03 2015 +0000

    add GCC5 patches
---
 debian/patches/0001-fix_gcc5.patch.patch           | 24 ++++++++++++++++++++++
 debian/patches/0002-fix_istream_failure_call.patch | 24 ++++++++++++++++++++++
 debian/patches/series                              |  2 ++
 3 files changed, 50 insertions(+)

diff --git a/debian/patches/0001-fix_gcc5.patch.patch b/debian/patches/0001-fix_gcc5.patch.patch
new file mode 100644
index 0000000..1465d7e
--- /dev/null
+++ b/debian/patches/0001-fix_gcc5.patch.patch
@@ -0,0 +1,24 @@
+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(+)
+
+diff --git a/Chrysalis/Makefile b/Chrysalis/Makefile
+index 448b2d1..11eae21 100644
+--- a/Chrysalis/Makefile
++++ b/Chrysalis/Makefile
+@@ -302,6 +302,10 @@ ifeq ($(COMPILER),g++)
+   ifeq ($(GPP_MAJOR_VERSION),4)
+        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/0002-fix_istream_failure_call.patch b/debian/patches/0002-fix_istream_failure_call.patch
new file mode 100644
index 0000000..a6ccaf9
--- /dev/null
+++ b/debian/patches/0002-fix_istream_failure_call.patch
@@ -0,0 +1,24 @@
+From: Olivier Sallou <osallou at debian.org>
+Date: Thu, 20 Aug 2015 13:05:48 +0000
+Subject: fix_istream_failure_call
+
+Upstream is using wrong test gor file open failure, comparing an int instead
+of calling fail() method
+---
+ Inchworm/src/sequenceUtil.cpp | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/Inchworm/src/sequenceUtil.cpp b/Inchworm/src/sequenceUtil.cpp
+index 7ba9c1f..a24c250 100644
+--- a/Inchworm/src/sequenceUtil.cpp
++++ b/Inchworm/src/sequenceUtil.cpp
+@@ -52,7 +52,8 @@ bool contains_non_gatc (string kmer) {
+ string read_sequence_from_file (string filename) {
+   
+   ifstream fileReader (filename.c_str());
+-  if (fileReader == 0) { // couldn't open file
++  //if (fileReader == 0) { // couldn't open file
++  if (fileReader.fail()) { // couldn't open file
+ 	throw(stacktrace() + "\n\nCould not open " + filename + "\n");
+   }
+   
diff --git a/debian/patches/series b/debian/patches/series
index 26aa8b3..8ce756e 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,5 @@ noExitTester
 jellyfish-path
 update-paths
 collections15-to-4
+0001-fix_gcc5.patch.patch
+0002-fix_istream_failure_call.patch

-- 
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