sga-0.10.14-1

- updates rpath patch
- explicitly sets C++ standard

4 files changed, 33 insertions, 10 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 43603e276612..0d65b7ca6ca1 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,6 +1,8 @@
+# Generated by mksrcinfo v8
+# Thu Aug  4 07:25:44 UTC 2016
 pkgbase = sga
 	pkgdesc = de novo sequence assembler using string graphs
-	pkgver = 0.10.13
+	pkgver = 0.10.14
 	pkgrel = 1
 	url = https://github.com/jts/sga
 	arch = x86_64
@@ -10,9 +12,11 @@ pkgbase = sga
 	depends = bamtools
 	depends = jemalloc
 	depends = python
-	source = sga-0.10.13.tar.gz::https://github.com/jts/sga/archive/v0.10.13.tar.gz
+	source = sga-0.10.14.tar.gz::https://github.com/jts/sga/archive/v0.10.14.tar.gz
+	source = set-standard.patch
 	source = configure-rpath.patch
-	md5sums = d4f6aefc48c940dba96cc6513649ecdd
+	md5sums = 211edb372898d6515dcde98d17078b7b
+	md5sums = SKIP
 	md5sums = SKIP
 
 pkgname = sga
diff --git a/PKGBUILD b/PKGBUILD
index f879c950fecc..5d94b6ea7d8f 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,7 +1,7 @@
 # Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com>
 
 pkgname=sga
-pkgver=0.10.13
+pkgver=0.10.14
 pkgrel=1
 pkgdesc="de novo sequence assembler using string graphs"
 arch=('x86_64' 'i686')
@@ -10,20 +10,26 @@ license=('GPL3')
 depends=('bamtools' 'jemalloc' 'python')
 makedepends=('sparsehash')
 source=("$pkgname-$pkgver.tar.gz::https://github.com/jts/sga/archive/v$pkgver.tar.gz"
+        'set-standard.patch'
         'configure-rpath.patch')
-md5sums=('d4f6aefc48c940dba96cc6513649ecdd'
+md5sums=('211edb372898d6515dcde98d17078b7b'
+         'SKIP'
          'SKIP')
 
 prepare() {
-  cd $srcdir/$pkgname-$pkgver/src
+  cd $srcdir/$pkgname-$pkgver
+
+  patch -p1 -i $srcdir/set-standard.patch
+  patch -p1 -i $srcdir/configure-rpath.patch
+
+  cd src
 
-  patch -p0 -i $srcdir/configure-rpath.patch
+  ./autogen.sh
 }
 
 build() {
   cd $srcdir/$pkgname-$pkgver/src
 
-  ./autogen.sh
   ./configure --prefix=/usr --with-bamtools=/usr --with-jemalloc=/usr
 
   make
diff --git a/configure-rpath.patch b/configure-rpath.patch
index 2ec981c5fb14..76c08bf9a6b2 100644
--- a/configure-rpath.patch
+++ b/configure-rpath.patch
@@ -1,5 +1,5 @@
---- configure.ac	2014-01-17 21:16:36.000000000 +0100
-+++ /tmp/configure.ac.patched	2014-11-07 14:04:25.882803929 +0100
+--- a/src/configure.ac	2014-01-17 21:16:36.000000000 +0100
++++ b/src/configure.ac	2014-11-07 14:04:25.882803929 +0100
 @@ -32,8 +32,8 @@
  	[specify directory containing the bamtools library (http://github.com/pezmaster31/bamtools)]))
  
diff --git a/set-standard.patch b/set-standard.patch
new file mode 100644
index 000000000000..3e6dc2a690fa
--- /dev/null
+++ b/set-standard.patch
@@ -0,0 +1,13 @@
+--- a/src/configure.ac
++++ b/src/configure.ac
+@@ -92,8 +92,8 @@ fi
+ 
+ # Set compiler flags.
+ AC_SUBST(AM_CXXFLAGS, "-Wall -Wextra $fail_on_warning -Wno-unknown-pragmas")
+-AC_SUBST(CXXFLAGS, "-O3")
+-AC_SUBST(CFLAGS, "-O3")
++AC_SUBST(CXXFLAGS, "-std=c++98 -O3")
++AC_SUBST(CFLAGS, "-std=gnu99 -O3")
+ AC_SUBST(CPPFLAGS, "$CPPFLAGS $openmp_cppflags $sparsehash_include $bamtools_include")
+ AC_SUBST(LDFLAGS, "$openmp_cppflags $external_malloc_ldflags $bamtools_ldflags $LDFLAGS")
+