Backport some compiler fixes from master

1 files changed, 18 insertions, 10 deletions

diff --git a/PKGBUILD b/PKGBUILD
index e7c636065740..6bea3959d79c 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,29 +1,37 @@
-# Maintainer: Alex Peltzer ("alexpe87") <alexpe.aur@mailbox.org>
+# Maintainer: Maël Kerbiriou <m431.kerbiriou@gmail.com>
+# Previous maintainer: Alex Peltzer ("alexpe87") <alexpe.aur@mailbox.org>
 # Contributor: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com>
 
 pkgname=bwa
 pkgver=0.7.17
 _pkgver=${pkgver}
-pkgrel=1
+pkgrel=2
 pkgdesc="Burrows-Wheeler Aligner maps low-divergent sequences against a large reference genome"
 arch=('i686' 'x86_64')
 url="http://bio-bwa.sourceforge.net/"
 license=('GPL3')
 depends=('perl' 'zlib')
-source=(https://github.com/lh3/bwa/releases/download/v$pkgver/bwa-${_pkgver}.tar.bz2)
-md5sums=('82cba7ef695538e6a38b9d4156837381')
+source=("https://github.com/lh3/bwa/releases/download/v$pkgver/bwa-${_pkgver}.tar.bz2"
+        'backported.patch')
+sha256sums=('de1b4d4e745c0b7fc3e107b5155a51ac063011d33a5d82696331ecf4bed8d0fd'
+            'ec91adc478cbf207c694c5b7e46738dcbd77cd77180c7a6279d3e000108fe8c2')
+
+prepare() {
+    patch --directory="$pkgname-$_pkgver" --forward --strip=1 --input="${srcdir}/backported.patch"
+}
 
 build() {
-  cd $srcdir/$pkgname-$_pkgver
+  cd "$srcdir/$pkgname-$_pkgver"
 
   make
 }
 
 package() {
-  cd $srcdir/$pkgname-$_pkgver
+  cd "$srcdir/$pkgname-$_pkgver"
 
-  install -Dm755 bwa          $pkgdir/usr/bin/bwa
-  install -Dm755 qualfa2fq.pl $pkgdir/usr/bin/qualfa2fq
-  install -Dm755 xa2multi.pl  $pkgdir/usr/bin/xa2multi
-  install -Dm644 bwa.1        $pkgdir/usr/share/man/man1/bwa.1
+  install -Dm755 bwa          "$pkgdir/usr/bin/bwa"
+  install -Dm755 qualfa2fq.pl "$pkgdir/usr/bin/qualfa2fq"
+  install -Dm755 xa2multi.pl  "$pkgdir/usr/bin/xa2multi"
+  install -Dm644 bwa.1        "$pkgdir/usr/share/man/man1/bwa.1"
+  install -Dm644 COPYING      "$pkgdir/usr/share/licenses/${pkgname}"
 }