Fix for now JEMalloc seg fault when using jemalloc package

2 files changed, 15 insertions, 8 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 2fcd5affdebf..6b11688b49df 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,7 +1,7 @@
 pkgbase = salmon
 	pkgdesc = Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments
-	pkgver = 0.11.2
-	pkgrel = 2
+	pkgver = 0.11.3
+	pkgrel = 1
 	url = https://combine-lab.github.io/salmon/
 	arch = x86_64
 	license = GPL
@@ -12,8 +12,8 @@ pkgbase = salmon
 	depends = intel-tbb
 	depends = xz
 	options = !emptydirs
-	source = salmon-0.11.2.tar.gz::https://github.com/COMBINE-lab/salmon/archive/v0.11.2.tar.gz
-	md5sums = d81f083e71adc6d46a21ed14df624136
+	source = salmon-0.11.3.tar.gz::https://github.com/COMBINE-lab/salmon/archive/v0.11.3.tar.gz
+	md5sums = 99e95233be7f8510bed5c4d0c46a5074
 
 pkgname = salmon
 
diff --git a/PKGBUILD b/PKGBUILD
index 3297660358fb..7e745440ab1e 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,16 +1,23 @@
 # Maintainer: Thiago L. A. Miller <thiago_leisrael@hotmail.com>
 pkgname=salmon
-pkgver=0.11.2
-pkgrel=2
+pkgver=0.11.3
+pkgrel=1
 pkgdesc="Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments"
 arch=('x86_64')
 url="https://combine-lab.github.io/$pkgname/"
 license=('GPL')
-depends=('bzip2' 'intel-tbb' 'jemalloc' 'xz')
+depends=('bzip2' 'intel-tbb' 'xz')
 makedepends=('boost>=1.55' 'cmake' 'unzip')
 options=('!emptydirs')
 source=("$pkgname-$pkgver.tar.gz"::"https://github.com/COMBINE-lab/$pkgname/archive/v$pkgver.tar.gz")
-md5sums=('d81f083e71adc6d46a21ed14df624136')
+md5sums=('99e95233be7f8510bed5c4d0c46a5074')
+
+prepare() {
+  # Fix for now JEMalloc seg fault when using jemalloc package
+  # Force cmake to statically build JEMalloc from salmon's dev sources
+	cd "$pkgname-$pkgver"
+  sed -i '/^find_package(Jemalloc)/,/^endif()/s/\(.\+\)/#\1/' CMakeLists.txt
+}
 
 build() {
   cd "$pkgname-$pkgver"