Fix for version 3.04

3 files changed, 8 insertions, 37 deletions

diff --git a/.SRCINFO b/.SRCINFO
index e1a333ceff90..84a2e2d35119 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,6 +1,6 @@
 pkgbase = percolator-git
 	pkgdesc = Software for postprocessing of shotgun proteomics data + format converters + Elude tool
-	pkgver = 3.02.01.r8.gf97ae1d
+	pkgver = 3.04
 	pkgrel = 1
 	url = http://percolator.ms/
 	arch = x86_64
@@ -14,9 +14,7 @@ pkgbase = percolator-git
 	depends = libtirpc-compat
 	depends = boost
 	source = source::git+https://github.com/percolator/percolator
-	source = percolator.patch
 	md5sums = SKIP
-	md5sums = 53c592a9db82da8474907a617ea688fb
 
 pkgname = percolator-git
 	pkgdesc = Percolator and qvality, two post processors for shotgun proteomics data.
diff --git a/PKGBUILD b/PKGBUILD
index 3c8cc0515bc0..00c595e5b901 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,7 +1,7 @@
 # Maintainer: Lev Levitsky <levlev@mail.ru>
 pkgbase="percolator-git"
 pkgname=('percolator-git' 'percolator-converters-git' 'elude-git')
-pkgver=3.02.01.r8.gf97ae1d
+pkgver=3.04
 pkgrel=1
 pkgdesc="Software for postprocessing of shotgun proteomics data + format converters + Elude tool"
 url="http://percolator.ms/"
@@ -9,10 +9,8 @@ license=('Apache')
 depends=('xerces-c' 'sqlite' 'libtirpc-compat' 'boost')
 arch=('x86_64')
 makedepends=('git' 'xsd' 'cmake' 'zlib')
-source=('source::git+https://github.com/percolator/percolator'
-        'percolator.patch')
-md5sums=('SKIP'
-         '53c592a9db82da8474907a617ea688fb')
+source=('source::git+https://github.com/percolator/percolator')
+md5sums=('SKIP')
 
 pkgver() {
     cd "${srcdir}/source"
@@ -21,7 +19,6 @@ pkgver() {
 
 prepare() {
     cd "${srcdir}/source"
-    patch -p1 -i "$srcdir/${pkgname%-git}.patch"
     cd "$BUILDDIR"
     for d in "${pkgname[@]}"; do
         mkdir "${d%-git}"
@@ -36,10 +33,10 @@ build() {
     echo "------------------------"
     echo "Running cmake for percolator ..."
     echo "................................"
-    cmake -DTARGET_ARCH=x86_64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr -DXML_SUPPORT=ON "${srcdir}/source"
+    cmake -DTARGET_ARCH=x86_64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr -DXML_SUPPORT=ON -DCMAKE_PREFIX_PATH="/usr/include;/usr/lib" -DCMAKE_CXX_FLAGS="-l tirpc" "${srcdir}/source"
     echo "Running make for percolator ..."
     echo "..............................."
-    make
+    make -j 4
     echo "------------------------"
     echo "Building converters ..."
     echo "------------------------"
@@ -49,7 +46,7 @@ build() {
     cmake -DTARGET_ARCH=x86_64 -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release "${srcdir}/source/src/converters"
     echo "Running make for percolator-converters ..."
     echo ".........................................."
-    make
+    make -j 4
     echo "------------------------"
     echo "Building Elude ..."
     echo "------------------------"
@@ -59,7 +56,7 @@ build() {
     cmake -DTARGET_ARCH=x86_64 -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release "${srcdir}/source/src/elude_tool"
     echo "Running make for elude ..."
     echo ".........................."
-    make
+    make -j 4
 }
 
 package_percolator-git() {
diff --git a/percolator.patch b/percolator.patch
deleted file mode 100644
index 22fdc38b4a89..000000000000
--- a/percolator.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-diff --git a/cmake/FindXsd.cmake b/cmake/FindXsd.cmake
-index 5b4e084..d11970b 100755
---- a/cmake/FindXsd.cmake
-+++ b/cmake/FindXsd.cmake
-@@ -20,7 +20,7 @@ PATH_SUFFIXES
- 
- FIND_PROGRAM(XSD_EXECUTABLE 
-   NAMES 
--    xsd xsdcxx
-+    xsdcxx xsd
-   PATHS
-     $ENV{XSDDIR}/bin
-     /usr/local/bin
-diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
-index 09aa167..80f6105 100755
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -161,4 +161,5 @@ ENDIF(CRUX)
- ###############################################################################
- 
- add_subdirectory(qvality)
--
-+include_directories(/usr/include/rpc)
-+target_link_libraries(percolator tirpc)