Update OpenMS to 2.3 release from 2018-01-02

4 files changed, 58 insertions, 52 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 66f758d4c0b5..a0c1d8d4ea9f 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,29 +1,33 @@
 pkgbase = openms
 	pkgdesc = C++ library and tools for LC/MS data management and analyses
-	pkgver = 2.0.0
-	pkgrel = 2
-	url = http://open-ms.sourceforge.net/
+	pkgver = 2.3.0
+	pkgrel = 1
+	url = http://www.openms.de
 	arch = i686
 	arch = x86_64
 	license = BSD
+	makedepends = autoconf
+	makedepends = automake
+	makedepends = binutils
 	makedepends = cmake
-	makedepends = boost
-	depends = boost-libs
-	depends = libsvm
-	depends = glpk
-	depends = xerces-c
+	makedepends = fakeroot
+	makedepends = gcc
+	makedepends = make
+	makedepends = patch
+	depends = boost
+	depends = qt4
 	depends = qtwebkit
+	depends = xerces-c
+	depends = bzip2
 	depends = eigen
-	optdepends = dot2tex: Create package documentation during compilation
-	optdepends = texlive-core: Create package documentation during compilation
-	optdepends = texlive-latexextra: Create package documentation during compilation
-	optdepends = doxygen: Create package documentation during compilation
-	source = http://download.sourceforge.net/project/open-ms/OpenMS/OpenMS-2.0/OpenMS-2.0.0_src.tar.gz
+	depends = glpk
+	depends = zlib
+	source = https://download.sourceforge.net/project/open-ms/OpenMS/OpenMS-2.3/OpenMS-2.3.0-src.tar.gz
 	source = OpenMS-TOPPView.desktop
 	source = OpenMS-TOPPAS.desktop
-	sha256sums = 957bbb28bf484b9e288986c103109298f9aeac8e4d5e68b8b58ac2e365d7ab3d
-	sha256sums = 76fab06730720c786a0b874ba6bb8b85adae85b11dde9c68c35a0d3e76d7f049
-	sha256sums = ba63c4aa90b1c055141cb0ef5bd199e390912595e7fdb8d30e9bb777f189ca30
+	sha256sums = 6ddc56811e1bcb67f28b8c55781229bbe10cc8250b59e76ba1f2a3b52e142ba5
+	sha256sums = 06819f1899b6122d513e67f2427c0c07bab522f859a79b6c7dd56e7d627d0d23
+	sha256sums = 866f5c99e9516af943e06f3407bad6abbb24167f90e351e4727edb2c5cf058cf
 
 pkgname = openms
 
diff --git a/OpenMS-TOPPAS.desktop b/OpenMS-TOPPAS.desktop
index 8ebb76cedc99..b04056fd17c2 100755
--- a/OpenMS-TOPPAS.desktop
+++ b/OpenMS-TOPPAS.desktop
@@ -4,7 +4,8 @@ GenericName=
 Comment=Software for LC-MS data management and analyses
 Exec=TOPPAS
 Icon=applications-science
-Terminal=false
 Type=Application
+Terminal=false
 Categories=Science;
-StartupNotify=false
\ No newline at end of file
+StartupNotify=false
+
diff --git a/OpenMS-TOPPView.desktop b/OpenMS-TOPPView.desktop
index 0d2c21c99c65..ff088c7e26e7 100755
--- a/OpenMS-TOPPView.desktop
+++ b/OpenMS-TOPPView.desktop
@@ -7,4 +7,5 @@ Icon=applications-science
 Terminal=false
 Type=Application
 Categories=Science;
-StartupNotify=false
\ No newline at end of file
+StartupNotify=false
+
diff --git a/PKGBUILD b/PKGBUILD
index f6163cb576c4..8a90d5b32962 100755
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,41 +1,41 @@
- # Maintainer: saxonbeta <saxonbeta at gmail dot com>
+# Maintainer: lukaszimmermann <luk.zim91 at gmail dot com>
+# Contributor: saxonbeta <saxonbeta at gmail dot com>
 pkgname=openms
 _pkgname=OpenMS
-pkgver=2.0.0
-pkgrel=2
+pkgver=2.3.0
+_pkgver=2.3
+pkgrel=1
 pkgdesc="C++ library and tools for LC/MS data management and analyses"
 arch=('i686' 'x86_64')
-url="http://open-ms.sourceforge.net/"
+url="http://www.openms.de"
 license=('BSD')
-depends=('boost-libs' 'libsvm' 'glpk' 'xerces-c' 'qtwebkit' 'eigen')
-makedepends=('cmake' 'boost')
-optdepends=('dot2tex: Create package documentation during compilation'
-	    'texlive-core: Create package documentation during compilation'
-	    'texlive-latexextra: Create package documentation during compilation'
-	    'doxygen: Create package documentation during compilation')
-source=("http://download.sourceforge.net/project/open-ms/${_pkgname}/${_pkgname}-2.0/${_pkgname}-${pkgver}_src.tar.gz"
-        'OpenMS-TOPPView.desktop' 'OpenMS-TOPPAS.desktop')
-sha256sums=('957bbb28bf484b9e288986c103109298f9aeac8e4d5e68b8b58ac2e365d7ab3d'
-	    '76fab06730720c786a0b874ba6bb8b85adae85b11dde9c68c35a0d3e76d7f049'
-	    'ba63c4aa90b1c055141cb0ef5bd199e390912595e7fdb8d30e9bb777f189ca30')
-
-	    
-
-
+depends=('boost' 'qt4' 'qtwebkit' 'xerces-c' 'bzip2' 'eigen' 'glpk' 'zlib')
+makedepends=('autoconf' 'automake' 'binutils' 'cmake' 'fakeroot' 'gcc' 'make' 'patch')
+source=("https://download.sourceforge.net/project/open-ms/${_pkgname}/${_pkgname}-${_pkgver}/${_pkgname}-${pkgver}-src.tar.gz"
+        OpenMS-TOPPView.desktop OpenMS-TOPPAS.desktop)
+sha256sums=('6ddc56811e1bcb67f28b8c55781229bbe10cc8250b59e76ba1f2a3b52e142ba5'
+            '06819f1899b6122d513e67f2427c0c07bab522f859a79b6c7dd56e7d627d0d23'
+            '866f5c99e9516af943e06f3407bad6abbb24167f90e351e4727edb2c5cf058cf')
 build() {
-  cd "$srcdir/$_pkgname-$pkgver"
-  cd contrib
-  cmake -DBUILD_TYPE=WILDMAGIC
-  cmake -DBUILD_TYPE=SEQAN
-  cd ..
-  cmake -DBOOST_USE_STATIC=OFF -DINSTALL_PREFIX=/usr -DCMAKE_FIND_ROOT_PATH=/usr -DCMAKE_INSTALL_PREFIX=/usr
-  make
+  cd "${srcdir}/"
+  rm -rf ${_pkgname}-${pkgver}-build
+  mkdir  ${_pkgname}-${pkgver}-build
+  rm -rf contrib-build
+  mkdir contrib-build
+  cd contrib-build
+  cmake -DBUILD_TYPE=SEQAN     $(realpath -P ../${_pkgname}-${pkgver}/contrib)
+  cmake -DBUILD_TYPE=LIBSVM    $(realpath -P ../${_pkgname}-${pkgver}/contrib)
+  cmake -DBUILD_TYPE=COINOR    $(realpath -P ../${_pkgname}-${pkgver}/contrib)
+  cmake -DBUILD_TYPE=KISSFFT   $(realpath -P ../${_pkgname}-${pkgver}/contrib)
+  cmake -DBUILD_TYPE=WILDMAGIC $(realpath -P ../${_pkgname}-${pkgver}/contrib)
+  cd ../${_pkgname}-${pkgver}-build
+  cmake -DCMAKE_BUILD_TYPE=Release -DOPENMS_CONTRIB_LIBS=$(realpath -P ../contrib-build) -DCMAKE_INSTALL_PREFIX=$(realpath -P ${pkgdir}/usr)  $(realpath -P ../${_pkgname}-${pkgver})
+  make OpenMS TOPP UTILS GUI
 }
-
 package() {
-  cd "$srcdir/$_pkgname-$pkgver"
-  make DESTDIR="$pkgdir/" install
-  install -D -m644 LICENSE "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
-  install -D -m644 $srcdir/OpenMS-TOPPView.desktop ${pkgdir}/usr/share/applications/OpenMS-TOPPView.desktop
-  install -D -m644 $srcdir/OpenMS-TOPPAS.desktop ${pkgdir}/usr/share/applications/OpenMS-TOPPAS.desktop
-}
\ No newline at end of file
+  cd "${srcdir}/${_pkgname}-${pkgver}-build"
+  make DESTDIR=${pkgdir}/usr install
+  install -D -m644 ${srcdir}/${_pkgname}-${pkgver}/LICENSE "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
+  install -D -m644 ${srcdir}/OpenMS-TOPPView.desktop ${pkgdir}/usr/share/applications/OpenMS-TOPPView.desktop
+  install -D -m644 ${srcdir}/OpenMS-TOPPAS.desktop ${pkgdir}/usr/share/applications/OpenMS-TOPPAS.desktop
+}