fixed compilation without icc

2 files changed, 159 insertions, 109 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 47933972f668..0a96a275acd1 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,7 +1,7 @@
 # Generated by mksrcinfo v8
-# Fri Jan 15 13:05:52 UTC 2016
+# Wed Jan 20 20:55:51 UTC 2016
 pkgbase = r-mkl
-	pkgdesc = Language and environment for statistical computing and graphics, set up to use Intel's MKL
+	pkgdesc = Language and environment for statistical computing and graphics, set up to use Intel's MKL by default.
 	pkgver = 3.2.3
 	pkgrel = 1
 	url = http://www.r-project.org/
@@ -9,7 +9,7 @@ pkgbase = r-mkl
 	arch = i686
 	arch = x86_64
 	license = GPL
-	makedepends = jdk8-openjdk-infinality
+	makedepends = jdk8-openjdk
 	makedepends = gcc-fortran
 	makedepends = tk
 	depends = intel-mkl
@@ -30,6 +30,7 @@ pkgbase = r-mkl
 	depends = desktop-file-utils
 	depends = zip
 	depends = unzip
+	depends = openmp
 	optdepends = tk: tcl/tk interface
 	optdepends = texlive-bin: latex sty files
 	optdepends = icc: intel compiler
diff --git a/PKGBUILD b/PKGBUILD
index 34f4f135307b..be97f71c4717 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,62 +1,91 @@
-# Maintainer: halfhorn <mwellsa -at- gmail -dot- com>
+# Maintainer: alexanderp <alexisph -at- gmail -dot- com>
+# Contributor: halfhorn <mwellsa -at- gmail -dot- com>
 # Contributor: jdarch <jda -dot- cloud -plus- archlinux -at- gmail -dot- com>
 # Based on the PKGBUILD for R
 
 pkgname=r-mkl
 pkgver=3.2.3
 pkgrel=1
-pkgdesc="Language and environment for statistical computing and graphics, set up to use Intel's MKL"
+pkgdesc="Language and environment for statistical computing and graphics, set up to use Intel's MKL by default."
 arch=('i686' 'x86_64')
 license=('GPL')
 url=('http://www.r-project.org/')
 provides=("r=${pkgver}","r-mkl=${pkgver}")
 conflicts=('r')
-depends=('intel-mkl' 'bzip2'  'libpng' 'libjpeg' 'libtiff'
-         'ncurses' 'pcre' 'readline' 'zlib' 'perl' 'gcc-libs'
-         'libxt' 'libxmu' 'pango' 'xz' 'desktop-file-utils' 'zip' 'unzip')
-makedepends=('jdk8-openjdk-infinality' 'gcc-fortran' 'tk')
-optdepends=('tk: tcl/tk interface' 'texlive-bin: latex sty files'
-            'icc: intel compiler' 'icpc: intel compiler' 'xiar: intel compiler'
+depends=('intel-mkl'
+        'bzip2'
+        'libpng'
+        'libjpeg'
+        'libtiff'
+        'ncurses'
+        'pcre'
+        'readline'
+        'zlib'
+        'perl'
+        'gcc-libs'
+        'libxt'
+        'libxmu'
+        'pango'
+        'xz'
+        'desktop-file-utils'
+        'zip'
+        'unzip'
+        'openmp')
+makedepends=('jdk8-openjdk'
+            'gcc-fortran'
+            'tk')
+optdepends=('tk: tcl/tk interface'
+            'texlive-bin: latex sty files'
+            'icc: intel compiler'
+            'icpc: intel compiler'
+            'xiar: intel compiler'
             'xild: intel compiler')
-backup=('etc/R/Makeconf' 'etc/R/Renviron' 'etc/R/ldpaths' 'etc/R/repositories' 'etc/R/javaconf')
+backup=('etc/R/Makeconf'
+        'etc/R/Renviron'
+        'etc/R/ldpaths'
+        'etc/R/repositories'
+        'etc/R/javaconf')
 options=('!makeflags' '!emptydirs')
 install=r-mkl.install
 
 source=("http://cran.r-project.org/src/base/R-${pkgver%%.*}/R-${pkgver}.tar.gz"
-	'r.desktop'
-	'r.png'
-	'R.conf')
+        'r.desktop'
+        'r.png'
+        'R.conf')
 
 md5sums=('1ba3dac113efab69e706902810cc2970'
-         '44ca875140b148543148b7749c7d6f5e'
-         '00659f39e90627fe87f1645df5d4e3a7'
-         '1dfa62c812aed9642f6e4ac34999b9fe')
+        '44ca875140b148543148b7749c7d6f5e'
+        '00659f39e90627fe87f1645df5d4e3a7'
+        '1dfa62c812aed9642f6e4ac34999b9fe')
 sha512sums=('9d7294af860204f4d84e25eb503111c9607beedbc42f01de073c915945a6342c3e24e25a9cc038a2e58442036bee931975d93dc327081ed02afe5ffa365170ea'
             '1a90aed5411d72dd3e7708db0cb92c518e656e1a510ece02ad934131e05b8e683b4a36da8d37198263dc19fb2f3f19656c19c01f9b67974f0d7755974076d0b7'
             '55ed6e819dcbb231d842d825134b84d1a24db177558d5dad9369d57fd21d0239d6433c4311531171a101ca3c7c0685493e9cc6c1fe9e4e0df59f2331cff150ba'
             'aae388c5b6c02d9fb857914032b0cd7d68a9f21e30c39ba11f5a29aaf1d742545482054b57ce18872eabb6605bbb359b2fc1e9be5ce6881443fdbdf6b67fab3b')
 
 if [ "$CARCH" == "x86_64" ]; then
-    _intel_arch=intel64
-    _intel_lib=mkl_intel_lp64
+  _intel_arch=intel64
+  _intel_lib=mkl_intel_lp64
 elif [ "$CARCH" == "i686" ]; then
-    _intel_arch=ia32
-    _intel_lib=mkl_gf
+  _intel_arch=ia32
+  _intel_lib=mkl_gf
 fi
 
-_CC="icc" # uncomment to build with the Intel compiler
+_CC="icc" # comment to build without the Intel compiler
 
 prepare() {
-    cd R-${pkgver}
-    # set texmf dir correctly in makefile
-    sed -i 's|$(rsharedir)/texmf|${datarootdir}/texmf|' share/Makefile.in
-    # fix for texinfo 5.X
-    sed -i 's|test ${makeinfo_version_min} -lt 7|test ${makeinfo_version_min} -lt 0|' configure
-    # Fix the config script to look in Makeconf for LDFLAGS
-    sed -i '/LIBS=`eval $query VAR=LIBS`/a\LDFLAGS=`eval $query VAR=LDFLAGS`' src/scripts/config
+  cd R-${pkgver}
+  # set texmf dir correctly in makefile
+  sed -i 's|$(rsharedir)/texmf|${datarootdir}/texmf|' share/Makefile.in
+  # fix for texinfo 5.X
+  sed -i 's|test ${makeinfo_version_min} -lt 7|test ${makeinfo_version_min} -lt 0|' configure
+  # Fix the config script to look in Makeconf for LDFLAGS
+  sed -i '/LIBS=`eval $query VAR=LIBS`/a\LDFLAGS=`eval $query VAR=LDFLAGS`' src/scripts/config
 }
 
 build() {
+  cd R-${pkgver}
+
+  if [ $_CC = "icc" ]; then
     # Set up the environment for MKL
     source /opt/intel/mkl/bin/mklvars.sh ${_intel_arch}
     source /opt/intel/composerxe/linux/bin/ifortvars.sh ${_intel_arch}
@@ -64,93 +93,113 @@ build() {
     _mkllibpath=$MKLROOT/lib/${_intel_arch}
     _openmplibpath=${PROD_DIR}/compiler/lib/intel64
     _mkllibs="-L${_mkllibpath} -L${_openmplibpath} -Wl,--no-as-needed \
-              -l${_intel_lib} \
-              -lmkl_intel_thread \
-              -lmkl_core \
-              -liomp5 -ldl -lpthread -lm"
+      -l${_intel_lib} \
+      -lmkl_intel_thread \
+      -lmkl_core \
+      -liomp5 -ldl -lpthread -lm"
     LDFLAGS="${LDFLAGS} -L${_icclibpath}"
     export MAIN_LDFLAGS="-qopenmp"
-    
-    
-    if [ $_CC = "icc" ]; then
-        export CC="icc"
-        export CXX="icpc"
-        export AR="xiar"
-        export LD="xild"
-        export _F77="ifort"
-        export _FC="ifort"
-        export CFLAGS="-O3 -ipo -qopenmp -parallel -xHost -fp-model strict -qopt-mem-layout-trans=3 -I${MKLROOT}/include"
-        export CXXFLAGS="-O3 -ipo -qopenmp -parallel -xHost -fp-model strict -qopt-mem-layout-trans=3 -I${MKLROOT}/include"
-        export FFLAGS="-O3 -ipo -qopenmp -parallel -xHost -fp-model strict -qopt-mem-layout-trans=3 -I${MKLROOT}/include"
-        export FCFLAGS="-O3 -ipo -qopenmp -parallel -xHost -fp-model strict -qopt-mem-layout-trans=3 -I${MKLROOT}/include"
-    else
-        export _F77="gfortran"
-        export _FC="gfortran"
-    fi
-    
-    cd R-${pkgver}
+
+    export CC="icc"
+    export CXX="icpc"
+    export AR="xiar"
+    export LD="xild"
+    export _F77="ifort"
+    export _FC="ifort"
+    export CFLAGS="-O3 -ipo -qopenmp -parallel -xHost -fp-model strict -qopt-mem-layout-trans=3 -I${MKLROOT}/include"
+    export CXXFLAGS="-O3 -ipo -qopenmp -parallel -xHost -fp-model strict -qopt-mem-layout-trans=3 -I${MKLROOT}/include"
+    export FFLAGS="-O3 -ipo -qopenmp -parallel -xHost -fp-model strict -qopt-mem-layout-trans=3 -I${MKLROOT}/include"
+    export FCFLAGS="-O3 -ipo -qopenmp -parallel -xHost -fp-model strict -qopt-mem-layout-trans=3 -I${MKLROOT}/include"
+
     ./configure  --prefix=/usr \
-     	--libdir=/usr/lib \
-     	--sysconfdir=/etc/R \
-     	--datarootdir=/usr/share \
-     	rsharedir=/usr/share/R/ \
-     	rincludedir=/usr/include/R/ \
-     	rdocdir=/usr/share/doc/R/ \
-     	--with-x \
-        --with-blas="${_mkllibs}" \
-        --with-lapack \
-        --enable-R-shlib \
-        --enable-memory-profiling \
-        --enable-BLAS-shlib \
-        --enable-openmp \
-        F77=${_F77} \
-        FC=${_FC} \
-     	LIBnn=lib
-    
-    # Place Intel's basic math library prior to GLIBC libm 
+      --libdir=/usr/lib \
+      --sysconfdir=/etc/R \
+      --datarootdir=/usr/share \
+        rsharedir=/usr/share/R/ \
+        rincludedir=/usr/include/R/ \
+        rdocdir=/usr/share/doc/R/ \
+      --with-x \
+      --with-blas="${_mkllibs}" \
+      --with-lapack \
+      --enable-R-shlib \
+      --enable-memory-profiling \
+      --enable-BLAS-shlib \
+      --enable-openmp \
+      F77=${_F77} \
+      FC=${_FC} \
+      LIBnn=lib
+
+    # Place Intel's basic math library prior to GLIBC libm
     sed -i "s/\(^\| \)-lm\( \|$\)/\1-limf -lm\2/g" {./,etc/}Makeconf
-    
-    # Build the package
-    make
-    
-    # make libRmath.so
-    cd src/nmath/standalone
-    make shared
+
+  else
+    export _F77="gfortran"
+    export _FC="gfortran"
+    export CFLAGS="-O3 -fopenmp"
+    export CXXFLAGS="-O3 -fopenmp"
+    export FFLAGS="-O3 -fopenmp"
+    export FCFLAGS="-O3 -fopenmp"
+
+    ./configure  --prefix=/usr \
+      --libdir=/usr/lib \
+      --sysconfdir=/etc/R \
+      --datarootdir=/usr/share \
+        rsharedir=/usr/share/R/ \
+        rincludedir=/usr/include/R/ \
+        rdocdir=/usr/share/doc/R/ \
+      --with-x \
+      --with-blas \
+      --with-lapack \
+      --enable-R-shlib \
+      --enable-memory-profiling \
+      --enable-openmp \
+      F77=${_F77} \
+      FC=${_FC} \
+      LIBnn=lib
+  fi
+
+  # Build the package
+  make
+
+  # make libRmath.so
+  cd src/nmath/standalone
+  make shared
 }
 
 check() {
-    cd R-${pkgver}
-    make check-recommended
+  cd R-${pkgver}
+  make check-recommended
 }
 
 package() {
-    cd R-${pkgver}
-    make DESTDIR="${pkgdir}" install
-    
-    # install libRmath.so
-    cd src/nmath/standalone
-    make DESTDIR="${pkgdir}" install
-    
-    #  Fixup R wrapper scripts.
-    sed -i "s|${pkgdir} ||" "${pkgdir}/usr/bin/R"
-    rm "${pkgdir}/usr/lib/R/bin/R"
-    cd "${pkgdir}/usr/lib/R/bin"
-    ln -s ../../../bin/R
-    
-    # install some freedesktop.org compatibility
-    install -Dm644 "${srcdir}/r.desktop" \
-     "${pkgdir}/usr/share/applications/r.desktop"
-    install -Dm644 "${srcdir}/r.png" \
-     "${pkgdir}/usr/share/pixmaps/r.png"
-    
-    # move the config directory to /etc and create symlinks
-    install -d "${pkgdir}/etc/R"
-    cd "${pkgdir}/usr/lib/R/etc"
-    for i in *; do
-        mv -f ${i} "${pkgdir}/etc/R"
-        ln -s /etc/R/${i} ${i}
-    done
-    
-    # Install ld.so.conf.d file to ensure other applications access the shared lib
-    install -Dm644 "${srcdir}/R.conf" "${pkgdir}/etc/ld.so.conf.d/R.conf"
+  cd R-${pkgver}
+  make DESTDIR="${pkgdir}" install
+
+  # install libRmath.so
+  cd src/nmath/standalone
+  make DESTDIR="${pkgdir}" install
+
+  # Fixup R wrapper scripts.
+  sed -i "s|${pkgdir} ||" "${pkgdir}/usr/bin/R"
+  rm "${pkgdir}/usr/lib/R/bin/R"
+  cd "${pkgdir}/usr/lib/R/bin"
+  ln -s ../../../bin/R
+
+  # install some freedesktop.org compatibility
+  install -Dm644 "${srcdir}/r.desktop" \
+    "${pkgdir}/usr/share/applications/r.desktop"
+  install -Dm644 "${srcdir}/r.png" \
+    "${pkgdir}/usr/share/pixmaps/r.png"
+
+  # move the config directory to /etc and create symlinks
+  install -d "${pkgdir}/etc/R"
+  cd "${pkgdir}/usr/lib/R/etc"
+  for i in *; do
+    mv -f ${i} "${pkgdir}/etc/R"
+    ln -s /etc/R/${i} ${i}
+  done
+
+  # Install ld.so.conf.d file to ensure other applications access the shared lib
+  install -Dm644 "${srcdir}/R.conf" "${pkgdir}/etc/ld.so.conf.d/R.conf"
 }
+