cran-packages: restructured

18 files changed, 344 insertions, 0 deletions

diff --git a/pkgs/development/r-modules/patches/BayesBridge.patch b/pkgs/development/r-modules/patches/BayesBridge.patch
new file mode 100644
index 00000000000..2fb0392bf3e
--- /dev/null
+++ b/pkgs/development/r-modules/patches/BayesBridge.patch
@@ -0,0 +1,9 @@
+diff -ru -x '*~' BayesBridge_orig/src/Makevars BayesBridge/src/Makevars
+--- BayesBridge_orig/src/Makevars	2014-07-19 05:08:55.000000000 +0900
++++ BayesBridge/src/Makevars	2014-10-25 18:35:01.398539305 +0900
+@@ -9,4 +9,4 @@
+ # PKG_CPPFLAGS = -DUSE_R -DDISABLE_FIO -I../inst/include/ -DDISABLE_SINGLE -DNTHROW
+ PKG_CPPFLAGS = -DUSE_R -DDISABLE_FIO -DDISABLE_SINGLE -DNTHROW
+ # PKG_CPPFLAGS = -DUSE_R -DDISABLE_SINGLE -DNTHROW -Wall -pedantic -Wshadow  -ansi -Wsequence-point
+-PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS) 
++PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
diff --git a/pkgs/development/r-modules/patches/BayesBridge_cblas.patch b/pkgs/development/r-modules/patches/BayesBridge_cblas.patch
new file mode 100644
index 00000000000..418a6b95ee7
--- /dev/null
+++ b/pkgs/development/r-modules/patches/BayesBridge_cblas.patch
@@ -0,0 +1,9 @@
+diff -ru -x '*~' BayesBridge_orig/src/Makevars BayesBridge/src/Makevars
+--- BayesBridge_orig/src/Makevars	2014-07-19 05:08:55.000000000 +0900
++++ BayesBridge/src/Makevars	2014-10-25 14:44:23.422592445 +0900
+@@ -9,4 +9,4 @@
+ # PKG_CPPFLAGS = -DUSE_R -DDISABLE_FIO -I../inst/include/ -DDISABLE_SINGLE -DNTHROW
+ PKG_CPPFLAGS = -DUSE_R -DDISABLE_FIO -DDISABLE_SINGLE -DNTHROW
+ # PKG_CPPFLAGS = -DUSE_R -DDISABLE_SINGLE -DNTHROW -Wall -pedantic -Wshadow  -ansi -Wsequence-point
+-PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS) 
++PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS) -lcblas
diff --git a/pkgs/development/r-modules/patches/BayesLogit.patch b/pkgs/development/r-modules/patches/BayesLogit.patch
new file mode 100644
index 00000000000..83c865e479c
--- /dev/null
+++ b/pkgs/development/r-modules/patches/BayesLogit.patch
@@ -0,0 +1,12 @@
+diff -ru -x '*~' BayesLogit_orig/src/Makevars BayesLogit/src/Makevars
+--- BayesLogit_orig/src/Makevars	2014-04-24 23:31:13.000000000 +0900
++++ BayesLogit/src/Makevars	2014-10-25 18:33:32.398572641 +0900
+@@ -6,7 +6,7 @@
+ ## W/OUT Dynamic Stuff
+ OBJECTS = Matrix.o MatrixFrame.o RRNG.o RNG.o FSF_nmix.o LogitWrapper.o \
+ 	PolyaGamma.o PolyaGammaAlt.o PolyaGammaSP.o InvertY.o
+-PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS) 
++PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+ # PKG_CPPFLAGS = -DUSE_R -DNDEBUG -DDISABLE_SINGLE -DNTHROW -Wall -pedantic -Wextra
+ PKG_CPPFLAGS = -DUSE_R -DNDEBUG -DDISABLE_SINGLE -DNTHROW 
+ 
diff --git a/pkgs/development/r-modules/patches/BayesLogit_cblas.patch b/pkgs/development/r-modules/patches/BayesLogit_cblas.patch
new file mode 100644
index 00000000000..4c8778c4697
--- /dev/null
+++ b/pkgs/development/r-modules/patches/BayesLogit_cblas.patch
@@ -0,0 +1,12 @@
+diff -ru -x '*~' BayesLogit_orig/src/Makevars BayesLogit/src/Makevars
+--- BayesLogit_orig/src/Makevars	2014-04-24 23:31:13.000000000 +0900
++++ BayesLogit/src/Makevars	2014-10-21 21:00:15.570699136 +0900
+@@ -6,7 +6,7 @@
+ ## W/OUT Dynamic Stuff
+ OBJECTS = Matrix.o MatrixFrame.o RRNG.o RNG.o FSF_nmix.o LogitWrapper.o \
+ 	PolyaGamma.o PolyaGammaAlt.o PolyaGammaSP.o InvertY.o
+-PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS) 
++PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS) -llapack -lf77blas -lcblas -latlas -lgfortran
+ # PKG_CPPFLAGS = -DUSE_R -DNDEBUG -DDISABLE_SINGLE -DNTHROW -Wall -pedantic -Wextra
+ PKG_CPPFLAGS = -DUSE_R -DNDEBUG -DDISABLE_SINGLE -DNTHROW 
+ 
diff --git a/pkgs/development/r-modules/patches/BayesXsrc.patch b/pkgs/development/r-modules/patches/BayesXsrc.patch
new file mode 100644
index 00000000000..b357d7f83fc
--- /dev/null
+++ b/pkgs/development/r-modules/patches/BayesXsrc.patch
@@ -0,0 +1,55 @@
+diff -ru -x '*~' BayesXsrc_org/MD5 BayesXsrc/MD5
+--- BayesXsrc_org/MD5	2013-11-22 21:59:01.000000000 +0900
++++ BayesXsrc/MD5	2014-10-14 22:50:46.040754675 +0900
+@@ -4,7 +4,7 @@
+ cba21fc7e2d39608d0241d8cedc4fd43 *R/run.bayesx.R
+ 112cb3aff0f8f0cd60bb146b14df1fcf *inst/CITATION
+ cf04425475f03ee67c06efcebbd8d476 *man/run.bayesx.Rd
+-1f73de4dba1228cdaa8d5435d1c1656b *src/Makefile
++658152ec0b336198a2654385bb27666d *src/Makefile
+ 2971212d003d1d647110264fb471e63b *src/Makefile.win
+ e0fd1515e0d2f8553d4034c3f7544fc5 *src/bayesxsrc/adaptiv/fullcond_adaptiv.cpp
+ 08cd954d541c3c0d635bbbd61cd05d15 *src/bayesxsrc/adaptiv/fullcond_adaptiv.h
+@@ -320,7 +320,7 @@
+ 465ac930657299f89a0a164232dc15d2 *src/dev-Makefile
+ d9aafe726622cd8c46bab760fef0d813 *src/dev-Makefile.win
+ 50413e579bc999d49037293a612190c0 *src/install.libs.R
+-1f73de4dba1228cdaa8d5435d1c1656b *src/rel-Makefile
++658152ec0b336198a2654385bb27666d *src/rel-Makefile
+ 2971212d003d1d647110264fb471e63b *src/rel-Makefile.win
+ 4d675785837670b6a9b2b3405812a910 *tests/data.raw
+ 1d3777462fcefa39559aa645305a65f2 *tests/mcmc.R
+diff -ru -x '*~' BayesXsrc_org/src/Makefile BayesXsrc/src/Makefile
+--- BayesXsrc_org/src/Makefile	2013-11-22 21:49:16.000000000 +0900
++++ BayesXsrc/src/Makefile	2014-10-14 22:47:15.458766001 +0900
+@@ -137,11 +137,11 @@
+ 	${PSPLINES_OBJS}\
+ 	${STRUCTADD_OBJS}\
+ 	bayesxsrc/main.o\
+-       	bayesxsrc/samson/multgaussian.o\
++	bayesxsrc/samson/multgaussian.o\
+ 	bayesxsrc/adaptiv/fullcond_adaptiv.o\
+ 	bayesxsrc/alex/mixture.o
+ 
+-LDFLAGS  += -L${R_HOME}/lib -lreadline -lcurses
++LDFLAGS  += -L${R_HOME}/lib -lreadline -lncurses
+ CPPFLAGS +=  -Ibayesxsrc/. -I"bayesxsrc/bib"  -I"bayesxsrc/alex"  -I"bayesxsrc/adaptiv"  -I"bayesxsrc/andrea"  -I"bayesxsrc/dag"  -I"bayesxsrc/graph"  -I"bayesxsrc/mcmc"  -I"bayesxsrc/psplines"  -I"bayesxsrc/samson"  -I"bayesxsrc/leyre"  -I"bayesxsrc/structadd"
+ CPPFLAGS += -D__BUILDING_GNU -D__BUILDING_LINUX -DTEMPL_INCL_DEF -D_MSC_VER2 -DNO_TEMPLATE_FRIENDS -DINCLUDE_REML -DINCLUDE_MCMC
+ # CXXFLAGS += -O3 -ansi
+diff -ru -x '*~' BayesXsrc_org/src/rel-Makefile BayesXsrc/src/rel-Makefile
+--- BayesXsrc_org/src/rel-Makefile	2013-10-08 21:28:09.000000000 +0900
++++ BayesXsrc/src/rel-Makefile	2014-10-14 22:47:04.601766431 +0900
+@@ -137,11 +137,11 @@
+ 	${PSPLINES_OBJS}\
+ 	${STRUCTADD_OBJS}\
+ 	bayesxsrc/main.o\
+-       	bayesxsrc/samson/multgaussian.o\
++	bayesxsrc/samson/multgaussian.o\
+ 	bayesxsrc/adaptiv/fullcond_adaptiv.o\
+ 	bayesxsrc/alex/mixture.o
+ 
+-LDFLAGS  += -L${R_HOME}/lib -lreadline -lcurses
++LDFLAGS  += -L${R_HOME}/lib -lreadline -lncurses
+ CPPFLAGS +=  -Ibayesxsrc/. -I"bayesxsrc/bib"  -I"bayesxsrc/alex"  -I"bayesxsrc/adaptiv"  -I"bayesxsrc/andrea"  -I"bayesxsrc/dag"  -I"bayesxsrc/graph"  -I"bayesxsrc/mcmc"  -I"bayesxsrc/psplines"  -I"bayesxsrc/samson"  -I"bayesxsrc/leyre"  -I"bayesxsrc/structadd"
+ CPPFLAGS += -D__BUILDING_GNU -D__BUILDING_LINUX -DTEMPL_INCL_DEF -D_MSC_VER2 -DNO_TEMPLATE_FRIENDS -DINCLUDE_REML -DINCLUDE_MCMC
+ # CXXFLAGS += -O3 -ansi
diff --git a/pkgs/development/r-modules/patches/CARramps.patch b/pkgs/development/r-modules/patches/CARramps.patch
new file mode 100644
index 00000000000..901ab1f69b7
--- /dev/null
+++ b/pkgs/development/r-modules/patches/CARramps.patch
@@ -0,0 +1,24 @@
+diff -ru -x '*~' CARramps_orig/configure CARramps/configure
+--- CARramps_orig/configure	2011-12-01 22:27:06.000000000 +0900
++++ CARramps/configure	2014-10-25 14:56:04.599337748 +0900
+@@ -2395,7 +2395,7 @@
+ 
+ 
+ NCFLAGS="-arch=sm_13 -O2"
+-CUDA_INC=${CUDA_HOME}/include
++CUDA_INC=${CUDA_HOME}/usr_include
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for CUDA headers" >&5
+ $as_echo_n "checking for CUDA headers... " >&6; }
+ as_ac_File=`$as_echo "ac_cv_file_${CUDA_INC}/cublas.h" | $as_tr_sh`
+diff -ru -x '*~' CARramps_orig/src/combo1colForR1Q_d.cu CARramps/src/combo1colForR1Q_d.cu
+--- CARramps_orig/src/combo1colForR1Q_d.cu	2011-12-01 22:27:06.000000000 +0900
++++ CARramps/src/combo1colForR1Q_d.cu	2014-10-25 14:59:06.869299163 +0900
+@@ -4,7 +4,7 @@
+ #include <cuda.h>
+ #include <R.h>
+ #include <Rmath.h>
+-#include <combo1colForR1Q_d.h>
++#include "combo1colForR1Q_d.h"
+ 
+ #define BLOCKSIZE 256 
+ 
diff --git a/pkgs/development/r-modules/patches/EMCluster.patch b/pkgs/development/r-modules/patches/EMCluster.patch
new file mode 100644
index 00000000000..afc9de3a95a
--- /dev/null
+++ b/pkgs/development/r-modules/patches/EMCluster.patch
@@ -0,0 +1,6 @@
+diff -ru -x '*~' EMCluster_orig/src/Makevars EMCluster/src/Makevars
+--- EMCluster_orig/src/Makevars	2013-07-05 02:43:25.000000000 +0900
++++ EMCluster/src/Makevars	2014-10-25 18:10:19.190992120 +0900
+@@ -1 +1 @@
+-PKG_LIBS = $(FLIBS) $(BLAS_LIBS) $(LAPACK_LIBS)
++PKG_LIBS = $(FLIBS) $(LAPACK_LIBS) $(BLAS_LIBS)
diff --git a/pkgs/development/r-modules/patches/RAppArmor.patch b/pkgs/development/r-modules/patches/RAppArmor.patch
new file mode 100644
index 00000000000..f2dc49bd476
--- /dev/null
+++ b/pkgs/development/r-modules/patches/RAppArmor.patch
@@ -0,0 +1,20 @@
+diff -ru -x '*~' RAppArmor_orig/configure RAppArmor/configure
+--- RAppArmor_orig/configure	2013-12-17 11:23:00.000000000 +0900
++++ RAppArmor/configure	2014-10-18 22:22:39.641341244 +0900
+@@ -1,15 +1,2 @@
+-if [ ! -e /usr/include/sys/apparmor.h ]
+-then
+-  echo "sys/apparmor.h not found. Make sure libapparmor-dev is installed."
+-  exit 1
+-fi
+-
+-LIBFILE=$(/sbin/ldconfig -p | egrep -oh " [-_a-zA-Z0-9/]*/libapparmor.so(.1)?$")
+-
+-if [ -z "$LIBFILE" ]
+-then
+-  echo "libapparmor.so not found. Make sure libapparmor-dev is installed."
+-  exit 1
+-fi 
+-
++LIBFILE="$LIBAPPARMOR_HOME/lib/libapparmor.so.1"
+ echo "PKG_LIBS="$LIBFILE > src/Makevars
diff --git a/pkgs/development/r-modules/patches/Rserve.patch b/pkgs/development/r-modules/patches/Rserve.patch
new file mode 100644
index 00000000000..1ffe17e5542
--- /dev/null
+++ b/pkgs/development/r-modules/patches/Rserve.patch
@@ -0,0 +1,15 @@
+diff -ru -x '*~' Rserve_orig/src/Makevars.in Rserve/src/Makevars.in
+--- Rserve_orig/src/Makevars.in	2013-08-22 06:09:33.000000000 +0900
++++ Rserve/src/Makevars.in	2014-11-09 21:36:31.184590320 +0900
+@@ -12,8 +12,9 @@
+ 	$(CC) -DSTANDALONE_RSERVE -DRSERV_DEBUG -DNODAEMON -I. -Iinclude $(ALL_CPPFLAGS) $(ALL_CFLAGS) $(PKG_CPPFLAGS) $(PKG_CFLAGS) -o Rserve.dbg $(SERVER_SRC) $(ALL_LIBS) $(PKG_LIBS)
+ 
+ # merging to bin/Rserve works only if installed from sources, won't work for binary
+-	-./mergefat Rserve "$(R_HOME)/bin/Rserve"
+-	-./mergefat Rserve.dbg "$(R_HOME)/bin/Rserve.dbg"
++	mkdir $(out)/bin
++	-./mergefat Rserve "$(out)/bin/Rserve"
++	-./mergefat Rserve.dbg "$(out)/bin/Rserve.dbg"
+ 
+ client: config.h
+ 	cp config.h client/cxx/
diff --git a/pkgs/development/r-modules/patches/WideLM.patch b/pkgs/development/r-modules/patches/WideLM.patch
new file mode 100644
index 00000000000..f86d66bf746
--- /dev/null
+++ b/pkgs/development/r-modules/patches/WideLM.patch
@@ -0,0 +1,19 @@
+diff -ru -x '*~' WideLM_orig/src/Makefile.in WideLM/src/Makefile.in
+--- WideLM_orig/src/Makefile.in	2012-02-17 04:28:05.000000000 +0900
++++ WideLM/src/Makefile.in	2014-10-25 18:54:49.110011921 +0900
+@@ -12,12 +12,12 @@
+ #compiler/preprocessor options
+ R_INCS := @R_INCL@ @RCPP_INCL@
+ CC_ARGS := @CU_PARAMS@ -Xcompiler @R_CPIC@
+-CU_INCS := -I@CUDA_HOME@/include
++CU_INCS := -I@CUDA_HOME@/usr_include
+ CU_ARCH := -gencode arch=compute_20,code=sm_20
+ 
+ #linker options
+-LD_PARAMS := -Xlinker "@RCPP_LDFLAGS@"
+-RCU_LIBS :=  @R_LIB@ -L@CU_LIBDIR@ -lcublas
++LD_PARAMS := -Xlinker "--export-dynamic -fopenmp -L${R_HOME}/lib -lR"
++RCU_LIBS := -Xlinker "-L@CU_LIBDIR@ -lcublas"
+ 
+ all : WideLM.so
+ 
diff --git a/pkgs/development/r-modules/patches/dbarts.patch b/pkgs/development/r-modules/patches/dbarts.patch
new file mode 100644
index 00000000000..f80f6b38929
--- /dev/null
+++ b/pkgs/development/r-modules/patches/dbarts.patch
@@ -0,0 +1,12 @@
+diff -ru -x '*~' dbarts_orig/src/Makevars.in dbarts/src/Makevars.in
+--- dbarts_orig/src/Makevars.in	2014-07-01 02:30:57.000000000 +0900
++++ dbarts/src/Makevars.in	2014-10-25 19:25:58.910704279 +0900
+@@ -6,7 +6,7 @@
+ 
+ PKG_CPPFLAGS=-I$(INST_DIR)/include -Iinclude @PTHREAD_CFLAGS@ $(THREAD_SAFE_UNLOAD)
+ PKG_CPPXXFLAGS=-I$(INST_DIR)/include -Iinclude @PTHREAD_CFLAGS@ $(THREAD_SAFE_UNLOAD)
+-PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) dbarts/libdbarts.a external/libexternal.a @PTHREAD_LIBS@ 
++PKG_LIBS=dbarts/libdbarts.a external/libexternal.a $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) @PTHREAD_LIBS@ 
+ 
+ .PHONY: all dbarts/libdbarts.a external/libexternal.a clean
+ 
diff --git a/pkgs/development/r-modules/patches/gmatrix.patch b/pkgs/development/r-modules/patches/gmatrix.patch
new file mode 100644
index 00000000000..990debb8a42
--- /dev/null
+++ b/pkgs/development/r-modules/patches/gmatrix.patch
@@ -0,0 +1,48 @@
+diff -ru -x '*~' gmatrix_orig/src/Makefile gmatrix/src/Makefile
+--- gmatrix_orig/src/Makefile	2014-08-27 02:42:04.000000000 +0900
++++ gmatrix/src/Makefile	2014-10-25 15:35:29.797202981 +0900
+@@ -21,6 +21,7 @@
+ # to the manual on the gmatrix install instructions)
+ CUDA_LIB_PATH ?= /usr/local/cuda/lib64
+ R_INC_PATH    ?= /usr/include/R
++CUDA_INC_PATH ?= /usr/local/cuda/include
+ 
+ 
+ # Nvidia CUDA Compiler
+@@ -49,25 +50,25 @@
+ # Build rules
+ build: $(OUT_OBJ)
+ 	$(R_CC) $(OUT_OBJ) -o $(OUT_SO) $(LIBS) -L$(CUDA_LIB_PATH)
+-	
++
+ conversions.o: 
+-	$(NVCC) -c conversions.cu -o conversions.o $(NVCC_FLAGS)  -I$(R_INC_PATH)
+-	
++	$(NVCC) -c conversions.cu -o conversions.o $(NVCC_FLAGS)  -I$(R_INC_PATH) -I${CUDA_INC_PATH}
++
+ manipulation.o: 
+-	$(NVCC) -c manipulation.cu -o manipulation.o $(NVCC_FLAGS)  -I$(R_INC_PATH)
++	$(NVCC) -c manipulation.cu -o manipulation.o $(NVCC_FLAGS)  -I$(R_INC_PATH) -I${CUDA_INC_PATH}
+ 
+ general.o:
+-	$(NVCC) -c general.cu -o general.o $(NVCC_FLAGS) -I$(R_INC_PATH)
++	$(NVCC) -c general.cu -o general.o $(NVCC_FLAGS) -I$(R_INC_PATH) -I${CUDA_INC_PATH}
+ 
+ matrix.o: 
+-	$(NVCC) -c matrix.cu -o matrix.o $(NVCC_FLAGS) -I$(R_INC_PATH)
+- 	
++	$(NVCC) -c matrix.cu -o matrix.o $(NVCC_FLAGS) -I$(R_INC_PATH) -I${CUDA_INC_PATH}
++
+ ops.o: 
+-	$(NVCC) -c ops.cu -o ops.o $(NVCC_FLAGS) -I$(R_INC_PATH)
+-	
++	$(NVCC) -c ops.cu -o ops.o $(NVCC_FLAGS) -I$(R_INC_PATH) -I${CUDA_INC_PATH}
++
+ dist.o: 
+-	$(NVCC) -c dist.cu -o dist.o $(NVCC_FLAGS) -I$(R_INC_PATH)
+- 	
++	$(NVCC) -c dist.cu -o dist.o $(NVCC_FLAGS) -I$(R_INC_PATH) -I${CUDA_INC_PATH}
++
+ 
+ clean:
+ 	-rm -f *.o core
diff --git a/pkgs/development/r-modules/patches/gputools.patch b/pkgs/development/r-modules/patches/gputools.patch
new file mode 100644
index 00000000000..61cbcea9370
--- /dev/null
+++ b/pkgs/development/r-modules/patches/gputools.patch
@@ -0,0 +1,13 @@
+diff -ru -x '*~' gputools_orig/src/Makefile gputools/src/Makefile
+--- gputools_orig/src/Makefile	2013-05-09 01:43:32.000000000 +0900
++++ gputools/src/Makefile	2014-10-21 21:41:23.067148490 +0900
+@@ -6,6 +6,9 @@
+ 
+ R_HOME := $(shell R RHOME)
+ 
++CUDA_INC := $(CUDA_HOME)/usr_include
++CUDA_LIB := $(CUDA_HOME)/lib
++
+ #compiler/preprocessor options
+ INCS := -I. -I"$(CUDA_INC)" -I"$(R_INC)"
+ PARAMS := $(DEVICEOPTS) -Xcompiler $(CPICFLAGS)
diff --git a/pkgs/development/r-modules/patches/magma_cuda_include.patch b/pkgs/development/r-modules/patches/magma_cuda_include.patch
new file mode 100644
index 00000000000..67552325ae9
--- /dev/null
+++ b/pkgs/development/r-modules/patches/magma_cuda_include.patch
@@ -0,0 +1,12 @@
+diff -ru -x '*~' magma_orig/configure magma/configure
+--- magma_orig/configure	2013-04-03 11:07:42.000000000 +0900
++++ magma/configure	2014-10-18 21:58:48.745890187 +0900
+@@ -2377,7 +2377,7 @@
+ 
+ 
+ NCFLAGS="-arch=sm_13 -O2 -DADD_"
+-CUDA_INC=${CUDA_HOME}/include
++CUDA_INC=${CUDA_HOME}/usr_include
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for CUDA headers" >&5
+ $as_echo_n "checking for CUDA headers... " >&6; }
+ as_ac_File=`$as_echo "ac_cv_file_${CUDA_INC}/cublas.h" | $as_tr_sh`
diff --git a/pkgs/development/r-modules/patches/openssl.patch b/pkgs/development/r-modules/patches/openssl.patch
new file mode 100644
index 00000000000..61dc641023b
--- /dev/null
+++ b/pkgs/development/r-modules/patches/openssl.patch
@@ -0,0 +1,28 @@
+diff -ru -x '*~' openssl_orig/configure openssl/configure
+--- openssl_orig/configure	2014-10-18 08:14:15.000000000 +0900
++++ openssl/configure	2014-11-03 15:05:25.122906126 +0900
+@@ -1,23 +1 @@
+-# Check for include
+-if [ ! -e /usr/include/openssl/rand.h ]
+-then
+-  echo "openssl/rand.h not found. Make sure libssl-dev (deb) or openssl-devel (rpm) is installed."
+-  exit 1
+-fi
+-
+-# Not linux. Probably OSX.
+-if [ ! -e /sbin/ldconfig ]
+-then
+-  exit 0
+-fi
+-
+-# looks like unix
+-LIBFILE=$(/sbin/ldconfig -p | egrep -ohm1 " [-_a-zA-Z0-9/]*/libssl[0-9]*.so$")
+-
+-if [ -z "$LIBFILE" ]
+-then
+-  echo "libssl.so not found. Make sure libssl-dev (deb) or openssl-devel (rpm) is installed."
+-  exit 1
+-fi
+-
+-echo "PKG_LIBS= -L"$(dirname $LIBFILE)" -lssl -lcrypto" > src/Makevars
++echo "PKG_LIBS= -L"${OPENSSL_HOME}/lib" -lssl -lcrypto" > src/Makevars
diff --git a/pkgs/development/r-modules/patches/qtbase.patch b/pkgs/development/r-modules/patches/qtbase.patch
new file mode 100644
index 00000000000..14427b72630
--- /dev/null
+++ b/pkgs/development/r-modules/patches/qtbase.patch
@@ -0,0 +1,13 @@
+diff -ru -x '*~' qtbase_orig/src/Makefile qtbase/src/Makefile
+--- qtbase_orig/src/Makefile	2012-03-03 03:57:47.000000000 +0900
++++ qtbase/src/Makefile	2014-11-01 23:06:51.383876323 +0900
+@@ -10,6 +10,9 @@
+ 	      -DR_INCLUDES=${R_INCLUDE_DIR} \
+ 	      -DCMAKE_INSTALL_PREFIX=../src; \
+ 	make install
++# I could not control RPATH via CMake. HELP WANTED!
++	patchelf --set-rpath ${CMAKE_LIBRARY_PATH} qtbase.so
++	find ../inst/local/ -executable -type f -print0 | xargs -0 patchelf --set-rpath ${CMAKE_LIBRARY_PATH} 
+ 
+ clean:
+ 	rm -rf ../kdebindings-build
diff --git a/pkgs/development/r-modules/patches/rpud.patch b/pkgs/development/r-modules/patches/rpud.patch
new file mode 100644
index 00000000000..45d20e6bd67
--- /dev/null
+++ b/pkgs/development/r-modules/patches/rpud.patch
@@ -0,0 +1,29 @@
+diff -ru -x '*~' rpud_orig/configure rpud/configure
+--- rpud_orig/configure	2010-09-08 02:14:55.000000000 +0900
++++ rpud/configure	2014-10-25 16:46:39.479098648 +0900
+@@ -1794,7 +1794,7 @@
+ fi
+ 
+ LIBS="-L${CUDA_HOME}${CUDA_LIB_DIR} -lcublas -lcuda"
+-RPATHFLAG="-Wl,-rpath,${CUDA_HOME}${CUDA_LIB_DIR}"
++RPATHFLAG="-Xlinker -rpath=${CUDA_HOME}${CUDA_LIB_DIR}"
+ 
+ 
+ 
+diff -ru -x '*~' rpud_orig/src/Makefile.in rpud/src/Makefile.in
+--- rpud_orig/src/Makefile.in	2010-08-31 01:53:50.000000000 +0900
++++ rpud/src/Makefile.in	2014-10-25 16:45:30.248109883 +0900
+@@ -3,11 +3,11 @@
+ OBJS := rpud.o rpudist.o
+ 
+ #compiler/preprocessor options
+-INCS := -I@CUDA_HOME@/include
++INCS := -I@CUDA_HOME@/usr_include
+ PARAMS := -Xcompiler "@R_INCLUDE@ @CPICFLAGS@"
+ 
+ #linker options
+-LD_PARAMS := -Xlinker "@R_LIB@ @RPATHFLAG@"
++LD_PARAMS := -Xlinker "--export-dynamic -fopenmp -L${R_HOME}/lib -lR @RPATHFLAG@" 
+ LIBS :=  @LIBS@
+ 
+ TARGETS := rpud.so
diff --git a/pkgs/development/r-modules/patches/spMC.patch b/pkgs/development/r-modules/patches/spMC.patch
new file mode 100644
index 00000000000..04239d721c0
--- /dev/null
+++ b/pkgs/development/r-modules/patches/spMC.patch
@@ -0,0 +1,8 @@
+Only in spMC_orig: spMC
+diff -ru -x '*~' spMC_orig/src/Makevars spMC/src/Makevars
+--- spMC_orig/src/Makevars	2014-09-19 21:23:30.000000000 +0900
++++ spMC/src/Makevars	2014-10-25 18:14:48.366954769 +0900
+@@ -1,2 +1,2 @@
+ PKG_CFLAGS=$(SHLIB_OPENMP_CFLAGS)
+-PKG_LIBS=$(SHLIB_OPENMP_CFLAGS) $(BLAS_LIBS) $(LAPACK_LIBS) $(FLIBS)
++PKG_LIBS=$(SHLIB_OPENMP_CFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)