Merge recent 'staging' into closure-size

Let's get rid of those merge conflicts.

5 files changed, 0 insertions, 81 deletions

diff --git a/pkgs/development/r-modules/patches/BayesBridge_cblas.patch b/pkgs/development/r-modules/patches/BayesBridge_cblas.patch
deleted file mode 100644
index 418a6b95ee71..000000000000
--- a/pkgs/development/r-modules/patches/BayesBridge_cblas.patch
+++ /dev/null
@@ -1,9 +0,0 @@
-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_cblas.patch b/pkgs/development/r-modules/patches/BayesLogit_cblas.patch
deleted file mode 100644
index ef776f3531da..000000000000
--- a/pkgs/development/r-modules/patches/BayesLogit_cblas.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-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) $(LAPACK_LIBS) -lopenblas
- # PKG_CPPFLAGS = -DUSE_R -DNDEBUG -DDISABLE_SINGLE -DNTHROW -Wall -pedantic -Wextra
- PKG_CPPFLAGS = -DUSE_R -DNDEBUG -DDISABLE_SINGLE -DNTHROW 
- 
diff --git a/pkgs/development/r-modules/patches/CARramps.patch b/pkgs/development/r-modules/patches/CARramps.patch
deleted file mode 100644
index add01b28fc15..000000000000
--- a/pkgs/development/r-modules/patches/CARramps.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -ru -x '*~' CARramps_orig/src/combo1colForR1Q_d.cu CARramps/src/combo1colForR1Q_d.cu
---- CARramps_orig/src/combo1colForR1Q_d.cu	2011-12-01 22:27:06.000000000 +0900
-+++ CARramps/src/combo1colForR1Q_d.cu	2014-10-25 14:59:06.869299163 +0900
-@@ -4,7 +4,7 @@
- #include <cuda.h>
- #include <R.h>
- #include <Rmath.h>
--#include <combo1colForR1Q_d.h>
-+#include "combo1colForR1Q_d.h"
- 
- #define BLOCKSIZE 256 
- 
diff --git a/pkgs/development/r-modules/patches/WideLM.patch b/pkgs/development/r-modules/patches/WideLM.patch
deleted file mode 100644
index 02bbfb7e0dab..000000000000
--- a/pkgs/development/r-modules/patches/WideLM.patch
+++ /dev/null
@@ -1,19 +0,0 @@
-diff -ru -x '*~' WideLM_orig/src/Makefile.in WideLM/src/Makefile.in
---- WideLM_orig/src/Makefile.in	2012-02-17 04:28:05.000000000 +0900
-+++ WideLM/src/Makefile.in	2014-10-25 18:54:49.110011921 +0900
-@@ -12,12 +12,12 @@
- #compiler/preprocessor options
- R_INCS := @R_INCL@ @RCPP_INCL@
- CC_ARGS := @CU_PARAMS@ -Xcompiler @R_CPIC@
--CU_INCS := -I@CUDA_HOME@/include
-+CU_INCS := -I@CUDA_HOME@/include
- CU_ARCH := -gencode arch=compute_20,code=sm_20
- 
- #linker options
--LD_PARAMS := -Xlinker "@RCPP_LDFLAGS@"
--RCU_LIBS :=  @R_LIB@ -L@CU_LIBDIR@ -lcublas
-+LD_PARAMS := -Xlinker "--export-dynamic -fopenmp -L${R_HOME}/lib -lR"
-+RCU_LIBS := -Xlinker "-L@CU_LIBDIR@ -lcublas"
- 
- all : WideLM.so
- 
diff --git a/pkgs/development/r-modules/patches/rpud.patch b/pkgs/development/r-modules/patches/rpud.patch
deleted file mode 100644
index bb904b68989c..000000000000
--- a/pkgs/development/r-modules/patches/rpud.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-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@/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