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Merge recent 'staging' into closure-size

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Let's get rid of those merge conflicts.
This commit is contained in:
Vladimír Čunát
2016-02-03 16:54:03 +01:00
parent c979012631 53e0f8b1cd
commit ae74c356d9
637 changed files with 123880 additions and 83341 deletions
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9
pkgs/development/r-modules/patches/BayesBridge_cblas.patch
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@@ -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

12
pkgs/development/r-modules/patches/BayesLogit_cblas.patch
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@@ -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

12
pkgs/development/r-modules/patches/CARramps.patch
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@@ -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

19
pkgs/development/r-modules/patches/WideLM.patch
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@@ -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

29
pkgs/development/r-modules/patches/rpud.patch
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@@ -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