Add 'nixpkgs/' from commit 'abf060725d7614bd3b9f96764262dfbc2f9c2199'

git-subtree-dir: nixpkgs
git-subtree-mainline: 4e31070265257dc67d120c27e0f75c2344fdfa9a
git-subtree-split: abf060725d7614bd3b9f96764262dfbc2f9c2199

8 files changed, 142 insertions, 0 deletions

diff --git a/nixpkgs/pkgs/development/r-modules/patches/BayesXsrc.patch b/nixpkgs/pkgs/development/r-modules/patches/BayesXsrc.patch
new file mode 100644
index 000000000000..b357d7f83fcc
--- /dev/null
+++ b/nixpkgs/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/nixpkgs/pkgs/development/r-modules/patches/EMCluster.patch b/nixpkgs/pkgs/development/r-modules/patches/EMCluster.patch
new file mode 100644
index 000000000000..afc9de3a95a9
--- /dev/null
+++ b/nixpkgs/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) $(BLAS_LIBS)
diff --git a/nixpkgs/pkgs/development/r-modules/patches/RAppArmor.patch b/nixpkgs/pkgs/development/r-modules/patches/RAppArmor.patch
new file mode 100644
index 000000000000..f2dc49bd4766
--- /dev/null
+++ b/nixpkgs/pkgs/development/r-modules/patches/RAppArmor.patch
@@ -0,0 +1,20 @@
+diff -ru -x '*~' RAppArmor_orig/configure RAppArmor/configure
+--- RAppArmor_orig/configure	2013-12-17 11:23:00.000000000 +0900
++++ RAppArmor/configure	2014-10-18 22:22:39.641341244 +0900
+@@ -1,15 +1,2 @@
+-if [ ! -e /usr/include/sys/apparmor.h ]
+-then
+-  echo "sys/apparmor.h not found. Make sure libapparmor-dev is installed."
+-  exit 1
+-fi
+-
+-LIBFILE=$(/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/nixpkgs/pkgs/development/r-modules/patches/RMySQL.patch b/nixpkgs/pkgs/development/r-modules/patches/RMySQL.patch
new file mode 100644
index 000000000000..dc93b902cd5c
--- /dev/null
+++ b/nixpkgs/pkgs/development/r-modules/patches/RMySQL.patch
@@ -0,0 +1,13 @@
+diff -ru3 RMySQL_orig/configure RMySQL/configure
+--- RMySQL_orig/configure	2015-02-19 22:49:15.812455730 +0300
++++ RMySQL/configure	2015-02-19 22:49:42.066407256 +0300
+@@ -1,7 +1,7 @@
+ # If $MYSQL_DIR is specified, use that
+ if [ "$MYSQL_DIR" ]; then
+-  echo "PKG_CPPFLAGS= -I$MYSQL_DIR/include" > src/Makevars
+-  echo "PKG_LIBS= -L$MYSQL_DIR/lib -lmysqlclient -lz" >> src/Makevars
++  echo "PKG_CPPFLAGS= -I$MYSQL_DIR/include/mysql" > src/Makevars
++  echo "PKG_LIBS= -L$MYSQL_DIR/lib/mysql -lmysqlclient -lz" >> src/Makevars
+   exit 0
+ fi
+ 
diff --git a/nixpkgs/pkgs/development/r-modules/patches/Rhdf5lib.patch b/nixpkgs/pkgs/development/r-modules/patches/Rhdf5lib.patch
new file mode 100644
index 000000000000..dcd9b61798bd
--- /dev/null
+++ b/nixpkgs/pkgs/development/r-modules/patches/Rhdf5lib.patch
@@ -0,0 +1,12 @@
+diff --git a/configure b/configure
+index e2d292e..b13c0db 100755
+--- a/configure
++++ b/configure
+@@ -2880,6 +2880,7 @@ $MAKE
+ echo "building the hdf5 library...";
+ cd ../;
+ ## we add the '-w' flag to suppress all the warnings hdf5 prints
++sed -i 's#/bin/mv#mv#' configure
+ ./configure --with-pic --enable-shared=no --enable-cxx \
+     --with-szlib \
+     CXX="${CXX}" CXFLAGS="${CXXFLAGS} -w" \
diff --git a/nixpkgs/pkgs/development/r-modules/patches/Rserve.patch b/nixpkgs/pkgs/development/r-modules/patches/Rserve.patch
new file mode 100644
index 000000000000..1ffe17e55420
--- /dev/null
+++ b/nixpkgs/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 "$(out)/bin/Rserve.dbg"
+ 
+ client: config.h
+ 	cp config.h client/cxx/
diff --git a/nixpkgs/pkgs/development/r-modules/patches/qtbase.patch b/nixpkgs/pkgs/development/r-modules/patches/qtbase.patch
new file mode 100644
index 000000000000..14427b72630e
--- /dev/null
+++ b/nixpkgs/pkgs/development/r-modules/patches/qtbase.patch
@@ -0,0 +1,13 @@
+diff -ru -x '*~' qtbase_orig/src/Makefile qtbase/src/Makefile
+--- qtbase_orig/src/Makefile	2012-03-03 03:57:47.000000000 +0900
++++ qtbase/src/Makefile	2014-11-01 23:06:51.383876323 +0900
+@@ -10,6 +10,9 @@
+ 	      -DR_INCLUDES=${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 ${CMAKE_LIBRARY_PATH} 
+ 
+ clean:
+ 	rm -rf ../kdebindings-build
diff --git a/nixpkgs/pkgs/development/r-modules/patches/spMC.patch b/nixpkgs/pkgs/development/r-modules/patches/spMC.patch
new file mode 100644
index 000000000000..04239d721c07
--- /dev/null
+++ b/nixpkgs/pkgs/development/r-modules/patches/spMC.patch
@@ -0,0 +1,8 @@
+Only in spMC_orig: spMC
+diff -ru -x '*~' spMC_orig/src/Makevars spMC/src/Makevars
+--- spMC_orig/src/Makevars	2014-09-19 21:23:30.000000000 +0900
++++ spMC/src/Makevars	2014-10-25 18:14:48.366954769 +0900
+@@ -1,2 +1,2 @@
+ PKG_CFLAGS=$(SHLIB_OPENMP_CFLAGS)
+-PKG_LIBS=$(SHLIB_OPENMP_CFLAGS) $(BLAS_LIBS) $(LAPACK_LIBS) $(FLIBS)
++PKG_LIBS=$(SHLIB_OPENMP_CFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)