refactor R installation

examples/meta/generator/targets/r.json

@@ -28,12 +28,12 @@
     },
     "Element": {
         "Access": {
-            "Vector": "$identifier[$indices]",
-            "Matrix": "$identifier[$indices]"
+            "Vector": "$identifier$$get_element($indices)",
+            "Matrix": "$identifier$$get_element($indices)"
         },
         "Assign": {
-            "Vector": "$identifier[$indices] = $expr",
-            "Matrix": "$identifier[$indices] = $expr"
+            "Vector": "$identifier$$set_element($expr, $indices)",
+            "Matrix": "$identifier$$set_element($expr, $indices)"
         },
         "ZeroIndexed": false
     },

src/interfaces/r/CMakeLists.txt

@@ -11,6 +11,28 @@ ENDIF()
 GENERATE_INTERFACE_TARGET(r ${CMAKE_CURRENT_SOURCE_DIR} ${R_LIBRARIES})
 set_target_properties(interface_r PROPERTIES PREFIX "")
 
+EXECUTE_PROCESS(COMMAND ${R_EXECUTABLE} --slave -e "with(R.version, cat(sprintf('%s.%s', major, minor)))"
+	OUTPUT_VARIABLE R_VERSION
+	OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+EXECUTE_PROCESS(COMMAND ${R_EXECUTABLE} --slave -e "cat(R.version\$platform)"
+	OUTPUT_VARIABLE PLATFORM
+	OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+EXECUTE_PROCESS(COMMAND ${R_EXECUTABLE} --slave -e "cat(.Platform\$OS.type)"
+	OUTPUT_VARIABLE OSTYPE
+	OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+EXECUTE_PROCESS(COMMAND ${PYTHON_EXECUTABLE} -c "from time import gmtime, strftime; print(strftime(\"%Y-%m-%d %H:%M:%S\", gmtime()))"
+	OUTPUT_VARIABLE DATE
+	OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/DESCRIPTION.in ${CMAKE_CURRENT_BINARY_DIR}/DESCRIPTION @ONLY)
+
 ADD_CUSTOM_COMMAND(TARGET interface_r
 	POST_BUILD
 	COMMAND echo 'wd="${CMAKE_CURRENT_BINARY_DIR}" \; setwd( wd ) \; f="shogun.R" \; fdata="shogun.RData" \; source( f ) \; save( list=ls( all=TRUE ) , file=fdata , compress=TRUE ) \; q( save="no" ) \;' | ${R_EXECUTABLE} --silent --no-save
@@ -26,6 +48,10 @@ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/shogun.RData
 	DESTINATION ${R_COMPONENT_LIB_PATH}/shogun/R
 	COMPONENT r)
 
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/DESCRIPTION ${CMAKE_CURRENT_SOURCE_DIR}/NAMESPACE
+	DESTINATION ${R_COMPONENT_LIB_PATH}/shogun
+	COMPONENT r)
+
 install(CODE "FILE(MAKE_DIRECTORY \$ENV{DESTDIR}/${R_COMPONENT_LIB_PATH}/shogun/Meta)")
 
 install(CODE "EXECUTE_PROCESS(COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/r-install.sh \$ENV{DESTDIR}/${R_COMPONENT_LIB_PATH} shogun so saveRDS WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})")

src/interfaces/r/DESCRIPTION.in

@@ -0,0 +1,26 @@
+Package: shogun
+Version: @VERSION@
+Date: @DATE@
+Title: The SHOGUN Machine Learning Toolbox
+Author: Shogun Team
+Maintainer: Shogun Team <shogun-team@shogun-toolbox.org>
+Depends: R (>= 2.10.0)
+Suggests:
+Description: SHOGUN - is a new machine learning toolbox with focus on large
+        scale kernel methods and especially on Support Vector Machines (SVM) with focus
+        to bioinformatics. It provides a generic SVM object interfacing to several
+        different SVM implementations. Each of the SVMs can be combined with a variety
+        of the many kernels implemented. It can deal with weighted linear combination
+        of a number of sub-kernels, each of which not necessarily working on the same
+        domain, where  an optimal sub-kernel weighting can be learned using Multiple
+        Kernel Learning.  Apart from SVM 2-class classification and regression
+        problems, a number of linear methods like Linear Discriminant Analysis (LDA),
+        Linear Programming Machine (LPM), (Kernel) Perceptrons and also algorithms to
+        train hidden markov models are implemented. The input feature-objects can be
+        dense, sparse or strings and of type int/short/double/char and can be converted
+        into different feature types. Chains of preprocessors (e.g.  substracting the
+        mean) can be attached to each feature object allowing for on-the-fly
+        pre-processing.
+License: GPL Version 3 or later.
+URL: http://www.shogun-toolbox.org
+Built: @R_VERSION@; @PLATFORM@; @OSTYPE@;

src/interfaces/r/NAMESPACE

@@ -0,0 +1 @@
+useDynLib(shogun, .registration = TRUE)

src/interfaces/r/r-install.sh

@@ -9,35 +9,6 @@ DATE="`date '+%Y-%m-%d %H:%M:%S'`"
 PKGFILE="$1/$2/Meta/package.rds"
 SAVERDS="$4"
 
-cat >"$1/$2/DESCRIPTION" <<EOF
-Package: $2
-Version: $VERSION
-Date: $DATE
-Title: The SHOGUN Machine Learning Toolbox
-Author: Shogun Team
-Maintainer: Shogun Team <shogun-team@shogun-toolbox.org>
-Depends: R (>= 2.10.0)
-Suggests:
-Description: SHOGUN - is a new machine learning toolbox with focus on large
-        scale kernel methods and especially on Support Vector Machines (SVM) with focus
-        to bioinformatics. It provides a generic SVM object interfacing to several
-        different SVM implementations. Each of the SVMs can be combined with a variety
-        of the many kernels implemented. It can deal with weighted linear combination
-        of a number of sub-kernels, each of which not necessarily working on the same
-        domain, where  an optimal sub-kernel weighting can be learned using Multiple
-        Kernel Learning.  Apart from SVM 2-class classification and regression
-        problems, a number of linear methods like Linear Discriminant Analysis (LDA),
-        Linear Programming Machine (LPM), (Kernel) Perceptrons and also algorithms to
-        train hidden markov models are implemented. The input feature-objects can be
-        dense, sparse or strings and of type int/short/double/char and can be converted
-        into different feature types. Chains of preprocessors (e.g.  substracting the
-        mean) can be attached to each feature object allowing for on-the-fly
-        pre-processing.
-License: GPL Version 3 or later.
-URL: http://www.shogun-toolbox.org
-Built: $RVERSION; $PLATFORM; $OSTYPE;
-EOF
-
 echo "x=structure(list(DESCRIPTION = c(Package='$2',\
 		Version=\"$VERSION\",\
 		Date=\"$DATE\",\
@@ -58,10 +29,6 @@ echo "x=structure(list(DESCRIPTION = c(Package='$2',\
 # R-MODULAR
 echo "Installing modular shogun interface for R"
 
-cat >"$1/$2/NAMESPACE" <<EOF
-useDynLib(shogun, .registration = TRUE)
-EOF
-
 cat >"$1/$2/R/$2" <<EOF
 .packageName <- "$2"
 #$2 <- function(...) .External("$2",...,PACKAGE="$2")