[GR-13573] Script configure_fastr also generates files Renviron and ldpaths.

PullRequest: fastr/1918

Author: steve-s

CHANGELOG.md

@@ -4,11 +4,22 @@ New features:
 
 * new JUL-like logging infrastructure backed by Truffle
 * FastR options backed by Truffle now. New command-line format - i.e. bin/r --R.PerformanceWarning="true". Also configurable via org.graal.polyglot.Context.Builder.
+* script configure_fastr also regenerates etc/Renviron and etc/ldpaths
+* FastR vectors are not writeable from other languages
+  * in order to update FastR vectors from other languages:
+    retrieve reference to the subset assign function `` `[<-` `` and execute it.
+    Note that it will return the new vector with the updated values.
+
+Added missing R builtins and C API
+
+* `polyroot`
+* dummy implementation of `pcre_config`
 
 Bug fixes:
 
-* when using GNU-R graphics (-UseInternalGridGraphics) FastR would still override the graphics package R functions
+* when using GNU-R graphics (--R.UseInternalGridGraphics=false) FastR would still override the graphics package R functions
 * cannot install RcppParallel #52
+* visibility propagation in `tryCatch`
 
 # 1.0 RC 12
 

com.oracle.truffle.r.native/run/Darwin/Renviron

@@ -0,0 +1,49 @@
+### Default etc/Renviron file provided with FastR configured for generic MacOS
+###
+### ${R_HOME}/etc/Renviron
+###
+### Record R system environment variables.
+
+R_PLATFORM=${R_PLATFORM-'x86_64-apple-darwin18.2.0'}
+## Default printer paper size: first record if user set R_PAPERSIZE
+R_PAPERSIZE_USER=${R_PAPERSIZE}
+R_PAPERSIZE=${R_PAPERSIZE-'a4'}
+## Default print command
+R_PRINTCMD=${R_PRINTCMD-'lpr'}
+# for Rd2pdf, reference manual
+R_RD4PDF=${R_RD4PDF-'times,inconsolata,hyper'}
+## used for options("texi2dvi")
+R_TEXI2DVICMD=${R_TEXI2DVICMD-${TEXI2DVI-'/usr/bin/texi2dvi'}}
+## used by INSTALL, untar() and installing grDevices
+R_GZIPCMD=${R_GZIPCMD-'/usr/bin/gzip'}
+## Default zip/unzip commands
+R_UNZIPCMD=${R_UNZIPCMD-'/usr/bin/unzip'}
+R_ZIPCMD=${R_ZIPCMD-'/usr/bin/zip'}
+R_BZIPCMD=${R_BZIPCMD-'/usr/bin/bzip2'}
+## Default browser
+R_BROWSER=${R_BROWSER-'/usr/bin/open'}
+## Default editor
+EDITOR=${EDITOR-${VISUAL-vi}}
+## Default pager
+PAGER=${PAGER-'/usr/bin/less'}
+## Default PDF viewer
+R_PDFVIEWER=${R_PDFVIEWER-'/usr/bin/open'}
+## Used by libtool
+LN_S='ln -s'
+MAKE=${MAKE-'make'}
+## Prefer a POSIX-compliant sed on e.g. Solaris
+SED=${SED-'/usr/bin/sed'}
+## Prefer a tar that can automagically read compressed archives
+## Used in R CMD INSTALL for binary packages
+TAR=${TAR-'/usr/bin/tar'}
+
+## System and compiler types.
+R_SYSTEM_ABI='osx,gcc,gxx,gfortran,?'
+
+R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-apple-darwin18.2.0-library/3.5'}
+#R_LIBS_USER=${R_LIBS_USER-'~/Library/R/3.5/library'}
+
+### Local Variables: ***
+### mode: sh ***
+### sh-indentation: 2 ***
+### End: ***

com.oracle.truffle.r.native/run/Linux/Renviron

@@ -0,0 +1,48 @@
+### Default etc/Renviron file provided with FastR configured for generic Linux
+###
+### ${R_HOME}/etc/Renviron
+###
+### Record R system environment variables.
+
+R_PLATFORM=${R_PLATFORM-'x86_64-pc-linux-gnu'}
+## Default printer paper size: first record if user set R_PAPERSIZE
+R_PAPERSIZE_USER=${R_PAPERSIZE}
+R_PAPERSIZE=${R_PAPERSIZE-'a4'}
+## Default print command
+R_PRINTCMD=${R_PRINTCMD-'lpr'}
+# for Rd2pdf, reference manual
+R_RD4PDF=${R_RD4PDF-'times,inconsolata,hyper'}
+## used for options("texi2dvi")
+R_TEXI2DVICMD=${R_TEXI2DVICMD-${TEXI2DVI-'texi2dvi'}}
+## used by INSTALL, untar() and installing grDevices
+R_GZIPCMD=${R_GZIPCMD-'/bin/gzip'}
+## Default zip/unzip commands
+R_UNZIPCMD=${R_UNZIPCMD-'/usr/bin/unzip'}
+R_ZIPCMD=${R_ZIPCMD-'/usr/bin/zip'}
+R_BZIPCMD=${R_BZIPCMD-'/bin/bzip2'}
+## Default browser
+R_BROWSER=${R_BROWSER-'/usr/bin/firefox'}
+## Default editor
+EDITOR=${EDITOR-${VISUAL-vi}}
+## Default pager
+PAGER=${PAGER-'/usr/bin/less'}
+## Default PDF viewer
+R_PDFVIEWER=${R_PDFVIEWER-'/usr/bin/xdg-open'}
+## Used by libtool
+LN_S='ln -s'
+MAKE=${MAKE-'make'}
+## Prefer a POSIX-compliant sed on e.g. Solaris
+SED=${SED-'/bin/sed'}
+## Prefer a tar that can automagically read compressed archives
+## Used in R CMD INSTALL for binary packages
+TAR=${TAR-'/bin/tar'}
+
+## System and compiler types.
+R_SYSTEM_ABI='linux,gcc,gxx,gfortran,?'
+
+R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/3.5'}
+
+### Local Variables: ***
+### mode: sh ***
+### sh-indentation: 2 ***
+### End: ***

com.oracle.truffle.r.native/run/Makefile

@@ -48,9 +48,6 @@ BIN_FILES := $(wildcard $(GNUR_HOME_BINARY)/bin/*)
 
 DOC_FILES := $(wildcard $(GNUR_HOME_BINARY)/doc/*)
 
-# Not all of these work unchanged
-ETC_FILES := $(addprefix $(GNUR_HOME_BINARY)/etc/,javaconf ldpaths Renviron repositories)
-
 SHARE_FILES := $(addprefix $(GNUR_HOME_BINARY)/share/,R Rd make java encodings)
 
 LLVM_TOOLS := $(wildcard $(FASTR_NATIVE_DIR)/llvm_tools/llvm-*)
@@ -64,13 +61,13 @@ rundirs:
 	mkdir -p $(FASTR_BIN_DIR)/execRextras
 	mkdir -p $(FASTR_ETC_DIR)
 	mkdir -p $(FASTR_SHARE_DIR)
-	
+
 rcmds: $(FASTR_BIN_DIR)/R
 
 $(FASTR_BIN_DIR)/R: Makefile R.sh Rscript.sh Rscript_exec.sh Rclasspath.sh
 	cp -r $(BIN_FILES) $(FASTR_BIN_DIR)
-	
-    # overide bin/R
+
+	# overide bin/R
 	cp R.sh $(FASTR_BIN_DIR)/exec/R
 	# override bin/Rscript
 	cp Rscript_exec.sh $(FASTR_BIN_DIR)/execRextras/Rscript
@@ -82,18 +79,22 @@ $(FASTR_BIN_DIR)/R: Makefile R.sh Rscript.sh Rscript_exec.sh Rclasspath.sh
 	(sed -e 's!^\(R_HOME_DIR=\)\(.*\)!\1"$(FASTR_R_HOME)"!' | \
 	 sed -e 's/    -h.--help./    --r-help\)/' | \
 	 sed -e 's!      exec sh "$${R_HOME}/bin/Rcmd" "$${@}" ;;!      FASTR_INTERNAL_ARGS=`echo "$${FASTR_INTERNAL_ARGS} $${args}" | $${SED} -e 's/^[[:space:]]*//' | $${SED} -e 's/[[:blank:]]*$$//'` exec sh "$${R_HOME}/bin/Rcmd" "$${@}" ;;!') < $(R_SCRIPT) > $(FASTR_BIN_DIR)/R
-	chmod +x $(FASTR_BIN_DIR)/R 
+	chmod +x $(FASTR_BIN_DIR)/R
 	touch $(FASTR_ETC_DIR)/ldpaths
-	sed -e "s|\(R_LIBS_USER=.*-'\)\(.*\)'}|\1$(FASTR_R_HOME)/library'}|" < $(GNUR_HOME_BINARY)/etc/Renviron > $(FASTR_ETC_DIR)/Renviron
+	sed -e "s|\(R_LIBS_USER=.*-'\)\(.*\)'}|\1$(FASTR_R_HOME)/library'}|" < $(shell uname)/Renviron > $(FASTR_ETC_DIR)/Renviron
+	mkdir -p $(FASTR_ETC_DIR)/src/include
+	cp config.h.in $(FASTR_ETC_DIR)/src/include
+	cp $(GNUR_HOME_BINARY)/etc/Renviron.in $(FASTR_ETC_DIR)/Renviron.in
+	cp $(GNUR_HOME_BINARY)/etc/ldpaths.in $(FASTR_ETC_DIR)/ldpaths.in
 	cp $(GNUR_HOME_BINARY)/etc/Makeconf Makeconf.etc
 	cp $(GNUR_HOME_BINARY)/etc/javaconf $(FASTR_ETC_DIR)/javaconf
 	cp $(GNUR_HOME_BINARY)/etc/repositories $(FASTR_ETC_DIR)/repositories
 	cp $(GNUR_HOME_BINARY)/etc/ldpaths $(FASTR_ETC_DIR)/ldpaths
 	# the ed script adds -DFASTR to compiler options and removes JAVA related variables
 	ed Makeconf.etc < edMakeconf.etc
-	
+
 	echo $(DEFAULT_CRAN_MIRROR) > $(FASTR_ETC_DIR)/DEFAULT_CRAN_MIRROR
-	
+
 ifeq ($(FASTR_RFFI),llvm)
 	ed Makeconf.etc < edMakeconf.etc.llvm
 	cp $(LLVM_TOOLS) $(FASTR_BIN_DIR)
@@ -102,7 +103,7 @@ endif
 
 	## deploy helper script that can build native-image of FastR and update the launchers in GraalVM
 	cp install_r_native_image $(FASTR_BIN_DIR)
-    ## prepare the configuration artefacts for the manual FastR configuration in GraalVM 
+	## prepare the configuration artefacts for the manual FastR configuration in GraalVM
 	cp configure_fastr $(FASTR_BIN_DIR)
 	chmod +x $(FASTR_BIN_DIR)/configure_fastr
 	cp configure.ac $(FASTR_ETC_DIR)