Merge 3.2.3 feature branch into dev

R-src/Makeconf.in

@@ -19,6 +19,8 @@ CPICFLAGS = @CPICFLAGS@
 CPPFLAGS = @CPPFLAGS@
 CURL_CPPFLAGS = @CURL_CPPFLAGS@
 CURL_LIBS = @CURL_LIBS@
+## in case we want to link with this for UBSAN checks
+CXX = @CXX@
 DEFS = @DEFS@ @R_DEFS@
 DISTDIR_TAR_EXCLUDE = --exclude=.svn --exclude=Makefile --exclude="*.o" --exclude="*$(SHLIB_EXT)" --exclude="*~"
 DYLIB_EXT = @DYLIB_EXT@
@@ -66,11 +68,13 @@ MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LIBR0) $(LDFLAGS)
 MKINSTALLDIRS = @R_SHELL@ $(top_srcdir)/src/scripts/mkinstalldirs.in
 NOTANGLE = @NOTANGLE@
 R_ARCH = @R_ARCH@
+R_DYLIB_EXT = @R_DYLIB_EXT@
 R_FRAMEWORK_DIR = $(prefix)/R.framework
 R_GZIPCMD = @R_GZIPCMD@
 ## needed for AIX only
 @USE_EXPORTFILES_TRUE@ R_HOME = $(top_builddir)
 R_OPENMP_CFLAGS = @R_OPENMP_CFLAGS@
+## if ever used, need to check that this is compatible with C OpenMP
 R_OPENMP_FFLAGS = @R_OPENMP_FFLAGS@
 R_OSTYPE = @R_OSTYPE@
 R_PKGS = $(R_PKGS_BASE) @USE_RECOMMENDED_PACKAGES_TRUE@ $(R_PKGS_RECOMMENDED)
@@ -102,6 +106,7 @@ YACC = @YACC@
 
 ALL_CFLAGS = $(R_XTRA_CFLAGS) $(R_OPENMP_CFLAGS) $(MAIN_CFLAGS) $(CFLAGS)
 ALL_CPPFLAGS = $(R_XTRA_CPPFLAGS) $(CPPFLAGS) $(DEFS)
+## R_OPENMP_FFLAGS should not really be here: see above
 ALL_FFLAGS = $(R_XTRA_FFLAGS) $(R_OPENMP_FFLAGS) $(MAIN_FFLAGS) $(FFLAGS)
 ALL_CFLAGS_LO = $(R_XTRA_CFLAGS) $(R_OPENMP_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(CFLAGS)
 ALL_FFLAGS_LO = $(R_XTRA_FFLAGS) $(R_OPENMP_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS)

R-src/Makefile.in

@@ -40,6 +40,7 @@ ACINCLUDE_DEPENDENCIES = \
 	m4/cxx_11.m4 \
 	m4/gettext.m4 m4/gettext-lib.m4 \
 	m4/libtool.m4 m4/ltoptions.m4 m4/ltversion.m4 m4/ltsugar.m4 m4/lt~obsolete.m4 \
+	m4/openmp.m4 \
 	m4/stat-time.m4
 CONFIGURE_DEPENDENCIES = $(srcdir)/VERSION
 config.status: $(srcdir)/configure
@@ -82,8 +83,8 @@ vignettes: stamp-recommended
 ## This needs packages built, hence 'R' dependence on 'javaconf'
 ## javareconf gets remade often.
 stamp-java : etc/javaconf $(srcdir)/src/scripts/javareconf.in
-	@$(ECHO) "configuring Java ..."
-	@-bin/R CMD javareconf
+@WANT_JAVA_TRUE@	@$(ECHO) "configuring Java ..."
+@WANT_JAVA_TRUE@	@-bin/R CMD javareconf
 	@touch stamp-java
 
 javaconf: R
@@ -123,7 +124,7 @@ svnonly:
 	  fi \
 	fi
 
-@WANT_R_STATIC_FALSE@libR_la = libR$(DYLIB_EXT)
+@WANT_R_STATIC_FALSE@libR_la = libR$(R_DYLIB_EXT)
 @WANT_R_STATIC_TRUE@libR_la = libR.a
 install-libR:
 	@if test -f lib$(R_ARCH)/$(libR_la); then $(MAKE) install-libR-exists; fi
@@ -144,7 +145,7 @@ uninstall:
 	@rm -rf "$(DESTDIR)$(Rexecbindir)" "$(DESTDIR)$(rhome)/lib"
 	@rmdir "$(DESTDIR)$(rhome)" 2>/dev/null \
           || $(ECHO) "  dir $(DESTDIR)$(rhome) not removed"
-	@rm -f "$(DESTDIR)${libdir}/libR$(DYLIB_EXT)"
+	@rm -f "$(DESTDIR)${libdir}/libR$(R_DYLIB_EXT)"
 
 mostlyclean: clean
 clean:

R-src/SVN-REVISION

@@ -1,2 +1,2 @@
-Revision: 69053
-Last Changed Date: 2015-08-14
+Revision: 69752
+Last Changed Date: 2015-12-10

R-src/VERSION

@@ -1 +1 @@
-3.2.2
+3.2.3

R-src/VERSION-NICK

@@ -1 +1 @@
-Fire Safety
+Wooden Christmas-Tree

R-src/config.site

@@ -277,4 +277,15 @@
 ## CURL_LIBS=`curl-config --static-libs`
 
 ## Path to the version of pkg-config to be used for locating cairographics.
-## PKGCONF =
+## PKGCONF=
+
+## OpenMP settings.
+## The configure code is conservative about enabling OpenMP 
+## so use can be forced here (or non-use if set but empty).
+## For packages
+## SHLIB_OPENMP_CFLAGS=
+## SHLIB_OPENMP_CXXFLAGS=
+## SHLIB_OPENMP_FCFLAGS=
+## SHLIB_OPENMP_FFLAGS=
+## For R itself (src/main/array.c and src/library/stats/src/distance.c)
+## R_OPENMP_CFLAGS=