[GR-30277] Re-enable API checksum of recommended packages cache (2).

PullRequest: fastr/2626

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

@@ -85,19 +85,19 @@ ifdef FASTR_RECOMMENDED_BINARY
 $(info Using FastR recommended packages binary: $(FASTR_RECOMMENDED_BINARY))
 
 install.recommended: $(GNUR_RECOMMENDED_TARS)
-#	if ! (mx -p $(FASTR_R_HOME) r-pkgcache --print-api-checksum --vm fastr | tail -n 1 | diff -q $(FASTR_RECOMMENDED_BINARY)/api-checksum.txt -); then \
-#		echo "******************************"; \
-#		echo "ERROR:"; \
-#		echo "The checksum of FastR header files does not match the checksum that the recommended packages were build against."; \
-#		echo "You can run appropriate CI jobs in FastR repo to generate a new version of recommended packages binary and then upload it to the appropriate place."; \
-#		echo "******************************"; \
-#		echo "Actual checksum of FastR headers:"; \
-#		echo "$(mx -p $(FASTR_R_HOME) r-pkgcache --print-api-checksum --vm fastr)"; \
-#		echo "Expected checksum by the recommended pkgs:"; \
-#		cat $(FASTR_RECOMMENDED_BINARY)/api-checksum.txt; \
-#		echo "******************************"; \
-#		exit 1; \
-#	fi
+	@if ! (mx -p $(FASTR_R_HOME) r-pkgcache --print-api-checksum --vm fastr | tail -n 1 | diff -q $(FASTR_RECOMMENDED_BINARY)/api-checksum.txt -); then \
+		echo "******************************"; \
+		echo "ERROR:"; \
+		echo "The checksum of FastR header files does not match the checksum that the recommended packages were build against."; \
+		echo "You can run appropriate CI jobs in FastR repo to generate a new version of recommended packages binary and then upload it to the appropriate place."; \
+		echo "******************************"; \
+		echo "Actual checksum of FastR headers:"; \
+		mx -p $(FASTR_R_HOME) r-pkgcache --print-api-checksum --vm fastr; \
+		echo "Expected checksum by the recommended pkgs:"; \
+		cat $(FASTR_RECOMMENDED_BINARY)/api-checksum.txt; \
+		echo "******************************"; \
+		exit 1; \
+	fi
 	cp -R $(FASTR_RECOMMENDED_BINARY)/pkgs/* $(FASTR_R_HOME)/library
 	touch install.recommended
 

com.oracle.truffle.r.native/gnur/patch/Makeconf.in

@@ -21,18 +21,20 @@ CURL_CPPFLAGS = @CURL_CPPFLAGS@
 CURL_LIBS = @CURL_LIBS@
 ## in case we want to link with this for UBSAN checks
 CXX = @CXX@
+## DEFS is generated by autoconf as -DHAVE_CONFIG_H: R_DEFS is user's
 DEFS = @DEFS@ @R_DEFS@
 DISTDIR_TAR_EXCLUDE = --exclude=.svn --exclude=Makefile --exclude="*.o" --exclude="*$(SHLIB_EXT)" --exclude="*~"
 DYLIB_EXT = @DYLIB_EXT@
 DYLIB_LD = @DYLIB_LD@
-DYLIB_LDFLAGS = @DYLIB_LDFLAGS@@BUILD_LTO_TRUE@ $(DYLIBS_LTO)
+DYLIB_LDFLAGS = @DYLIB_LDFLAGS@@BUILD_LTO_TRUE@ $(DYLIB_LTO)
+## used for libR as a shared library
 DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS)
-DYLIBS_LTO = $(CFLAGS) $(CPICFLAGS)
+DYLIB_LTO = $(CFLAGS) $(CPICFLAGS) @LTO_LD@
 ECHO = echo
 ECHO_C = @ECHO_C@
 ECHO_N = @ECHO_N@
 ECHO_T = @ECHO_T@
-FFLAGS = @FFLAGS@ @LTO@
+FFLAGS = @FFLAGS@ @LTO_FC@
 FLIBS = @FLIBS@
 ## needed for some earlier Solaris compilers
 FLIBS_IN_SO = @FLIBS_IN_SO@
@@ -62,7 +64,7 @@ LIBTOOL = @LIBTOOL@
 LN_S = @LN_S@
 MAIN_CFLAGS = @MAIN_CFLAGS@
 MAIN_FFLAGS = @MAIN_FFLAGS@
-MAIN_LD = @MAIN_LD@@BUILD_LTO_TRUE@ $(CFLAGS)
+MAIN_LD = @MAIN_LD@@BUILD_LTO_TRUE@ $(CFLAGS) $(CPICFLAGS) @LTO_LD@
 MAIN_LDFLAGS = @MAIN_LDFLAGS@ @WANT_R_SHLIB_FALSE@ @USE_EXPORTFILES_TRUE@ -Wl,-bE:$(top_builddir)/etc/R.exp
 MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LIBR0) $(LDFLAGS)
 ## need this for bootstrapping
@@ -76,14 +78,14 @@ R_GZIPCMD = @R_GZIPCMD@
 @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
+## and add it to ALL_FFLAGS{,_LO}
 R_OPENMP_FFLAGS = @R_OPENMP_FFLAGS@
 R_OSTYPE = @R_OSTYPE@
 R_PKGS = $(R_PKGS_BASE) @USE_RECOMMENDED_PACKAGES_TRUE@ $(R_PKGS_RECOMMENDED)
 R_PLATFORM = @R_PLATFORM@
 R_XTRA_CFLAGS = @R_XTRA_CFLAGS@ 
 R_XTRA_CPPFLAGS = @R_XTRA_CPPFLAGS@ -I. -I$(top_builddir)/src/include -I$(top_srcdir)/src/include
 R_XTRA_FFLAGS = @R_XTRA_FFLAGS@
-R_XTRA_LIBS = @R_XTRA_LIBS@
 RANLIB = @RANLIB@
 READLINE_LIBS = @READLINE_LIBS@
 SED = @SED@
@@ -95,8 +97,8 @@ SHLIB_LD = @SHLIB_LD@
 SHLIB_LDFLAGS = @SHLIB_LDFLAGS@@BUILD_LTO_TRUE@ $(SHLIB_LTO)
 SHLIB_LINK = $(SHLIB_LD) $(SHLIB_LDFLAGS) $(LIBR0) $(LDFLAGS)
 SHLIB_LTO = $(CFLAGS) $(CPICFLAGS)
-STRIP_LIBS = @striplib@
-STRIP_STATIC_LIBS = @stripstaticlib@
+STRIP_SHARED_LIB = @STRIP_SHARED_LIB@
+STRIP_STATIC_LIB = @STRIP_STATIC_LIB@
 TAR = @TAR@
 USE_NLS = @USE_NLS@
 X_CFLAGS = @X_CFLAGS@
@@ -105,12 +107,16 @@ X_PRE_LIBS = @X_PRE_LIBS@
 X_EXTRA_LIBS = @X_EXTRA_LIBS@
 YACC = @YACC@
 
+## MAIN_[CF]FLAGS are used on some systems when profiling R.
 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_FFLAGS = $(R_XTRA_FFLAGS) $(MAIN_FFLAGS) $(FFLAGS)
+
+## For use in src/{appl,main} when R is a shared library, src/modules/lapack
+## and src/extra/blas when internal BLAS is built as a shared library
+## SHLIB_CFLAGS and SHLIB_FFLAGS are apparently currently unused
 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)
+ALL_FFLAGS_LO = $(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS)
 
 .SUFFIXES:
 .SUFFIXES: .c .f .m .d .o

com.oracle.truffle.r.native/gnur/patch/Makefile.in

@@ -82,7 +82,8 @@ 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
+## If configure is re-run, etc/Makeconf gets reset to initial Java state
+stamp-java : etc/Makeconf etc/javaconf $(srcdir)/src/scripts/javareconf.in
 @WANT_JAVA_TRUE@	@$(ECHO) "configuring Java ..."
 @WANT_JAVA_TRUE@	@-bin/R CMD javareconf
 	@touch stamp-java
@@ -142,7 +143,7 @@ uninstall:
 	@for f in $(INSTFILES) $(NON_SVN_INSTFILES); do \
 	  rm -f "$(DESTDIR)$(rhome)/$${f}"; \
 	done
-	@rm -rf "$(DESTDIR)$(Rexecbindir)" "$(DESTDIR)$(rhome)/lib"
+	@rm -Rf "$(DESTDIR)$(Rexecbindir)" "$(DESTDIR)$(rhome)/lib"
 	@rmdir "$(DESTDIR)$(rhome)" 2>/dev/null \
           || $(ECHO) "  dir $(DESTDIR)$(rhome) not removed"
 	@rm -f "$(DESTDIR)${libdir}/libR$(R_DYLIB_EXT)"
@@ -158,15 +159,15 @@ distclean: clean
 	@(for d in $(SUBDIRS); do rsd="$${d} $${rsd}"; done; \
 	  for d in $${rsd}; do (cd $${d} && $(MAKE) $@); done)
 	@rm -f po/Makefile
-	-@rm -rf bin include lib library modules gnome
+	-@rm -Rf bin include lib library modules gnome
 	@if test -f non-tarball ; then \
 	  rm -f $(NON_SVN_INSTFILES) non-tarball doc/FAQ doc/RESOURCES doc/html/resources.html doc/html/NEWS.html; \
 	fi
 	@if test "$(BUILDDIR_IS_SRCDIR)" = no ; then \
 	  rm -f $(NON_SVN_INSTFILES); \
-	  rm -rf $(SUBDIRS) $(SUBDIRS_WITH_NO_BUILD); \
+	  rm -Rf $(SUBDIRS) $(SUBDIRS_WITH_NO_BUILD); \
 	fi
-	-@rm -rf libconftest.dSYM
+	-@rm -Rf libconftest.dSYM
 	-@rm -f Makeconf Makefile Makefile.bak Makefrag.* \
 	  config.cache config.log config.status libtool stamp-java \
 	  $(ACLOCAL_M4) acinclude.m4 $(distdir).tar.gz
@@ -175,9 +176,10 @@ maintainer-clean: distclean
 	@$(ECHO) "deletes files that may need special rules to rebuild"
 	@(for d in $(SUBDIRS); do rsd="$${d} $${rsd}"; done; \
 	  for d in $${rsd}; do (cd $${d} && $(MAKE) $@); done)
-	-@(cd $(srcdir) && rm -rf autom4te.cache)
+	-@(cd $(srcdir) && rm -Rf autom4te.cache)
 
 dist: dist-unix
+## GNU gzip 1.8 warns that env var GZIP is obsolescent for gzip, so use as arg
 dist-unix: distdir
 	-chmod -R a+r $(distdir)
 	-chmod -R go-w $(distdir)
@@ -186,11 +188,11 @@ dist-unix: distdir
           if test $(distdir) != $${dirname} ; then \
             mv $(distdir) $${dirname}; \
           fi ; \
-	  GZIP=$(GZIP) $(TAR) czf $${distname}.tar.gz $${dirname}; \
-	  rm -rf $${dirname}
+	  $(TAR) cf $${distname}.tar $${dirname} && $(R_GZIPCMD) $(GZIP) $${distname}.tar; \
+	  rm -Rf $${dirname}
 dist-win:
 distdir: $(DISTFILES) vignettes
-	@rm -rf $(distdir)
+	@rm -Rf $(distdir)
 	@mkdir $(distdir)
 	@-chmod 755 $(distdir)
 	@for f in $(DISTFILES); do \
@@ -220,6 +222,71 @@ distdir: $(DISTFILES) vignettes
 	done
 	@(cd $(distdir); tools/link-recommended)
 
+distcheck: distcheck-unix
+distcheck-unix: dist
+	distname=`$(srcdir)/tools/GETDISTNAME`; \
+	dirname=`$(ECHO) $${distname} | sed -e s/_.*//`; \
+	rm -Rf $${dirname}; \
+	$(R_GZIPCMD) -d -c $${distname}.tar.gz | $(TAR) -x -f -; \
+	chmod u+w $${dirname}; \
+	if test -f config.site; then \
+	  cp config.site $${dirname}; \
+	fi; \
+	mkdir $${dirname}/_build $${dirname}/_inst; \
+	test -d $${dirname}/_build || exit 0; \
+	dc_install_base=`cd $${dirname}/_inst && pwd` \
+	  && save__cwd=`pwd` \
+	  && cd $${dirname}/_build \
+	  && ../configure --srcdir=.. --prefix="$$dc_install_base" \
+	  && $(MAKE) \
+	  && $(MAKE) check-all \
+	  && $(MAKE) install \
+	  && $(MAKE) uninstall \
+	  && $(MAKE) distuninstallcheck_dir="$$dc_install_base" \
+	        distuninstallcheck \
+	  && $(MAKE) dist \
+	  && rm -f $${distname}.tar.gz \
+	  && $(MAKE) distcleancheck \
+	  && cd "$$save__cwd" \
+	  || exit 1; \
+	rm -Rf $${dirname}; \
+	$(ECHO) "$${distname}.tar.gz ready for distribution"
+
+distcheck-win:
+distuninstallcheck:
+	@test -n '$(distuninstallcheck_dir)' || { \
+	  echo 'ERROR: trying to run $@ with an empty' \
+	       '$$(distuninstallcheck_dir)' >&2; \
+	  exit 1; \
+	}; \
+	cd '$(distuninstallcheck_dir)' || { \
+	  $(ECHO) 'ERROR: cannot chdir into $(distuninstallcheck_dir)' >&2; \
+	  exit 1; \
+	}; \
+	test `find . -type f -print | wc -l` -eq 0 || \
+	  { $(ECHO) "ERROR: files left after uninstall:" ; \
+	    `find . -type f -print`; \
+	    exit 1; } >&2
+distcleancheck: distclean
+	@test `find . -type f -print | wc -l` -eq 0 || \
+	  { $(ECHO) "ERROR: files left in build directory after distclean:" ; \
+	    `find . -type f -print`; \
+	    exit 1; } >&2
+
+## For developers: from an svn checkout expect .svn to be only in the srcdir
+checkdistcomplete:
+	@distname=`$(srcdir)/tools/GETDISTNAME`; \
+	dirname=`$(ECHO) $${distname} | sed -e s/_.*//`; \
+	if test -d $${dirname}; then \
+	  echo "Please remove directory $${dirname} first"; \
+	  exit 1; \
+	fi; \
+	rm -Rf $${dirname}; \
+	echo "Checking $${distname}.tar.gz"; \
+	$(R_GZIPCMD) -d -c $${distname}.tar.gz | $(TAR) -x -f -; \
+	diff -r $${dirname} $(srcdir) | grep "^Only in $(srcdir)" | grep -v "^Only in.*[.]svn"; \
+	rm -Rf $${dirname}
+
 info pdf:
 	-@(cd doc && $(MAKE) $@)
 install-info install-pdf:

com.oracle.truffle.r.native/gnur/patch/SVN-REVISION

@@ -1,2 +1,2 @@
-Revision: 72570
-Last Changed Date: 2017-04-21
+Revision: 79318
+Last Changed Date: 2020-10-10

com.oracle.truffle.r.native/gnur/patch/VERSION

@@ -1 +1 @@
-3.4.0
+4.0.3

com.oracle.truffle.r.native/gnur/patch/VERSION-NICK

@@ -1 +1 @@
-You Stupid Darkness
+Bunny-Wunnies Freak Out