Merge branch 'master' into el5

#2781)

.gitignore

@@ -1,28 +1,8 @@
-R-2.11.1.tar.gz
-/R-2.12.0.tar.gz
-/R-2.12.1.tar.gz
-/R-2.12.2.tar.gz
-/R-2.13.0.tar.gz
-/R-2.13.1.tar.gz
-/R-2.13.2.tar.gz
-/R-2.14.0.tar.gz
-/R-2.14.1.tar.gz
-/R-2.15.0.tar.gz
-/R-2.15.1.tar.gz
-/R-2.15.2.tar.gz
-/R-3.0.0.tar.gz
-/R-3.0.1.tar.gz
-/R-3.0.2.tar.gz
-/R-3.0.3.tar.gz
-/R-3.1.1.tar.gz
-/R-3.1.2.tar.gz
-/R-3.1.3.tar.gz
-/R-3.2.0.tar.gz
-/R-3.2.1.tar.gz
-/R-3.2.2.tar.gz
-/R-3.2.3.tar.gz
-/R-3.2.4-revised.tar.gz
-/R-3.3.0.tar.gz
+/xz-5.2.2.tar.bz2
+/zlib-1.2.8.tar.gz
+/bzip2-1.0.6.tar.gz
+/curl-7.48.0.tar.bz2
+/pcre-8.38.tar.bz2
 /R-3.3.1.tar.gz
 /R-3.3.2.tar.gz
 /R-3.3.3.tar.gz

R-2.5.0-pkgconfig.patch

@@ -0,0 +1,149 @@
+diff -uNr R-2.5.0/src/nmath/standalone/Makefile.in R-2.5.0-patched/src/nmath/standalone/Makefile.in
+--- R-2.5.0/src/nmath/standalone/Makefile.in	2007-03-26 18:42:08.000000000 +0200
++++ R-2.5.0-patched/src/nmath/standalone/Makefile.in	2007-04-29 14:50:55.000000000 +0200
+@@ -67,7 +67,7 @@
+ libRmath_la_LDFLAGS =
+ 
+ CLEANFILES = Makedeps *.d *.o *.lo test $(SOURCES)
+-DISTCLEANFILES = Makefile $(Rexeclibdir_LIBRARIES) $(Rexeclibdir_LTLIBRARIES)
++DISTCLEANFILES = Makefile libRmath.pc $(Rexeclibdir_LIBRARIES) $(Rexeclibdir_LTLIBRARIES)
+ 
+ DEFS = -DHAVE_CONFIG_H -DMATHLIB_STANDALONE
+ ALL_CPPFLAGS = $(R_XTRA_CPPFLAGS) -I$(srcdir)/.. $(CPPFLAGS) $(DEFS)
+@@ -78,7 +78,7 @@
+ @r_cc_lo_rules_frag@
+ 
+ 
+-all: Makefile inc static shared
++all: Makefile inc static shared build-pc
+ 
+ inc:
+ 	(cd ../../include; $(MAKE) Rmath.h)
+@@ -100,6 +100,11 @@
+ shared: Makefile ../../include/Rconfig.h Copy Makedeps
+ 	@$(MAKE) $(Rexeclibdir_LTLIBRARIES)
+ 
++build-pc:
++	@$(SED) -e "s:@libdir:$(libdir):" -e "s:@includedir:$(includedir):" \
++	  -e 's/@VERSION/$(VERSION)/' -e 's/@libm/$(LIBM)/' $(srcdir)/libRmath.pc.in \
++	  > "libRmath.pc"
++
+ ../../include/Rconfig.h:
+ 	(cd $(@D); $(MAKE) $(@F))
+ 
+@@ -163,9 +168,7 @@
+ 
+ install-pc:
+ 	@$(MKINSTALLDIRS) "$(libdir)/pkgconfig"
+-	@$(SED) -e "s:@libdir:$(libdir):" -e "s:@includedir:$(includedir):" \
+-	  -e 's/@VERSION/$(VERSION)/' -e 's/@libm/$(LIBM)/' $(srcdir)/libRmath.pc.in \
+-	  > "$(libdir)/pkgconfig/libRmath.pc"
++	@$(INSTALL_DATA) libRmath.pc "$(libdir)/pkgconfig/libRmath.pc"
+ 
+ uninstall:
+ 	@rm -f $(includedir)/Rmath.h $(libdir)/$(libRmath_la) $(libdir)/libRmath.a "$(libdir)/pkgconfig/libRmath.pc"
+diff -uNr R-2.5.0/src/scripts/Makefile.in R-2.5.0-patched/src/scripts/Makefile.in
+--- R-2.5.0/src/scripts/Makefile.in	2007-03-26 18:42:09.000000000 +0200
++++ R-2.5.0-patched/src/scripts/Makefile.in	2007-04-29 14:50:14.000000000 +0200
+@@ -23,17 +23,22 @@
+ DISTFILES = Makefile.in Makefile.win $(SCRIPTS_S) $(SCRIPTS_B_IN) R.sh.in
+ 
+ CLEANFILES =
+-DISTCLEANFILES = Makefile R.fe R.sh $(SCRIPTS_B)
++DISTCLEANFILES = Makefile R.fe R.fe2 R.sh $(SCRIPTS_B)
+ 
+ all: Makefile R
+ 
+ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+ 	@cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
+ 
+-R: $(SCRIPTS_B) R.fe
++R: $(SCRIPTS_B) R.fe R.fe2
+ 	@$(MAKE) rhome=$(top_builddir) install-cmds
+ 	@$(INSTALL_SCRIPT) R.fe $(top_builddir)/bin/R
+ 
++R.fe2: 
++	@(d=`echo '$(rhome)' | sed 's,/,\\\/,g';`; \
++	  sed -e "s/\\(R_HOME_DIR=\\).*/\\1$${d}/;" -e "s+\\(R_SHARE_DIR=\\).*+\\1$(rsharedir)+;" -e  "s+\\(R_INCLUDE_DIR=\\).*+\\1$(rincludedir)+;" -e "s+\\(R_DOC_DIR=\\).*+\\1$(rdocdir)+;"\
++	  < R.fe > $@)
++
+ ## <NOTE>
+ ## Seems we need target rules for creating FOO from FOO.in: pattern
+ ## rules ('%:%.in') are not portable, and some versions of Make do not
+@@ -95,10 +100,8 @@
+ 
+ install: installdirs install-cmds
+ 	@rm -f $(bindir)/R
+-	@(d=`echo '$(rhome)' | sed 's,/,\\\/,g';`; \
+-	  sed -e "s/\\(R_HOME_DIR=\\).*/\\1$${d}/;" -e "s+\\(R_SHARE_DIR=\\).*+\\1$(rsharedir)+;" -e  "s+\\(R_INCLUDE_DIR=\\).*+\\1$(rincludedir)+;" -e "s+\\(R_DOC_DIR=\\).*+\\1$(rdocdir)+;"\
+-	  < R.fe > "$(Rexecbindir)/R")
+-	@$(INSTALL_SCRIPT)  "$(Rexecbindir)/R" "$(bindir)/R"
++	@$(INSTALL_SCRIPT)  R.fe2 "$(Rexecbindir)/R"
++	@$(INSTALL_SCRIPT)  R.fe2 "$(bindir)/R"
+ 	@chmod 755 "$(bindir)/R" "$(Rexecbindir)/R"
+ ## why of all the scriots does this alone chmod just one copy?
+ installdirs:
+diff -uNr R-2.5.0/src/unix/Makefile.in R-2.5.0-patched/src/unix/Makefile.in
+--- R-2.5.0/src/unix/Makefile.in	2007-03-26 18:41:33.000000000 +0200
++++ R-2.5.0-patched/src/unix/Makefile.in	2007-04-29 14:51:55.000000000 +0200
+@@ -26,7 +26,7 @@
+ 
+ @WANT_R_SHLIB_TRUE@ALL_CFLAGS = $(ALL_CFLAGS_LO)
+ 
+-all: Makefile Makedeps R
++all: Makefile Makedeps R 
+ 
+ Makefile: $(srcdir)/Makefile.in \
+   $(top_builddir)/config.status \
+@@ -38,11 +38,23 @@
+ 	@cat $(DEPENDS) >> Makefile
+ 	@touch $@
+ 
+-R: Makefile
++R: Makefile 
+ 	@$(MAKE) Makedeps
+ @WANT_R_SHLIB_FALSE@	@$(MAKE) libunix.a
+ @WANT_R_SHLIB_TRUE@	@$(MAKE) stamp-lo
++	@$(MAKE) rhome=$(abs_top_builddir) build-Rscript
+ 	@$(MAKE) rhome=$(abs_top_builddir) install-Rscript
++	@$(MAKE) build-Rscript
++	@$(MAKE) build-pc
++
++build-pc:
++	@$(SED) -e "s:@rhome:$(rhome):" -e "s:@rincludedir:$(rincludedir):" \
++	  -e 's/@VERSION/$(VERSION)/' $(srcdir)/libR.pc.in \
++	  > "libR.pc"
++
++build-Rscript:
++	$(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -DR_HOME='"$(rhome)"' -o Rscript \
++	  $(srcdir)/Rscript.c
+ 
+ ## is this portable?
+ ../include/Rversion.h:
+@@ -60,22 +72,19 @@
+ clean:
+ 	@-rm -rf .libs _libs
+ 	@-rm -f Makedeps *.d *.o *.a *.lo *.la stamp-lo
++	@-rm -f Rscript libR.pc
+ distclean: clean
+ 	@-rm -f Makefile
+ maintainer-clean: distclean
+ 
+-## we need to build at install time to capture the correct 'rhome'
++## install previously built Rscript
+ install-Rscript:
+-	$(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -DR_HOME='"$(rhome)"' -o Rscript \
+-	  $(srcdir)/Rscript.c
+ 	@$(MKINSTALLDIRS) "$(Rexecbindir)"
+ 	@$(INSTALL_PROGRAM) Rscript "$(Rexecbindir)/Rscript"
+-## substitute at install time to allow 'prefix' to be overridden
++## install previously built libR.pc
+ install-pc:
+ 	@$(MKINSTALLDIRS) "$(libdir)/pkgconfig"
+-	@$(SED) -e "s:@rhome:$(rhome):" -e "s:@rincludedir:$(rincludedir):" \
+-	  -e 's/@VERSION/$(VERSION)/' $(srcdir)/libR.pc.in \
+-	  > "$(libdir)/pkgconfig/libR.pc"
++	@$(INSTALL_DATA) libR.pc "$(libdir)/pkgconfig/libR.pc"
+ install: install-Rscript @WANT_R_SHLIB_TRUE@ install-pc
+ 	@$(MKINSTALLDIRS) "$(bindir)"
+ 	@$(INSTALL_PROGRAM) Rscript "$(bindir)/Rscript"

R-2.7.1-javareconf-tmpfix.patch

@@ -0,0 +1,27 @@
+diff -up R-2.7.1/src/scripts/javareconf.BAD R-2.7.1/src/scripts/javareconf
+--- R-2.7.1/src/scripts/javareconf.BAD	2008-08-29 11:04:21.000000000 -0400
++++ R-2.7.1/src/scripts/javareconf	2008-08-29 11:05:34.000000000 -0400
+@@ -125,16 +125,17 @@ fi
+ javac_works='not present'
+ if test -n "$JAVAC"; then
+     javac_works='not functional'
+-    rm -rf /tmp/A.java /tmp/A.class
+-    echo "public class A { }" > /tmp/A.java
+-    if test -e /tmp/A.java; then
+-	if "${JAVAC}" /tmp/A.java >/dev/null; then
+-	    if test -e /tmp/A.class; then
++    tempdir=`mktemp -d`
++    echo "public class A { }" > ${tempdir}/A.java
++    if test -e ${tempdir}/A.java; then
++	if "${JAVAC}" ${tempdir}/A.java >/dev/null; then
++	    if test -e ${tempdir}/A.class; then
+ 		javac_works=yes
+ 	    fi
+ 	fi
+     fi
+-    rm -rf /tmp/A.java /tmp/A.class
++    rm -rf ${tempdir}
++
+ fi
+ if test "${javac_works}" = yes; then
+     echo "Java compiler    : ${JAVAC}"

R-2.7.2-filter_asoption.patch

@@ -0,0 +1,11 @@
+--- R-2.7.2/configure.org	2008-09-25 15:00:20.000000000 +0900
++++ R-2.7.2/configure	2008-09-25 15:00:35.000000000 +0900
+@@ -26995,7 +26995,7 @@
+ 
+           ;;
+           # Ignore these flags.
+-        -lang* | -lcrt*.o | -lc | -lgcc* | -lSystem | -libmil | -LANG:=* | -LIST:* | -LNO:*)
++        -little | -lang* | -lcrt*.o | -lc | -lgcc* | -lSystem | -libmil | -LANG:=* | -LIST:* | -LNO:*)
+           ;;
+         -lkernel32)
+           test x"$CYGWIN" != xyes && ac_cv_f77_libs="$ac_cv_f77_libs $ac_arg"

R-2.8.0-HAVE_BZLIB_H.patch

@@ -0,0 +1,26 @@
+diff -up R-2.8.0/configure.BAD R-2.8.0/configure
+--- R-2.8.0/configure.BAD	2008-10-26 11:51:56.000000000 -0400
++++ R-2.8.0/configure	2008-10-26 11:52:31.000000000 -0400
+@@ -44779,6 +44779,11 @@ else
+   have_bzlib=no
+ fi
+ if test "x${have_bzlib}" = xyes; then
++
++cat >>confdefs.h <<\_ACEOF
++#define HAVE_BZLIB_H 1
++_ACEOF
++
+ { echo "$as_me:$LINENO: checking if bzip2 version >= 1.0.5" >&5
+ echo $ECHO_N "checking if bzip2 version >= 1.0.5... $ECHO_C" >&6; }
+ if test "${r_cv_have_bzlib+set}" = set; then
+diff -up R-2.8.0/m4/R.m4.BAD R-2.8.0/m4/R.m4
+--- R-2.8.0/m4/R.m4.BAD	2008-09-21 18:05:06.000000000 -0400
++++ R-2.8.0/m4/R.m4	2008-10-26 11:53:05.000000000 -0400
+@@ -3055,6 +3055,7 @@ else
+   have_bzlib=no
+ fi
+ if test "x${have_bzlib}" = xyes; then
++AC_DEFINE(HAVE_BZLIB_H, 1, [Define to 1 if you have bzlib.h.])
+ AC_CACHE_CHECK([if bzip2 version >= 1.0.5], [r_cv_have_bzlib],
+ [AC_LANG_PUSH(C)
+ r_save_LIBS="${LIBS}"

R-3.0.1-arm-compile-fix.patch

@@ -0,0 +1,32 @@
+diff -up R-3.0.1/src/library/tools/R/install.R.armfix R-3.0.1/src/library/tools/R/install.R
+--- R-3.0.1/src/library/tools/R/install.R.armfix	2013-08-12 13:57:17.956790673 -0400
++++ R-3.0.1/src/library/tools/R/install.R	2013-08-12 13:59:51.230800752 -0400
+@@ -108,7 +108,11 @@
+     SHLIB_EXT <- if (WINDOWS) ".dll" else {
+         ## can we do better?
+         mconf <- file.path(R.home(), paste0("etc", rarch), "Makeconf")
+-        sub(".*= ", "", grep("^SHLIB_EXT", readLines(mconf), value = TRUE))
++        if (substr( Sys.info()["machine"], 1, 3) == "arm") { 	# arm has broken regexps in libc
++            sub(".*= ", "", grep("^SHLIB_EXT", readLines(mconf), value = TRUE), perl = TRUE)
++        } else {
++            sub(".*= ", "", grep("^SHLIB_EXT", readLines(mconf), value = TRUE))
++        }
+     }
+ 
+     options(warn = 1)
+@@ -1627,8 +1631,13 @@
+         mconf <- readLines(file.path(R.home(),
+                                      paste0("etc", Sys.getenv("R_ARCH")),
+                                      "Makeconf"))
+-        SHLIB_EXT <- sub(".*= ", "", grep("^SHLIB_EXT", mconf, value = TRUE))
+-        SHLIB_LIBADD <- sub(".*= ", "", grep("^SHLIB_LIBADD", mconf, value = TRUE))
++        if (substr( Sys.info()["machine"], 1, 3) == "arm") { 	# arm has broken regexps in libc
++            SHLIB_EXT <- sub(".*= ", "", grep("^SHLIB_EXT", mconf, value = TRUE), perl = TRUE)
++            SHLIB_LIBADD <- sub(".*= ", "", grep("^SHLIB_LIBADD", mconf, value = TRUE), perl = TRUE)
++        } else {
++            SHLIB_EXT <- sub(".*= ", "", grep("^SHLIB_EXT", mconf, value = TRUE))
++            SHLIB_LIBADD <- sub(".*= ", "", grep("^SHLIB_LIBADD", mconf, value = TRUE))
++        }
+         MAKE <- Sys.getenv("MAKE")
+         rarch <- Sys.getenv("R_ARCH")
+     } else {