Import upstream R-3.0.0

Author: Ingo Korb

COPYING

@@ -0,0 +1,56 @@
+
+			INSTALLING R UNDER UNIX
+
+
+This document concerns building and installing R from sources.  Pre-made
+binaries are made available for some systems with varying regularity and
+can be obtained from CRAN (see the RESOURCES file).
+
+The main source of information on installation is the `R Installation
+and Administration Manual', an HTML copy of which is available as file
+`doc/html/R-admin.html'.  Please read that before installing R.  But
+if you are impatient, read on but please refer to the manual to
+resolve any problems.  (If you obtained R using Subversion, the manual
+is at doc/manual/R-admin.texi.)
+
+
+SIMPLE COMPILATION
+
+As you are reading this file, you have unpacked the R sources and are
+presumably in the top directory.  Issue the following commands:
+
+	./configure
+	make
+
+(If your make is not called `make', set the environment variable MAKE to
+its name, and use that name throughout these instructions.)
+This will take a while, giving you time to read `R-admin.html'.
+
+Then check the built system worked correctly, by
+
+	make check
+
+and make the manuals by (as many options as preferred from)
+
+	make pdf	to create PDF versions
+	make info	to create info files
+
+However, please read the notes in `R-admin.html' about making the
+reference manual.
+
+
+INSTALLATION
+
+You do not need to install R to run it: you can run R by the script
+`bin/R' which you can link or copy to any convenient place in your path.
+
+For a site-wide installation, use
+
+	make install
+	make install-info
+	make install-pdf
+
+choosing to install the manuals that you made.
+
+This installs to the default location (typically `/usr/local') for your
+platform: see the Installation and Administration Manual for other options.

ChangeLog

@@ -0,0 +1,140 @@
+PACKAGE = @PACKAGE@
+VERSION = @VERSION@
+
+abs_top_srcdir = @abs_top_srcdir@
+abs_top_builddir = @abs_top_builddir@
+
+include $(top_srcdir)/share/make/vars.mk
+
+AR = @AR@
+ACLOCAL = @ACLOCAL@
+AUTOCONF = @AUTOCONF@
+AUTOMAKE = @AUTOMAKE@
+AUTOHEADER = @AUTOHEADER@
+BLAS_LIBS = @BLAS_LIBS@
+BUILDDIR_IS_SRCDIR = @BUILDDIR_IS_SRCDIR@
+CC = @CC@
+CFLAGS = @CFLAGS@ @LTO@
+CPICFLAGS = @CPICFLAGS@
+CPPFLAGS = @CPPFLAGS@
+DEFS = @DEFS@ @R_DEFS@
+DISTDIR_TAR_EXCLUDE = --exclude=.svn --exclude=Makefile --exclude="*.o" --exclude="*$(SHLIB_EXT)" --exclude="*~"
+DYLIB_EXT = @DYLIB_EXT@
+DYLIB_LD = @DYLIB_LD@
+DYLIB_LDFLAGS = @DYLIB_LDFLAGS@@BUILD_LTO_TRUE@ $(DYLIBS_LTO)
+DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS)
+DYLIBS_LTO = $(CFLAGS) $(CPICFLAGS)
+ECHO = echo
+ECHO_C = @ECHO_C@
+ECHO_N = @ECHO_N@
+ECHO_T = @ECHO_T@
+FFLAGS = @FFLAGS@ @LTO@
+FLIBS = @FLIBS@
+FLIBS_IN_SO = @FLIBS_IN_SO@
+FPICFLAGS = @FPICFLAGS@
+F77 = @F77@
+GETWD = @GETWD@
+GZIP = --best
+INSTALL = @INSTALL@
+INSTALL_DATA = @INSTALL_DATA@
+INSTALL_PROGRAM = @INSTALL_PROGRAM@
+INSTALL_SCRIPT = @INSTALL_SCRIPT@
+INSTALL_DIR = ${INSTALL} -d
+LDFLAGS = @LDFLAGS@
+LIBINTL= @LIBINTL@
+LIBM = @LIBM@
+LIBR = @LIBR@
+LIBS = @LIBS@
+LIBnn = @LIBnn@
+LIBTOOL = @LIBTOOL@
+## AFAICS unused
+LN_S = @LN_S@
+MAIN_CFLAGS = @MAIN_CFLAGS@
+MAIN_FFLAGS = @MAIN_FFLAGS@
+MAIN_LD = @MAIN_LD@@BUILD_LTO_TRUE@ $(CFLAGS)
+MAIN_LDFLAGS = @MAIN_LDFLAGS@ @WANT_R_SHLIB_FALSE@ @USE_EXPORTFILES_TRUE@ -Wl,-bE:$(top_builddir)/etc/R.exp
+MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LDFLAGS)
+## need this for bootstrapping
+MKINSTALLDIRS = @R_SHELL@ $(top_srcdir)/src/scripts/mkinstalldirs.in
+NOTANGLE = @NOTANGLE@
+R_ARCH = @R_ARCH@
+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@
+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@
+SHELL = @R_SHELL@
+SHLIB_EXT = @SHLIB_EXT@
+SHLIB_CFLAGS = @SHLIB_CFLAGS@
+SHLIB_FFLAGS = @SHLIB_FFLAGS@
+SHLIB_LD = @SHLIB_LD@
+SHLIB_LDFLAGS = @SHLIB_LDFLAGS@@BUILD_LTO_TRUE@ $(SHLIB_LTO)
+SHLIB_LINK = $(SHLIB_LD) $(SHLIB_LDFLAGS) $(LDFLAGS)
+SHLIB_LTO = $(CFLAGS) $(CPICFLAGS)
+STRIP_LIBS = @striplib@
+STRIP_STATIC_LIBS = @stripstaticlib@
+TAR = @TAR@
+USE_NLS = @USE_NLS@
+X_CFLAGS = @X_CFLAGS@
+X_LIBS = @X_LIBS@
+X_PRE_LIBS = @X_PRE_LIBS@
+X_EXTRA_LIBS = @X_EXTRA_LIBS@
+YACC = @YACC@
+
+ALL_CFLAGS = $(R_XTRA_CFLAGS) $(R_OPENMP_CFLAGS) $(MAIN_CFLAGS) $(CFLAGS)
+ALL_CPPFLAGS = $(R_XTRA_CPPFLAGS) $(CPPFLAGS) $(DEFS)
+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)
+
+.SUFFIXES:
+.SUFFIXES: .c .f .m .d .o
+
+@r_cc_rules_frag@
+.f.o:
+	$(F77) $(ALL_FFLAGS) -c $< -o $@
+
+prefix = @prefix@
+exec_prefix = @exec_prefix@
+datarootdir = @datarootdir@
+## only used for installing 'R'.
+bindir = @bindir@
+## not used
+datadir = @datadir@
+## used for 'rhome' and installation of standalone Rmath
+libdir = @libdir@
+## used for man page
+mandir = @mandir@
+## used for installation of standalone Rmath headers
+includedir = @includedir@
+
+rhome = ${libdir}/R
+rsharedir = @rsharedir@
+rincludedir = @rincludedir@
+rdocdir = @rdocdir@
+
+## Overrides for installing R as a framework (MacOS X).
+@WANT_R_FRAMEWORK_TRUE@FW_VERSION = @FW_VERSION@
+@WANT_R_FRAMEWORK_TRUE@rhome = $(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources
+@WANT_R_FRAMEWORK_TRUE@bindir = $(rhome)
+@WANT_R_FRAMEWORK_TRUE@mandir = $(rhome)
+
+Rexecbindir = $(rhome)/bin
+Rexecbindir2 = $(rhome)/bin/exec$(R_ARCH)
+Rexeclibdir = $(rhome)/lib$(R_ARCH)
+## FIXME:
+## Alternatively, we could try to set pkglibdir = $(rhome)/lib when
+## switching to automake.
+## </FIXME>
+Rexecmodulesdir = $(rhome)/modules$(R_ARCH)

INSTALL

@@ -0,0 +1,92 @@
+#-*- Makefile -*-
+#
+# ${R_HOME}/Makefile.fw
+
+top_builddir = .
+
+include $(top_builddir)/Makeconf
+
+install install-strip: install-R-framework
+		@(sed 's|^LIBR =.*|LIBR = -F$(R_FRAMEWORK_DIR)/.. -framework R|' \
+		  $(top_builddir)/etc/Makeconf > "$(rhome)/etc${R_ARCH}/Makeconf")
+		@(sed 's/Versions\/$(FW_VERSION)\/Resources/Resources/' \
+		  "$(DESTDIR)$(R_FRAMEWORK_DIR)/Resources/bin/R" > \
+		  "$(DESTDIR)$(R_FRAMEWORK_DIR)/Resources/bin/RR")
+		@(mv "$(DESTDIR)$(R_FRAMEWORK_DIR)/Resources/bin/RR" "$(DESTDIR)$(R_FRAMEWORK_DIR)/Resources/bin/R")
+		@(chmod a+x "$(DESTDIR)$(R_FRAMEWORK_DIR)/Resources/bin/R")
+		@(chmod -R g+w "$(DESTDIR)$(R_FRAMEWORK_DIR)")
+
+
+install-R-framework:
+	@$(ECHO) "Creating R framework ..."
+	@(cd "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)" && \
+	  ln -f -s -n Resources/include Headers && \
+	  ln -f -s -n Resources/lib/libR.dylib R)
+	@if [ ! -e "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/PrivateHeaders" ]; then \
+	 mkdir "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/PrivateHeaders"; fi
+	@(cd "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions" && \
+	  ln -f -s -n $(FW_VERSION) Current)
+	@(if [ -e "$(DESTDIR)$(R_FRAMEWORK_DIR)/Resources" -a ! -L "$(DESTDIR)$(R_FRAMEWORK_DIR)/Resources" ]; then \
+	  rm -rf "$(DESTDIR)$(R_FRAMEWORK_DIR)/Resources.old"; mv "$(DESTDIR)$(R_FRAMEWORK_DIR)/Resources" "$(DESTDIR)$(R_FRAMEWORK_DIR)/Resources.old"; \
+	  fi)
+	@(cd "$(DESTDIR)$(R_FRAMEWORK_DIR)"  && \
+	  ln -f -s -n Versions/Current/PrivateHeaders PrivateHeaders&& \
+	  ln -f -s -n Versions/Current/Headers Headers&& \
+	  ln -f -s -n Versions/Current/R R && \
+	  ln -f -s -n Versions/Current/Resources/lib Libraries && \
+	  ln -f -s -n Versions/Current/Resources Resources)
+	@## the resulting libR will point dyld to the fat libR regardless of its origin
+	@(cd "$(DESTDIR)$(R_FRAMEWORK_DIR)/Resources/lib" && \
+	  install_name_tool -id "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/lib/libR.dylib" $(Rexeclibdir)/libR.dylib)
+	@( otool=otool ; if otool -D "$(DESTDIR)$(Rexeclibdir)/libR.dylib"|grep 'not an object'>/dev/null; then otool=otool64; fi; \
+	   for lib in Rlapack Rblas R; do \
+	   if test -e "$(DESTDIR)$(Rexeclibdir)/lib$${lib}.dylib"; then $(ECHO) "  lib$${lib}"; \
+	    find "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/" -name '*.so' -or -name '*.dylib' | \
+	    xargs -n 1 install_name_tool -change \
+	    `$${otool} -L "$(DESTDIR)$(Rexeclibdir)/lib$${lib}.dylib" |sed -n -e '2 s/.\(.*\) (compat.*/\1/p'` \
+	    "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/lib/lib$${lib}.dylib" ; \
+	    find "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/" -name '*.so' -or -name '*.dylib' | \
+	    xargs -n 1 install_name_tool -change lib$${lib}.dylib \
+	    "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/lib/lib$${lib}.dylib" ; \
+	    install_name_tool -id "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/lib/lib$${lib}.dylib" \
+	    "$(DESTDIR)$(Rexeclibdir)/lib$${lib}.dylib"; \
+	    if [ "$(Rexeclibdir)" != "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/lib" ]; then \
+	      $(top_srcdir)/tools/updatefat "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/lib/lib$${lib}.dylib" "$(DESTDIR)$(Rexeclibdir)/lib$${lib}.dylib"; \
+	      install_name_tool -id "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/lib/lib$${lib}.dylib" \
+	      "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/lib/lib$${lib}.dylib"; \
+	    fi; \
+	    for rexe in `ls "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)"/Resources/bin/exec/*/R "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/bin/exec/R" 2>/dev/null`; do \
+	     install_name_tool -change lib$${lib}.dylib \
+	     "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/lib/lib$${lib}.dylib" "$$rexe" ; \
+	    done; \
+           fi; \
+          done)
+	@(cp -R $(top_srcdir)/src/include/* "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/Current/PrivateHeaders/" && \
+	  cp src/include/config.h "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/Current/PrivateHeaders/" && \
+	  chmod a+r "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/Current/PrivateHeaders/config.h"; \
+	  find "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/Current/PrivateHeaders" -name .svn | xargs rm -rf)
+	@(install_name_tool -change libR.dylib \
+	    "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/lib/libR.dylib" \
+	    "$(DESTDIR)$(Rexecbindir2)/R")
+	@(if [ -n "${R_ARCH}" ]; then \
+	  rm -rf "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/Current/PrivateHeaders${R_ARCH}" && \
+	  mkdir "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/Current/PrivateHeaders${R_ARCH}" && \
+	  cp src/include/config.h "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/Current/PrivateHeaders${R_ARCH}/config.h"; \
+	  chmod a+r "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/Current/PrivateHeaders${R_ARCH}/config.h"; \
+	  sed -e "s|R_ARCH=${R_ARCH}|R_ARCH=/\`arch\`|" "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/bin/R" \
+	  > "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/bin/.tmp.R" && \
+	  chmod a+x "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/bin/.tmp.R" && \
+	  mv "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/bin/.tmp.R" "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/bin/R"; \
+	  if [ "${R_ARCH}" != /ppc -a "${R_ARCH}" != /i386 -a "${R_ARCH}" != /ppc64 -a "${R_ARCH}" != /x86_64 -a "${R_ARCH}" != /arm ]; then \
+	    $(ECHO) "\
+	*** WARNING: The architecture name is incompatible with Apple's naming~              convention. This may prevent applications from using the R~              framework. Please use i386, x86_64, ppc, ppc64 or arm as architecture~              names to allow universal builds."|sed 'y/~/\n/' >&2; \
+	  else \
+	    for f in `ls "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Headers/${R_ARCH}/"*.h|xargs basename` config.h; do \
+	      fn="Headers/$$f"; if [ "$$f" = "config.h" ]; then fn="PrivateHeaders/config.h"; fi; \
+	      $(ECHO) "/* This is an automatically generated universal stub for architecture-dependent headers. */~#ifdef __i386__~#include \"i386/$$f\"~#elif defined __ppc__~#include \"ppc/$$f\"~#elif defined __ppc64__~#include \"ppc64/$$f\"~#elif defined __x86_64__~#include \"x86_64/$$f\"~#elif defined __arm__~#include \"arm/$$f\"~#else~#error \"Unsupported architecture.\"~#endif" |sed -e 'y/~/\n/' > "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/$$fn"; \
+	    done; \
+	  fi; \
+	fi )
+	@( rm -f "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/R" && \
+	   ln -s bin/R "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/R" )
+	@( $(ECHO) "<?xml version=\"1.0\" encoding=\"UTF-8\"?>~<!DOCTYPE plist PUBLIC \"-//Apple Computer//DTD PLIST 1.0//EN\" \"http://www.apple.com/DTDs/PropertyList-1.0.dtd\">~<plist version=\"1.0\">~<dict>~ <key>CFBundleIdentifier</key>~ <string>org.r-project.R-framework</string>~ <key>CFBundleInfoDictionaryVersion</key>~ <string>6.0</string>~ <key>CFBundleName</key>~ <string>R</string>~ <key>CFBundlePackageType</key>~ <string>FMWK</string>~ <key>CFBundleVersion</key>~ <string>$(VERSION)</string>~</dict>~</plist>" |sed -e 'y/~/\n/' > "$(DESTDIR)$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/Info.plist")