Commit f3ad6726 authored by Dirk Eddelbuettel's avatar Dirk Eddelbuettel

Import Upstream version 2.7.0

parent 900cc981

Too many changes to show.

To preserve performance only 1000 of 1000+ files are displayed.

......@@ -12,7 +12,7 @@ AUTOCONF = @AUTOCONF@
AUTOMAKE = @AUTOMAKE@
AUTOHEADER = @AUTOHEADER@
AWK = @AWK@
BITMAP_LIBS = @BITMAP_LIBS@
BITMAP_LIBS = @BITMAP_LIBS@ @TIFF_LIBS@
BLAS_LIBS = @BLAS_LIBS@
BUILDDIR_IS_SRCDIR = @BUILDDIR_IS_SRCDIR@
BUILD_CC = @BUILD_CC@
......@@ -28,6 +28,7 @@ DYLIB_EXT = @DYLIB_EXT@
DYLIB_LD = @DYLIB_LD@
DYLIB_LDFLAGS = @DYLIB_LDFLAGS@
DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS)
ECHO = echo
ECHO_C = @ECHO_C@
ECHO_N = @ECHO_N@
ECHO_T = @ECHO_T@
......@@ -49,8 +50,7 @@ JAVA_LIBS = @JAVA_LIBS0@
JAVAC = @JAVAC@
LATEX = @LATEX@
LDFLAGS = @LDFLAGS@
## we only need this is if it is external, as otherwise link to R
LIBINTL= @BUILD_LIBINTL_FALSE@ @LIBINTL@
LIBINTL= @LIBINTL@
LIBM = @LIBM@
LIBR = @LIBR@
LIBS = @LIBS@
......@@ -91,6 +91,7 @@ SHLIB_LD = @SHLIB_LD@
SHLIB_LDFLAGS = @SHLIB_LDFLAGS@
SHLIB_LINK = $(SHLIB_LD) $(SHLIB_LDFLAGS) $(LDFLAGS)
STRIP_LIBS = @striplib@
STRIP_STATIC_LIBS = @stripstaticlib@
TAR = @TAR@
X_CFLAGS = @X_CFLAGS@
X_LIBS = @X_LIBS@
......@@ -101,6 +102,7 @@ YACC = @YACC@
ALL_CFLAGS = $(R_XTRA_CFLAGS) $(MAIN_CFLAGS) $(CFLAGS)
ALL_CPPFLAGS = $(R_XTRA_CPPFLAGS) $(CPPFLAGS) $(DEFS)
ALL_FFLAGS = $(R_XTRA_FFLAGS) $(MAIN_FFLAGS) $(FFLAGS)
ALL_OBJCFLAGS = $(R_XTRA_OBJCFLAGS) $(MAIN_OBJCFLAGS) $(OBJCFLAGS)
ALL_CFLAGS_LO = $(R_XTRA_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(CFLAGS)
ALL_FFLAGS_LO = $(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS)
......@@ -110,11 +112,7 @@ ALL_FFLAGS_LO = $(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS)
@r_cc_rules_frag@
.f.o:
$(F77) $(ALL_FFLAGS) -c $< -o $@
## mainly for OS X to allow us to include Obj-C/Cocoa code if necessary
## the (long-term) goal is to integrate the Obj-C R API in the framework
.m.o:
$(OBJC) $(ALL_CPPFLAGS) $(OBJCFLAGS) -c $< -o $@
@r_objc_rules_frag@
prefix = @prefix@
exec_prefix = @exec_prefix@
......
......@@ -30,11 +30,12 @@ Makeconf: $(srcdir)/Makeconf.in $(top_builddir)/config.status
ACLOCAL_M4 = aclocal.m4
ACINCLUDE_DEPENDENCIES = \
m4/R.m4 \
m4/cairo.m4 \
m4/clibs.m4 \
m4/codeset.m4 \
m4/gettext.m4 m4/gettext-lib.m4 \
m4/java.m4 \
m4/libtool.m4
m4/libtool.m4 m4/ltoptions.m4 m4/ltversion.m4 m4/ltsugar.m4 m4/lt~obsolete.m4
CONFIGURE_DEPENDENCIES = $(srcdir)/VERSION
config.status: $(srcdir)/configure
@$(SHELL) ./config.status --recheck
......@@ -59,7 +60,7 @@ R: Makefile svnonly
(cd $${d} && $(MAKE) R) || exit 1; \
done
@test -f src/library/stamp-docs || \
echo "you should 'make docs' now ..."
$(ECHO) "you should 'make docs' now ..."
docs: R FORCE
-@(cd doc && $(MAKE) $@)
......@@ -98,7 +99,7 @@ svnonly:
@if test ! -f "$(srcdir)/doc/FAQ" || test -f non-tarball ; then \
(cd doc/manual && $(MAKE) front-matter html-non-svn) ; \
touch non-tarball ; \
(cd $(srcdir); LC_ALL=C TZ=GMT svn info || echo "Revision: unknown") 2> /dev/null \
(cd $(srcdir); LC_ALL=C TZ=GMT svn info || $(ECHO) "Revision: unknown") 2> /dev/null \
| sed -n -e '/^Revision/p' -e '/^Last Changed Date/'p \
| cut -d' ' -f1,2,3,4 > SVN-REVISION-tmp ; \
$(top_srcdir)/tools/move-if-change SVN-REVISION-tmp SVN-REVISION ; \
......@@ -128,7 +129,7 @@ uninstall:
done
@rm -rf "$(DESTDIR)$(Rexecbindir)" "$(DESTDIR)$(rhome)/lib"
@rmdir "$(DESTDIR)$(rhome)" 2>/dev/null \
|| echo " dir $(DESTDIR)$(rhome) not removed"
|| $(ECHO) " dir $(DESTDIR)$(rhome) not removed"
@rm -f "$(DESTDIR)${libdir}/libR$(DYLIB_EXT)"
mostlyclean: clean
......@@ -152,8 +153,8 @@ distclean: clean
config.cache config.log config.status libtool \
$(ACLOCAL_M4) acinclude.m4 $(distdir).tar.gz
maintainer-clean: distclean
@echo "This command is intended for maintainers to use; it"
@echo "deletes files that may need special rules to rebuild"
@$(ECHO) "This command is intended for maintainers to use; it"
@$(ECHO) "deletes files that may need special rules to rebuild"
@(for d in $(SUBDIRS); do rsd="$${d} $${rsd}"; done; \
for d in $${rsd}; do (cd $${d} && $(MAKE) $@); done)
-@(cd $(srcdir) && rm -rf autom4te.cache)
......@@ -163,7 +164,7 @@ dist-unix: distdir
-chmod -R a+r $(distdir)
-chmod -R go-w $(distdir)
distname=`$(srcdir)/tools/GETDISTNAME`; \
dirname=`echo $${distname} | sed -e s/_.*//`; \
dirname=`$(ECHO) $${distname} | sed -e s/_.*//`; \
if test $(distdir) != $${dirname} ; then \
mv $(distdir) $${dirname}; \
fi ; \
......@@ -213,23 +214,26 @@ reset-recommended:
@(cd src/library/Recommended && $(MAKE) clean)
install-R-framework:
@echo "Creating R framework ..."
@$(ECHO) "Creating R framework ..."
@(cd "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)" && \
ln -f -s -n Resources/include Headers && \
ln -f -s -n Resources/lib/libR.dylib R)
@if [ ! -e "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/PrivateHeaders" ]; then \
mkdir "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/PrivateHeaders"; fi
@(cd "$(R_FRAMEWORK_DIR)/Versions" && \
ln -f -s -n $(FW_VERSION) Current)
@(cd "$(R_FRAMEWORK_DIR)" && \
ln -f -s -n Versions/Current/PrivateHeaders PrivateHeaders&& \
ln -f -s -n Versions/Current/Headers Headers&& \
ln -f -s -n Versions/Current/R R && \
ln -f -s -n Versions/Current/Resources/lib Libraries && \
ln -f -s -n Versions/Current/Resources Resources)
@## the resulting libR will point dyld to the fat libR regardless of its origin
@(cd "$(R_FRAMEWORK_DIR)/Resources/lib" && \
install_name_tool -id "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/lib/libR.dylib" $(Rexeclibdir)/libR.dylib)
@( otool=otool ; if otool -D "$(Rexeclibdir)/libR.dylib"|grep 'not an object'>/dev/null; then otool=otool64; fi; \
for lib in Rlapack Rblas R; do \
if test -e "$(Rexeclibdir)/lib$${lib}.dylib"; then echo " lib$${lib}"; \
if test -e "$(Rexeclibdir)/lib$${lib}.dylib"; then $(ECHO) " lib$${lib}"; \
find "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/" -name '*.so' -or -name '*.dylib' | \
xargs -n 1 install_name_tool -change \
`$${otool} -L $(Rexeclibdir)/lib$${lib}.dylib |sed -n -e '2 s/.\(.*\) (compat.*/\1/p'` \
......@@ -250,28 +254,34 @@ install-R-framework:
done; \
fi; \
done)
@(cp -R $(srcdir)/src/include $(R_FRAMEWORK_DIR)/Versions/Current/PrivateHeaders && \
@(cp -R $(srcdir)/src/include/* $(R_FRAMEWORK_DIR)/Versions/Current/PrivateHeaders/ && \
cp src/include/config.h $(R_FRAMEWORK_DIR)/Versions/Current/PrivateHeaders/ && \
chmod a+r $(R_FRAMEWORK_DIR)/Versions/Current/PrivateHeaders/config.h; \
find $(R_FRAMEWORK_DIR)/Versions/Current/PrivateHeaders -name .svn | xargs rm -rf)
@(install_name_tool -change libR.dylib \
"$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/lib/libR.dylib" \
$(Rexecbindir2)/R)
@(if [ -n "${R_ARCH}" ]; then \
rm -rf $(R_FRAMEWORK_DIR)/Versions/Current/PrivateHeaders${R_ARCH} && \
mkdir $(R_FRAMEWORK_DIR)/Versions/Current/PrivateHeaders${R_ARCH} && \
cp src/include/config.h $(R_FRAMEWORK_DIR)/Versions/Current/PrivateHeaders${R_ARCH}/config.h; \
chmod a+r $(R_FRAMEWORK_DIR)/Versions/Current/PrivateHeaders${R_ARCH}/config.h; \
sed -e "s|R_ARCH=${R_ARCH}|R_ARCH=/\`arch\`|" "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/bin/R" \
> "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/bin/.tmp.R" && \
chmod a+x "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/bin/.tmp.R" && \
mv "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/bin/.tmp.R" "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/bin/R"; \
if [ "${R_ARCH}" != /ppc -a "${R_ARCH}" != /i386 -a "${R_ARCH}" != /ppc64 -a "${R_ARCH}" != /x86_64 ]; then \
echo "\
*** WARNING: The architecture name is incompatible with Apple's naming~ convention. This may prevent applications from using the R~ framework. Please use i386, x86_64, ppc or ppc64 as architecture~ names to allow universal builds."|sed 'y/~/\n/' >&2; \
if [ "${R_ARCH}" != /ppc -a "${R_ARCH}" != /i386 -a "${R_ARCH}" != /ppc64 -a "${R_ARCH}" != /x86_64 -a "${R_ARCH}" != /arm ]; then \
$(ECHO) "\
*** WARNING: The architecture name is incompatible with Apple's naming~ convention. This may prevent applications from using the R~ framework. Please use i386, x86_64, ppc, ppc64 or arm as architecture~ names to allow universal builds."|sed 'y/~/\n/' >&2; \
else \
for f in `ls "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Headers/${R_ARCH}/"*.h|xargs basename`; do \
echo "/* This is an automatically generated universal stub for architecture-dependent headers. */~#ifdef __i386__~#include <i386/$$f>~#else~#ifdef __ppc__~#include <ppc/$$f>~#else~#ifdef __ppc64__~#include <ppc64/$$f>~#else~#ifdef __x86_64__~#include <x86_64/$$f>~#else~#error Cannot determine the correct architecture. To force a certain configuration, include architecture-specific include path *before* general R headers path.~#endif~#endif~#endif~#endif" |sed -e 'y/~/\n/' > "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Headers/$$f"; \
for f in `ls "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Headers/${R_ARCH}/"*.h|xargs basename` config.h; do \
fn="Headers/$$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/' > "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/$$fn"; \
done; \
fi; \
fi )
@( rm -f "$(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/R" && \
ln -s bin/R "$(R_FRAMEWORK_DIR)/Versions/$(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/' > $(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/Info.plist)
@( $(ECHO) "<?xml version=\"1.0\" encoding=\"UTF-8\"?>~<!DOCTYPE plist PUBLIC \"-//Apple Computer//DTD PLIST 1.0//EN\" \"http://www.apple.com/DTDs/PropertyList-1.0.dtd\">~<plist version=\"1.0\">~<dict>~ <key>CFBundleIdentifier</key>~ <string>org.r-project.R-framework</string>~ <key>CFBundleInfoDictionaryVersion</key>~ <string>6.0</string>~ <key>CFBundleName</key>~ <string>R</string>~ <key>CFBundlePackageType</key>~ <string>FMWK</string>~ <key>CFBundleVersion</key>~ <string>$(VERSION)</string>~</dict>~</plist>" |sed -e 'y/~/\n/' > $(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/Info.plist)
TAGS:
This diff is collapsed.
......@@ -4585,42 +4585,42 @@ BUG FIXES
o try() could fail in BATCH use due to use of fflush(stdin).
Only seen on Solaris. (PR#1934)
o title(main=list("main")) printed garbage, as did similar calls
o title(main=list("main")) printed garbage, as did similar calls
using quote() instead of expression() for plotmath. (PR#1939)
o deparse() dropped parentheses in some case where they were
o deparse() dropped parentheses in some case where they were
needed. (PR#1119, 1737, 1928, at least)
o pdf(onefile = FALSE) never incremented the file number beyond
o pdf(onefile = FALSE) never incremented the file number beyond
two.
o On Unix, protect against broken pipes where popen calls succeed
o On Unix, protect against broken pipes where popen calls succeed
even though the command does not exist (and the glibc manual
says it should return NULL). (PR#1959)
o data.frame() was allowing explicit row.names with missing
o data.frame() was allowing explicit row.names with missing
values, but row names are required to be unique.
o as.character(expression) was silently truncating to 60
o as.character(expression) was silently truncating to 60
characters: the help page claimed 500 which is now true.
o as.hclust(x) now also works (as identity) for "hclust" objects.
o as.hclust(x) now also works (as identity) for "hclust" objects.
o NextMethod didn't work right in Ops.
o NextMethod didn't work right in Ops.
o dotchart() now obeys `xlim ='.
o dotchart() now obeys `xlim ='.
o t(x) behaves when x is a (multivariate) time series. (PR#1998)
o t(x) behaves when x is a (multivariate) time series. (PR#1998)
o parse(text=x) no longer parses from stdin if length(x) is zero
o parse(text=x) no longer parses from stdin if length(x) is zero
o binom.test() miscalculated p-value in some extreme cases
o binom.test() miscalculated p-value in some extreme cases
o get("print.ts")(1) would segfault. It's now just an error.
o get("print.ts")(1) would segfault. It's now just an error.
o cbind(NULL) {and similar} gave an error instead of NULL.
o cbind(NULL) {and similar} gave an error instead of NULL.
o the complex version of solve(a,b) now also works if b is a
o the complex version of solve(a,b) now also works if b is a
vector
......@@ -7518,10 +7518,10 @@ NEW FEATURES
o The L-BFGS-B method of optim() now support tracing, at several
levels of detail.
o options(check.bounds = TRUE) makes each vector extension
o options(check.bounds = TRUE) makes each vector extension
by sub-assignment ("x[.] <- .") produce a warning.
o options(width) now admits to a limit (previously 200, now
o options(width) now admits to a limit (previously 200, now
10000) and gives a more informative message if out of range
(as it does now for digits and expressions).
......
Revision: 44383
Last Changed Date: 2008-02-08
Revision: 45424
Last Changed Date: 2008-04-22
......@@ -207,7 +207,7 @@
## Browser default
## Default setting for the R_BROWSER env variable
## If unset configure searches in turn for (currently)
## firefox mozilla netscape galeon kfmclient opera gnome-moz-remote open
## firefox mozilla galeon kfmclient opera gnome-moz-remote open
## and uses the full path.
## R_BROWSER=