branch update

git-svn-id: https://svn.r-project.org/R/trunk@3076 00db46b3-68df-0310-9c12-caf00c1e9a41

COPYRIGHTS

@@ -16,6 +16,10 @@ afm/*
 
 	Copyright (c) 1984 Adobe Systems Incorporated.
 
+src/library/base/R/mosaicplot.R
+
+	Copyright (C) 1998 John W. Emerson
+
 src/library/base/R/aov.R
 src/library/base/R/biplot.R
 src/library/base/R/contr.poly.R

INSTALL

@@ -72,7 +72,7 @@ This will install to the following directories:
 
 	$prefix/bin		(some) executables
 	$prefix/man/man1	man pages
-	$prefix/lib/R		all the rest (libraries, online help
+	$prefix/share/R		all the rest (libraries, online help
 				system, ...)
 
 where prefix is determined during configuration (typically /usr/local)
@@ -93,6 +93,14 @@ and so on, as described further above.  This has the advantage of always
 keeping your source tree `clean'.
 
 
+USING MAKE
+
+To compile R, you currently most likely need GNU make.  (To be more
+precise, you need a version of make which accepts shell wildcards in
+dependencies.)  On Solaris 2.6 in particular, you need a version of
+GNU make different from 3.77 (the current one); 3.76.1 works fine.
+
+
 USING FORTRAN
 
 To compile R, you need a FORTRAN compiler or f2c, the FORTRAN-to-C
@@ -105,20 +113,6 @@ compiler is in a non-standard location, you should set the enviroment
 vaiable PATH accordingly before running configure.
 
 
-TWO-LEVEL MAKE
-
-If you don't need to supply any special arguments to "configure", you
-can actually build R simply by typing "make", which will automatically
-run "configure" if the configuration files are absent. Since the build
-process depends on the results of "configure", the top-level Makefile
-does little more than passing control to Makefile.2nd after ensuring
-that "configure" has been run.
-
-This has the curious, but harmless, consequence that "make distclean"
-and the like may run "configure" and remove the configuration files a
-moment later. This looks odd, but is fairly hard to avoid.
-
-
 NEW PLATFORMS (Standards Hah!)
 
 There are a number of sources of problems when installing R on a new

Makeconf.in

@@ -50,4 +50,4 @@ datadir = @datadir@
 libdir = @libdir@
 mandir = @mandir@
 
-rhome = @datadir@/R
+rhome = @libdir@/R

Makefile.in

@@ -26,19 +26,13 @@ Makefile:
 	cd $(top_builddir) \
 	  && CONFIG_FILES=$@ CONFIG_HEADERS= $(SHELL) ./config.status
 
-R: stamp-R
-stamp-R: $(top_builddir)/src/include/Platform.h \
-	  $(top_srcdir)/src/*/*.[chfy] \
-	  $(top_srcdir)/src/library/*/R/*.R \
-	  $(top_srcdir)/src/library/*/src/*.[chf]
-	@rm -f $@
+R: 
 	@for d in afm demos doc etc src; do \
-	  (cd $$d && $(MAKE) R); \
+	  (cd $${d} && $(MAKE) R) || exit 1; \
 	done
 	@if [ ! -f src/library/stamp-docs ]; then \
 	  echo "You should \`make docs' now ..."; \
 	fi
-	@touch $@
 
 $(top_builddir)/src/include/Platform.h: $(srcdir)/date-stamp
 	$(top_srcdir)/configure --srcdir $(top_srcdir)
@@ -49,26 +43,26 @@ FORCE:
 
 install: all installdirs
 	@for d in afm demos doc etc; do \
-	  (cd $$d && $(MAKE) $@); \
+	  (cd $${d} && $(MAKE) $@) || exit 1; \
 	done
 	@(cd $(srcdir); \
 	  for f in COPYING COPYRIGHTS MIRROR-SITES RESOURCES; do \
-	    $(INSTALL_DATA) $$f $(rhome); \
+	    $(INSTALL_DATA) $${f} $(rhome); \
 	  done)
 	@echo "Installing executables ..."
 	@$(INSTALL_PROGRAM) bin/R.binary $(rhome)/bin
 	@cat bin/R | sed "s@RHOME=.*@RHOME=$(rhome)@" > $(rhome)/bin/R
 	@cat bin/R | sed "s@RHOME=.*@RHOME=$(rhome)@" > $(bindir)/R
 	@chmod 755 $(bindir)/R $(rhome)/bin
 	@for f in `ls bin/* | grep -v '^R\|R.binary'`; do \
-	  $(INSTALL) $$f $(rhome)/bin; \
+	  $(INSTALL) $${f} $(rhome)/bin; \
 	done
 	@for f in Rd2txt Rdconv Rdindex Sd2Rd; do \
-	  $(INSTALL) bin/$$f $(bindir); \
+	  $(INSTALL) bin/$${f} $(bindir); \
 	done
 	@echo "Installing headers ..."
 	@for f in include/*.h; do \
-	  $(INSTALL_DATA) $$f $(rhome)/include; \
+	  $(INSTALL_DATA) $${f} $(rhome)/include; \
 	done
 	@echo "Installing library ..."
 	@cd library; $(TAR) cf - [a-z]* | (cd $(rhome)/library; tar xf -)
@@ -86,7 +80,7 @@ install-strip:
 uninstall:
 	@echo "Uninstalling library ..."
 	@(cd $(rhome)/library; \
-	  for p in base eda modreg mva stepfun; do rm -rf $$p; done)
+	  for p in base eda modreg mva stepfun; do rm -rf $${p}; done)
 	@echo "  Rebuilding help index ..."
 	@(cd $(rhome)/library; cat */TITLE > LibIndex 2> /dev/null)
 	@echo "  Rebuilding HTML index ..."
@@ -96,21 +90,21 @@ uninstall:
 	@echo "Uninstalling executables ..."
 	@rm -rf $(rhome)/bin
 	@for f in R Rd2txt Rdconv Rdindex Sd2Rd; do \
-	  rm -f $(bindir)/$$f; \
+	  rm -f $(bindir)/$${f}; \
 	done
 	@for f in COPYING COPYRIGHTS MIRROR-SITES RESOURCES; do \
-	  rm -f $(rhome)/$$f; \
+	  rm -f $(rhome)/$${f}; \
 	done
 	@for d in afm demos doc etc; do \
-	  (cd $$d && $(MAKE) $@); \
+	  (cd $${d} && $(MAKE) $@); \
 	done
 
 mostlyclean: clean
 clean:
 	@for d in $(SUBDIRS); do \
-	  (cd $$d && $(MAKE) $@); \
+	  (cd $${d} && $(MAKE) $@); \
 	done
-	@rm -f stamp-R
+
 distclean: clean
 	@for d in $(SUBDIRS); do \
 	  (cd $${d} && $(MAKE) $@); \

NEWS

@@ -1,3 +1,89 @@
+		CHANGES IN R VERSION 0.63.1
+
+NEW FEATURES
+
+    o   new function mosaicplot().
+
+    o	xy.coords(.) has a  "recycle = FALSE" argument,	 used in text().
+
+    o	RNGtype() allows to choose different Random Number Generators.
+		__EXPERIMENTAL__
+
+    o	print.default(.) now also works with a `right = TRUE' argument.
+	{{ print.matrix(.) is bound to become deprecated... }}
+
+    o	new help page `Memory' on the usage of command line options
+	--vsize and --nsize. Error message if R runs out of memory
+	points to help(Memory).
+
+    o	rowsum() and improved na.omit() added from survival4
+
+    o	backsolve(.) has new arguments "upper.tri = TRUE,  transpose = FALSE"
+
+    o	hist() has new "right = TRUE" argument;	 
+	"right = FALSE" gives  [a,b) intervals
+
+    o	help() has "htmlhelp" argument, allowing to suppress htmlhelp after
+	help.start().  This is desired for ESS.
+
+    o   quantile(.) has an "names = TRUE" argument for speed.
+	It is much better documented now.
+
+
+BUG FIXES
+
+    o	build-help --dosnames should now also work for text help,
+	latex and examples.
+
+    o	seq() should work better now (fuzz-factor 1e-7 inserted)
+
+    o	multiple arguments to return caused value to be a pairlist
+
+    o	data.frame choked on long names from deparse()
+
+    o	data.edit now works (dataedit doesn't need pairlist()s anymore)
+
+    o	as.pairlist(NULL) is ok
+
+    o	ts(1:5, start=2, end=4) now work.  Further plot(ts(..), ts(..))
+
+    o	eigen() returns $vectors in any case [S compat].
+
+    o	apply(cbind(1,1:9, 2, quantile) doesn't drop quantile names anymore
+
+    o	array(1, dim=(1:3)[c(F,F,F)]) is now valid == array(1,NULL) == c(1);
+	the same for array(a,d, list())
+
+    o	fix problem with step() and offsets
+
+    o	drop attributes on matrix subsetting
+
+    o	kappa(.) now works [dtrco now in load table (ROUTINES)].
+
+    o	pmin() and pmax() now preserve attributes.
+
+    o	handle null models arising in drop1(), step, etc.
+
+    o	partial matching problem with $ indexing
+
+    o	matplot(.) works with lwd (vectors)
+
+    o	par("cex.axis") now has the desired effect...
+
+    o	which(.) now omits NAs in its argument.
+
+    o	rbind.data.frame caused character-to-factor coercion a bit too often
+
+    o	couple of messups in dotplot
+
+    o	z[[1]] <- ~x probl fixed as suggested by J.Lindsey 
+
+    o   do_modelframe could lose contrast attributes
+
+    o	"make check" needed standardisation of locale
+
+    o	unlist(...,recursive=F) got names wrong
+
 		CHANGES IN R VERSION 0.63
 
 NEW FEATURES
@@ -8,7 +94,7 @@ NEW FEATURES
     o	new  .Platform	variable  for better modularizing
 	platform dependence. __This_is_"beta"_and_bound_to_be_changed___
 
-    o	new arguments to colnames(..) and 
+    o	new arguments to colnames(..) and
 	rownames(x, do.NULL = TRUE, prefix = "row").
 			   _
     o	par(bty = "]") for _| box(.) in plots.
@@ -111,12 +197,12 @@ NEW FEATURES
 	and is subject to internal and interface changes.
 
     o	gctorture() for torturing the garbage collector to reveal
-	memory protection bugs. (Call GC on every memory allocation). 
+	memory protection bugs. (Call GC on every memory allocation).
 
-    o	B. Ripley's aov code (and more) has been added. This includes: 
+    o	B. Ripley's aov code (and more) has been added. This includes:
 
 	- aov() now handles models with Error terms, multiple
-	  responses. 
+	  responses.
 
 	- proj(), model.tables(), se.contrast(), replications(),
 	  eff.aovlist() are implemented for aov fits, and where
@@ -129,20 +215,20 @@ NEW FEATURES
 
 	- summary() and deviance() -- mlm methods.
 
-	- kappa()  for estimating condition numbers) 
+	- kappa()  for estimating condition numbers)
 
 	- labels() to find a suitable set of labels from an object
 
 	- C() for setting the contrasts of a factor
 
 	- anova(), plot(), summary() and deviance() methods for mlm fits
 
-    o	eval() semantics changed when envir= is a list. A 3rd argument is 
+    o	eval() semantics changed when envir= is a list. A 3rd argument is
 	now allowed, specifying the enclosure (i.e. where R looks for
-	variables *not* found in envir=) it defaults to the calling 
+	variables *not* found in envir=) it defaults to the calling
 	environment (was .GlobalEnv). Note that when used inside a function,
-	it is often desirable to set the enclosure to the parent 
-	environment instead. [ eval(e, data, sys.frame(sys.parent())) ] 
+	it is often desirable to set the enclosure to the parent
+	environment instead. [ eval(e, data, sys.frame(sys.parent())) ]
 
 
 BUG FIXES

PLATFORMS

@@ -17,7 +17,7 @@ our installation procedures.
 	sparc-sun-solaris2.5.1		gcc / g77
 		"			gcc / f77
 		"			cc  / f77
-
+	sparc-sun-solaris2.6		gcc / f77 
 
 	OLD (pre 0.62 systems)