Update to R-1.0.1. Move R library tree to ${PREFIX}/lib (a la perl5)

since it contains loadable shared object files that are platform-specific.
Lots of bug-fixes and additions ... it's getting closer to a usable
replacement for S-PLUS.

10 files changed, 3092 insertions, 2943 deletions

diff --git a/math/R/Makefile b/math/R/Makefile
index 29232303869..d9ec4391f80 100644
--- a/math/R/Makefile
+++ b/math/R/Makefile
@@ -1,47 +1,53 @@
-# $NetBSD: Makefile,v 1.11 2000/01/12 22:05:30 rh Exp $
+# $NetBSD: Makefile,v 1.12 2000/04/19 15:30:05 jlam Exp $
 #
 
-DISTNAME=	R-0.90.1
-CATEGORIES=	math
-MASTER_SITES=	http://cran.r-project.org/src/base/ \
-		ftp://cran.r-project.org/pub/R/src/base/ \
-		http://lib.stat.cmu.edu/R/CRAN/src/base/ \
-		ftp://ftp.biostat.washington.edu/mirrors/R/CRAN/src/base/ \
-		http://cran.stat.wisc.edu/src/base/ \
-		http://SunSITE.auc.dk/R/src/base/ \
-		http://www.stat.unipg.it/pub/stat/statlib/R/CRAN/src/base/ \
-		ftp://ftp.u-aizu.ac.jp/pub/lang/R/CRAN/src/base/ \
-		ftp://dola.snu.ac.kr/pub/R/CRAN/src/base/ \
-		http://stat.ethz.ch/CRAN/src/base/ \
-		http://www.stats.bris.ac.uk/R/src/base/ \
-		http://cran.at.r-project.org/src/base/ \
-		ftp://cran.at.r-project.org/pub/R/src/base/
-EXTRACT_SUFX=	.tgz
-
-MAINTAINER=	jlam@netbsd.org
-HOMEPAGE=	http://cran.r-project.org/
-
-DEPENDS+=	readline-4.0:../../devel/readline
-
-USE_FORTRAN=	yes
-USE_X11=	yes
-USE_PERL5=	yes
-USE_GMAKE=	yes
-GNU_CONFIGURE=	yes
-CONFIGURE_ARGS+=--enable-readline --with-x
+DISTNAME=		R-1.0.1
+CATEGORIES=		math
+MASTER_SITES=		http://cran.r-project.org/src/base/ \
+			ftp://cran.r-project.org/pub/R/src/base/ \
+			http://lib.stat.cmu.edu/R/CRAN/src/base/ \
+			http://cran.stat.wisc.edu/src/base/ \
+			http://SunSITE.auc.dk/R/src/base/ \
+			ftp://ftp.u-aizu.ac.jp/pub/lang/R/CRAN/src/base/ \
+			ftp://dola.snu.ac.kr/pub/R/CRAN/src/base/ \
+			http://stat.ethz.ch/CRAN/src/base/ \
+			http://www.stats.bris.ac.uk/R/src/base/ \
+			http://cran.at.r-project.org/src/base/ \
+			ftp://cran.at.r-project.org/pub/R/src/base/
+EXTRACT_SUFX=		.tgz
+
+MAINTAINER=		jlam@netbsd.org
+HOMEPAGE=		http://cran.r-project.org/
+
+DEPENDS+=		readline>=4.0:../../devel/readline
+
+USE_FORTRAN=		# defined
+USE_X11=		# defined
+USE_PERL5=		# defined
+USE_GMAKE=		# defined
+
+GNU_CONFIGURE=		# defined
+CONFIGURE_ARGS+=	--enable-readline --with-x
+CONFIGURE_ARGS+=	--without-gnome --without-libmoto
+CONFIGURE_ARGS+=	--without-blas --without-blas-risc
+CONFIGURE_ARGS+=	--without-dxml
+CONFIGURE_ENV+=		CPPFLAGS="${CPPFLAGS}"
+CONFIGURE_ENV+=		MAKE="${LOCALBASE}/bin/gmake"
+CPPFLAGS+=		-I${LOCALBASE}/include		# readline/readline.h
 
 .include "../../mk/bsd.prefs.mk"
 
 # R_PAPERSIZE can be: A4, Letter, Legal, Executive
 #
 .if defined(PAPERSIZE)
-R_PAPERSIZE?=	${PAPERSIZE}
+R_PAPERSIZE?=		${PAPERSIZE}
 .else
-R_PAPERSIZE?=	A4
+R_PAPERSIZE?=		A4
 .endif
 .if (${R_PAPERSIZE} == "Letterdj")
-R_PAPERSIZE=	Letter
+R_PAPERSIZE=		Letter
 .endif
+CONFIGURE_ENV+=		R_PAPERSIZE="${R_PAPERSIZE}"
 
 .if (${OPSYS} == "SunOS")
 BSD_INSTALL?=	/usr/ucb/install
@@ -51,12 +57,10 @@ BSD_INSTALL?=	/usr/bin/install
 INSTALL_OWN_SCRIPT=	${BSD_INSTALL} ${COPY} -o ${BINOWN} -g ${BINGRP} -m ${BINMODE}
 INSTALL_SCRIPT=		${BSD_INSTALL} ${COPY} -m ${BINMODE}
 INSTALL_DATA=		${BSD_INSTALL} ${COPY} -m 644
-LDFLAGS+=		-L${LOCALBASE}/lib	# for -lreadline
-CONFIGURE_ENV+=		CPPFLAGS="-I${LOCALBASE}/include" \
-			R_PAPERSIZE="${R_PAPERSIZE}"
+
 MAKE_ENV+=		INSTALL_OWN_SCRIPT="${INSTALL_OWN_SCRIPT}"
 
 post-install:
-	${CHOWN} -R ${SHAREOWN}:${SHAREGRP} ${PREFIX}/share/R
+	${CHOWN} -R ${SHAREOWN}:${SHAREGRP} ${PREFIX}/lib/R
 
 .include "../../mk/bsd.pkg.mk"
diff --git a/math/R/files/md5 b/math/R/files/md5
index 538804c453b..609a22d6ae0 100644
--- a/math/R/files/md5
+++ b/math/R/files/md5
@@ -1,3 +1,3 @@
-$NetBSD: md5,v 1.5 2000/01/12 22:05:32 rh Exp $
+$NetBSD: md5,v 1.6 2000/04/19 15:30:06 jlam Exp $
 
-MD5 (R-0.90.1.tgz) = 5ff7ed7ac53b7e968a373c9cf3099443
+MD5 (R-1.0.1.tgz) = f8cf4d9ef7324b0718456f5f8a21adad
diff --git a/math/R/files/patch-sum b/math/R/files/patch-sum
index 2d59e405484..8c710024197 100644
--- a/math/R/files/patch-sum
+++ b/math/R/files/patch-sum
@@ -1,8 +1,6 @@
-$NetBSD: patch-sum,v 1.4 2000/02/13 13:30:11 dmcmahill Exp $
+$NetBSD: patch-sum,v 1.5 2000/04/19 15:30:06 jlam Exp $
 
-MD5 (patch-aa) = f11a1756dbe1f0d3499cce6919f5fce5
-MD5 (patch-ab) = 6f9dbcb59868c9e42b60de2aa2831376
-MD5 (patch-ae) = 97a850f5efd0f91571361750e69b35eb
-MD5 (patch-af) = 67bcec4540b994104ba99b35667f6d10
-MD5 (patch-ag) = 62f3628549a1e9a4c1440e05548f2cb1
-MD5 (patch-ah) = 37e5d8f9aa3a296a62150a8269415807
+MD5 (patch-aa) = fb1673fe6c402a5ea29fa83e65eb2e82
+MD5 (patch-ab) = 9eb6830782e45b3e9bf243abc234ec53
+MD5 (patch-ae) = 376df20b745d8c9edf0a193a985a6865
+MD5 (patch-ag) = 0a7e7612fcf4bc72c459adaa57aff329
diff --git a/math/R/patches/patch-aa b/math/R/patches/patch-aa
index 431c0bfa1bb..efb51ae9550 100644
--- a/math/R/patches/patch-aa
+++ b/math/R/patches/patch-aa
@@ -1,8 +1,8 @@
-$NetBSD: patch-aa,v 1.2 1999/05/25 23:45:06 jlam Exp $
+$NetBSD: patch-aa,v 1.3 2000/04/19 15:30:06 jlam Exp $
 
---- Makeconf.in.orig	Tue Feb  2 19:16:51 1999
-+++ Makeconf.in	Tue May 25 02:52:48 1999
-@@ -20,6 +20,7 @@
+--- Makeconf.in.orig	Sat Jan 22 15:10:00 2000
++++ Makeconf.in	Mon Apr 17 16:04:58 2000
+@@ -23,6 +23,7 @@
  INSTALL = @INSTALL@
  INSTALL_DATA = @INSTALL_DATA@
  INSTALL_PROGRAM = @INSTALL_PROGRAM@
@@ -10,9 +10,3 @@ $NetBSD: patch-aa,v 1.2 1999/05/25 23:45:06 jlam Exp $
  INSTALL_DIR = ${INSTALL} -d
  LATEX = @LATEX@
  LDCMD = @LDCMD@
-@@ -53,4 +54,4 @@
- libdir = @libdir@
- mandir = @mandir@
- 
--rhome = @libdir@/R
-+rhome = @datadir@/R
diff --git a/math/R/patches/patch-ab b/math/R/patches/patch-ab
index 71ce50ab165..2ad9e22bcaf 100644
--- a/math/R/patches/patch-ab
+++ b/math/R/patches/patch-ab
@@ -1,22 +1,21 @@
-$NetBSD: patch-ab,v 1.5 2000/02/13 13:30:12 dmcmahill Exp $
+$NetBSD: patch-ab,v 1.6 2000/04/19 15:30:06 jlam Exp $
 
---- configure.orig	Wed Dec 15 07:29:04 1999
-+++ configure	Sun Feb 13 00:16:46 2000
-@@ -5378,8 +5378,9 @@
-   *netbsd*)
-     if ${CPP} - -dM < /dev/null | grep -q __ELF__; then
--      dllflags="-export-dynamic"
-+      dllflags="${LDFLAGS} -export-dynamic"
-       shlibldflags="-shared"
-     else
--      shlibldflags="-Bshareable"
-+      dllflags="${LDFLAGS}"
-+      shlibldflags="-shared"
-     fi
-     ;;
-@@ -6549,4 +6550,5 @@
- s%@INSTALL_PROGRAM@%$INSTALL_PROGRAM%g
- s%@INSTALL_DATA@%$INSTALL_DATA%g
-+s%@INSTALL_SCRIPT@%$INSTALL_SCRIPT%g
- s%@LN_S@%$LN_S%g
- s%@RANLIB@%$RANLIB%g
+--- configure.orig	Fri Apr 14 04:44:15 2000
++++ configure	Mon Apr 17 16:32:22 2000
+@@ -2676,6 +2676,7 @@
+ LIBS="$ac_save_LIBS"
+ 
+ fi
++if false; then
+ if eval "test \"`echo '$ac_cv_lib_'$ac_lib_var`\" = yes"; then
+   echo "$ac_t""yes" 1>&6
+     ac_tr_lib=HAVE_LIB`echo ncurses | sed -e 's/[^a-zA-Z0-9_]/_/g' \
+@@ -2685,7 +2686,7 @@
+ EOF
+ 
+   LIBS="-lncurses $LIBS"
+-
++fi
+ else
+   echo "$ac_t""no" 1>&6
+ echo $ac_n "checking for main in -ltermcap""... $ac_c" 1>&6
diff --git a/math/R/patches/patch-ae b/math/R/patches/patch-ae
index 06167e144b7..e9a3585b82a 100644
--- a/math/R/patches/patch-ae
+++ b/math/R/patches/patch-ae
@@ -1,26 +1,13 @@
-$NetBSD: patch-ae,v 1.3 2000/01/12 22:05:33 rh Exp $
+$NetBSD: patch-ae,v 1.4 2000/04/19 15:30:06 jlam Exp $
 
---- Makefile.in.orig	Wed Jan 12 20:01:29 2000
-+++ Makefile.in	Wed Jan 12 20:07:14 2000
-@@ -51,7 +51,7 @@
- 	    $(INSTALL_DATA) $${f} $(rhome); \
- 	  done)
- 	@echo "Installing executables ..."
--	@$(INSTALL_PROGRAM) bin/R.X11 $(rhome)/bin
-+	@$(INSTALL_PROGRAM) bin/R.X11 $(bindir)
- 	@if test -x bin/R.gnome; then \
- 	  $(INSTALL_PROGRAM) bin/R.gnome $(rhome)/bin; \
- 	fi
-@@ -61,10 +61,10 @@
+--- Makefile.in.orig	Mon Feb 21 02:03:26 2000
++++ Makefile.in	Mon Apr 17 16:11:47 2000
+@@ -74,7 +74,7 @@
  	@for f in `ls bin/* | grep -v '^bin/R\**$$' \
-                             | grep -v '^bin/R.X11\**$$' \
-                             | grep -v '^bin/R.gnome\**$$'`; do \
+ 	                    | grep -v '^bin/R.X11\**$$' \
+ 	                    | grep -v '^bin/R.GNOME\**$$'`; do \
 -	  $(INSTALL) $${f} $(rhome)/bin; \
 +	  $(INSTALL_SCRIPT) $${f} $(rhome)/bin; \
  	done
- 	@for f in Rd2txt Rdconv Rdindex Sd2Rd; do \
--	  $(INSTALL) bin/$${f} $(bindir); \
-+	  $(INSTALL_OWN_SCRIPT) bin/$${f} $(bindir); \
- 	done
- 	@echo "Installing headers ..."
+ 	@echo "installing headers ..."
  	@for f in include/*.h; do \
diff --git a/math/R/patches/patch-af b/math/R/patches/patch-af
deleted file mode 100644
index 9c029334f2c..00000000000
--- a/math/R/patches/patch-af
+++ /dev/null
@@ -1,21 +0,0 @@
-$NetBSD: patch-af,v 1.3 2000/01/12 22:05:33 rh Exp $
-
---- src/scripts/R.sh.in.orig	Wed Jan 12 20:12:45 2000
-+++ src/scripts/R.sh.in	Wed Jan 12 20:15:02 2000
-@@ -114,14 +114,14 @@
- fi
- 
- if test -z "${DBG}"; then
--  exec ${R_HOME}/bin/${R_BINARY} @R_BATCHSAVE@ ${ARGS}
-+  exec @prefix@/bin/${R_BINARY} @R_BATCHSAVE@ ${ARGS}
- else
-   if test -n "${ARGS}"; then
-     echo "*** Further command line arguments (\`${ARGS}') disregarded"
-     echo "*** (maybe use \`run ${ARGS}' from *inside* ${DBG})"
-     echo ""
-   fi
--  exec ${DBG} ${R_HOME}/bin/${R_BINARY}
-+  exec ${DBG} @prefix@/bin/${R_BINARY}
- fi
- 
- ### Local Variables: ***
diff --git a/math/R/patches/patch-ag b/math/R/patches/patch-ag
index b497b64ddbd..dfbf3367a87 100644
--- a/math/R/patches/patch-ag
+++ b/math/R/patches/patch-ag
@@ -1,7 +1,7 @@
-$NetBSD: patch-ag,v 1.2 2000/01/12 22:05:33 rh Exp $
+$NetBSD: patch-ag,v 1.3 2000/04/19 15:30:07 jlam Exp $
 
---- src/scripts/Makefile.in.orig	Wed Jan 12 20:16:55 2000
-+++ src/scripts/Makefile.in	Wed Jan 12 20:17:56 2000
+--- src/scripts/Makefile.in.orig	Mon Feb 21 05:49:10 2000
++++ src/scripts/Makefile.in	Mon Apr 17 16:13:11 2000
 @@ -38,10 +38,10 @@
  	  > $(top_builddir)/bin/R
  	@chmod +x $(top_builddir)/bin/R
diff --git a/math/R/patches/patch-ah b/math/R/patches/patch-ah
deleted file mode 100644
index 207f5e4b2d5..00000000000
--- a/math/R/patches/patch-ah
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-ah,v 1.1 1999/05/25 23:51:12 jlam Exp $
-
---- doc/Makefile.in.orig	Tue Mar 30 04:29:11 1999
-+++ doc/Makefile.in	Tue May 25 02:52:08 1999
-@@ -33,7 +33,7 @@
- 	fi
- 
- install: installdirs install-html install-man
--	@$(INSTALL) keyword-test $(rhome)/doc
-+	@$(INSTALL_SCRIPT) keyword-test $(rhome)/doc
- 	@$(INSTALL_DATA) $(srcdir)/KEYWORDS $(rhome)/doc
- 	@(cd manual && $(MAKE) $@)
- installdirs:
diff --git a/math/R/pkg/PLIST b/math/R/pkg/PLIST
index 06bc66db66a..0fa15f0939c 100644
--- a/math/R/pkg/PLIST
+++ b/math/R/pkg/PLIST
@@ -1,2811 +1,3012 @@
-@comment $NetBSD: PLIST,v 1.5 2000/01/12 22:05:33 rh Exp $
+@comment $NetBSD: PLIST,v 1.6 2000/04/19 15:30:07 jlam Exp $
 bin/R
-bin/R.X11
-bin/Rd2txt
-bin/Rdconv
-bin/Rdindex
-bin/Sd2Rd
-man/man1/R.1
-man/man1/Rdconv.1
-man/man1/Rd2txt.1
-man/man1/Sd2Rd.1
-man/man1/Rdindex.1
-share/R/bin/R
-share/R/bin/BATCH
-share/R/bin/COMPILE
-share/R/bin/INSTALL
-share/R/bin/REMOVE
-share/R/bin/Rd2contents
-share/R/bin/Rd2dvi
-share/R/bin/Rd2txt
-share/R/bin/Rdconv
-share/R/bin/Rdindex
-share/R/bin/Rman2Rd
-share/R/bin/SHLIB
-share/R/bin/Sd2Rd
-share/R/bin/build-help
-share/R/bin/check
-share/R/bin/filename
-share/R/bin/fwf2table
-share/R/bin/help
-share/R/bin/help.links
-share/R/bin/help.pretty
-share/R/bin/html2dos
-share/R/bin/massage-Examples
-share/R/bin/pager
-share/R/include/Applic.h
-share/R/include/Arith.h
-share/R/include/Blas.h
-share/R/include/Complex.h
-share/R/include/Error.h
-share/R/include/Errormsg.h
-share/R/include/Fortran.h
-share/R/include/Linpack.h
-share/R/include/Mathlib.h
-share/R/include/Memory.h
-share/R/include/PrtUtil.h
-share/R/include/Random.h
-share/R/include/Rconfig.h
-share/R/include/Rdefines.h
-share/R/include/Rinternals.h
-share/R/include/Rversion.h
-share/R/include/S.h
-share/R/include/S_compat.h
-share/R/include/Utils.h
-share/R/include/f2c.h
-share/R/library/nls/help/sortedXyData
-share/R/library/nls/help/00Titles
-share/R/library/nls/help/BOD
-share/R/library/nls/help/NLSstAsymptotic
-share/R/library/nls/help/NLSstClosestX
-share/R/library/nls/help/NLSstLfAsymptote
-share/R/library/nls/help/NLSstRtAsymptote
-share/R/library/nls/help/SSasymp
-share/R/library/nls/help/SSasympOff
-share/R/library/nls/help/SSasympOrig
-share/R/library/nls/help/SSbiexp
-share/R/library/nls/help/SSfol
-share/R/library/nls/help/SSfpl
-share/R/library/nls/help/SSlogis
-share/R/library/nls/help/SSmicmen
-share/R/library/nls/help/asOneSidedFormula
-share/R/library/nls/help/clearNames
-share/R/library/nls/help/formula.nls
-share/R/library/nls/help/getInitial
-share/R/library/nls/help/logLik
-share/R/library/nls/help/nls
-share/R/library/nls/help/nls.control
-share/R/library/nls/help/nlsModel
-share/R/library/nls/help/plot.profile.nls
-share/R/library/nls/help/predict.nls
-share/R/library/nls/help/profile.nls
-share/R/library/nls/help/profiler
-share/R/library/nls/help/profiler.nls
-share/R/library/nls/help/selfStart
-share/R/library/nls/help/selfStart.default
-share/R/library/nls/help/selfStart.formula
-share/R/library/nls/help/setNames
-share/R/library/nls/help/AnIndex
-share/R/library/nls/R-ex/sortedXyData.R
-share/R/library/nls/R-ex/NLSstAsymptotic.R
-share/R/library/nls/R-ex/NLSstClosestX.R
-share/R/library/nls/R-ex/NLSstLfAsymptote.R
-share/R/library/nls/R-ex/NLSstRtAsymptote.R
-share/R/library/nls/R-ex/SSasymp.R
-share/R/library/nls/R-ex/SSasympOff.R
-share/R/library/nls/R-ex/SSasympOrig.R
-share/R/library/nls/R-ex/SSbiexp.R
-share/R/library/nls/R-ex/SSfol.R
-share/R/library/nls/R-ex/SSfpl.R
-share/R/library/nls/R-ex/SSlogis.R
-share/R/library/nls/R-ex/SSmicmen.R
-share/R/library/nls/R-ex/asOneSidedFormula.R
-share/R/library/nls/R-ex/clearNames.R
-share/R/library/nls/R-ex/formula.nls.R
-share/R/library/nls/R-ex/getInitial.R
-share/R/library/nls/R-ex/logLik.R
-share/R/library/nls/R-ex/nls.R
-share/R/library/nls/R-ex/nls.control.R
-share/R/library/nls/R-ex/nlsModel.R
-share/R/library/nls/R-ex/BOD.R
-share/R/library/nls/R-ex/predict.nls.R
-share/R/library/nls/R-ex/plot.profile.nls.R
-share/R/library/nls/R-ex/profile.nls.R
-share/R/library/nls/R-ex/profiler.R
-share/R/library/nls/R-ex/profiler.nls.R
-share/R/library/nls/R-ex/selfStart.R
-share/R/library/nls/R-ex/selfStart.default.R
-share/R/library/nls/R-ex/selfStart.formula.R
-share/R/library/nls/R-ex/setNames.R
-share/R/library/nls/latex/sortedXyData.tex
-share/R/library/nls/latex/NLSstAsymptotic.tex
-share/R/library/nls/latex/NLSstClosestX.tex
-share/R/library/nls/latex/NLSstLfAsymptote.tex
-share/R/library/nls/latex/NLSstRtAsymptote.tex
-share/R/library/nls/latex/SSasymp.tex
-share/R/library/nls/latex/SSasympOff.tex
-share/R/library/nls/latex/SSasympOrig.tex
-share/R/library/nls/latex/SSbiexp.tex
-share/R/library/nls/latex/SSfol.tex
-share/R/library/nls/latex/SSfpl.tex
-share/R/library/nls/latex/SSlogis.tex
-share/R/library/nls/latex/SSmicmen.tex
-share/R/library/nls/latex/asOneSidedFormula.tex
-share/R/library/nls/latex/clearNames.tex
-share/R/library/nls/latex/formula.nls.tex
-share/R/library/nls/latex/getInitial.tex
-share/R/library/nls/latex/logLik.tex
-share/R/library/nls/latex/nls.tex
-share/R/library/nls/latex/nls.control.tex
-share/R/library/nls/latex/nlsModel.tex
-share/R/library/nls/latex/plot.profile.nls.tex
-share/R/library/nls/latex/predict.nls.tex
-share/R/library/nls/latex/profile.nls.tex
-share/R/library/nls/latex/profiler.tex
-share/R/library/nls/latex/profiler.nls.tex
-share/R/library/nls/latex/selfStart.tex
-share/R/library/nls/latex/selfStart.default.tex
-share/R/library/nls/latex/selfStart.formula.tex
-share/R/library/nls/latex/setNames.tex
-share/R/library/nls/latex/BOD.tex
-share/R/library/nls/html/sortedXyData.html
-share/R/library/nls/html/BOD.html
-share/R/library/nls/html/NLSstAsymptotic.html
-share/R/library/nls/html/NLSstClosestX.html
-share/R/library/nls/html/NLSstLfAsymptote.html
-share/R/library/nls/html/NLSstRtAsymptote.html
-share/R/library/nls/html/SSasymp.html
-share/R/library/nls/html/SSasympOff.html
-share/R/library/nls/html/SSasympOrig.html
-share/R/library/nls/html/SSbiexp.html
-share/R/library/nls/html/SSfol.html
-share/R/library/nls/html/SSfpl.html
-share/R/library/nls/html/SSlogis.html
-share/R/library/nls/html/SSmicmen.html
-share/R/library/nls/html/asOneSidedFormula.html
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