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Date:      Thu, 4 Jun 2009 10:54:38 GMT
From:      bf <bf2006a@yahoo.com>
To:        freebsd-gnats-submit@FreeBSD.org
Subject:   ports/135251: [PATCH]math/R : update to 2.9.0, miscellaneous fixes
Message-ID:  <200906041054.n54Asct5050843@www.freebsd.org>
Resent-Message-ID: <200906041100.n54B0BYk036771@freefall.freebsd.org>

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>Number:         135251
>Category:       ports
>Synopsis:       [PATCH]math/R : update to 2.9.0, miscellaneous fixes
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          sw-bug
>Submitter-Id:   current-users
>Arrival-Date:   Thu Jun 04 11:00:11 UTC 2009
>Closed-Date:
>Last-Modified:
>Originator:     bf
>Release:        8-CURRENT amd64
>Organization:
-
>Environment:
>Description:
Update to 2.9.0.  Add ICU,THREADS options.  Sort related options and option
handling. Fix WITHOUT_NLS. Fix plist for WITH_DVI_MANUALS.  Partially fix
NOPORTDOCS. Fix build when a threaded Tk is used. Switch to USE_TK.  More
cleanup to follow later.

Prodded by: Wen Heping (who also submitted a patch, independently)
>How-To-Repeat:

>Fix:


Patch attached with submission follows:

diff -ruN R.orig/Makefile R/Makefile
--- R.orig/Makefile	2009-01-22 05:56:59.000000000 -0500
+++ R/Makefile	2009-06-04 06:15:05.000000000 -0400
@@ -7,8 +7,7 @@
 #
 
 PORTNAME=	R
-PORTVERSION=	2.8.1
-PORTREVISION=	1
+PORTVERSION=	2.9.0
 CATEGORIES=	math lang
 MASTER_SITES=	http://cran.r-project.org/src/base/R-2/ \
 		ftp://cran.r-project.org/pub/R/src/base/R-2/ \
@@ -32,17 +31,20 @@
 MAINTAINER=	bf2006a@yahoo.com
 COMMENT=	A language for statistical computing and graphics
 
-OPTIONS=	ATLAS        "Use ATLAS instead of BLAS/LAPACK"           off \
-		TCLTK        "Use Tcl/Tk (for the tcltk package)"         on  \
-		JPEG         "Enable the jpeg() graphics device"          on  \
-		PNG          "Enable the png() graphics device"           on  \
-		X11          "Enable the X11() graphics device"           on  \
-		GHOSTSCRIPT  "Enable the [dev2]bitmap() graphics devices" on  \
-		PCRE_PORT    "Use PCRE port instead of bundled source"    on  \
-		DVI_MANUALS  "Install DVI manuals (requires TeX)"         off \
-		PDF_MANUALS  "Install PDF manuals (requires TeX)"         off \
-		INFO_MANUALS "Install GNU info manuals"                   on  \
-		LETTER_PAPER "Use US Letter paper"                        off
+OPTIONS=	ATLAS	"Use ATLAS instead of BLAS/LAPACK" off \
+		GHOSTSCRIPT  "Enable the [dev2]bitmap() graphics devices" on \
+		ICU		"Improve collation in multibyte locales with ICU" on \
+		JPEG         "Enable the jpeg() graphics device" on \
+		LETTER_PAPER	"Use US Letter paper" off \
+		NLS		"Build with NLS support" on \
+		PCRE_PORT	"Use PCRE port instead of bundled source" on \
+		PNG	"Enable the png() graphics device" on \
+		TCLTK	"Use Tcl/Tk (for the tcltk package)" on \
+		THREADS "Build a multithreaded R" on \
+		X11	"Enable the X11() graphics device" on \
+		DVI_MANUALS  "Install DVI manuals (requires TeX)" off \
+		INFO_MANUALS "Install GNU info manuals" on \
+		PDF_MANUALS	"Install PDF manuals (requires TeX)" off
 
 MAN1=		R.1 Rscript.1
 
@@ -54,7 +56,6 @@
 GNU_CONFIGURE=	yes
 USE_ICONV=	yes
 USE_PERL5=	yes
-USE_GETTEXT=	yes
 
 CONFIGURE_ENV=	INSTALL_DATA="${INSTALL} ${COPY} ${_SHROWNGRP} -m 644"
 CONFIGURE_ARGS=	--enable-R-shlib --with-system-bzlib --with-system-zlib \
@@ -62,14 +63,6 @@
 
 .include <bsd.port.pre.mk>
 
-.ifndef WITHOUT_NLS
-USE_GETTEXT=	yes
-PLIST_SUB+=	NLS=""
-.else
-CONFIGURE_ARGS+=--disable-nls
-PLIST_SUB+=	NLS="@comment "
-.endif
-
 .if defined(WITH_ATLAS)
 LIB_DEPENDS+=	atlas.2:${PORTSDIR}/math/atlas
 CONFIGURE_ARGS+=--with-blas="-lf77blas -latlas"
@@ -83,14 +76,15 @@
 CONFIGURE_ARGS+=--with-blas="-lblas" --with-lapack="-llapack -lblas"
 .endif
 
-.if defined(WITHOUT_TCLTK)
-CONFIGURE_ARGS+=--without-tcltk
-PLIST_SUB+=	TCLTK="@comment "
+.if !defined(WITHOUT_GHOSTSCRIPT)
+USE_GHOSTSCRIPT_RUN=yes
+.endif
+
+.if defined(WITHOUT_ICU)
+CONFIGURE_ARGS+=--without-ICU
 .else
-LIB_DEPENDS+=	tcl85:${PORTSDIR}/lang/tcl85 \
-		tk85:${PORTSDIR}/x11-toolkits/tk85
-CONFIGURE_ARGS+=--with-tcltk
-PLIST_SUB+=	TCLTK=""
+LIB_DEPENDS+=	icui18n:${PORTSDIR}/devel/icu
+CONFIGURE_ARGS+=--with-ICU
 .endif
 
 .if defined(WITHOUT_JPEG)
@@ -100,6 +94,25 @@
 CONFIGURE_ARGS+=--with-jpeglib
 .endif
 
+.if defined(WITH_LETTER_PAPER)
+CONFIGURE_ENV+=	R_PAPERSIZE=letter
+.endif
+
+.if !defined(WITHOUT_NLS)
+USE_GETTEXT=	yes
+PLIST_SUB+=	NLS=""
+.else
+CONFIGURE_ARGS+=--disable-nls
+PLIST_SUB+=	NLS="@comment "
+.endif
+
+.if defined(WITHOUT_PCRE_PORT)
+CONFIGURE_ARGS+=--without-system-pcre
+.else
+LIB_DEPENDS+=	pcre.0:${PORTSDIR}/devel/pcre
+CONFIGURE_ARGS+=--with-system-pcre
+.endif
+
 .if defined(WITHOUT_PNG)
 CONFIGURE_ARGS+=--without-libpng
 .else
@@ -107,6 +120,22 @@
 CONFIGURE_ARGS+=--with-libpng
 .endif
 
+.if defined(WITHOUT_TCLTK)
+CONFIGURE_ARGS+=--without-tcltk
+PLIST_SUB+=	TCLTK="@comment "
+.else
+USE_TK =	83+
+.include "${PORTSDIR}/Mk/bsd.tcl.mk"
+CONFIGURE_ARGS+=--with-tcltk
+PLIST_SUB+=	TCLTK=""
+.endif
+
+.if defined(WITHOUT_THREADS)
+CONFIGURE_ARGS+=--disable-threads
+.else
+CONFIGURE_ARGS+=--enable-threads=posix
+.endif
+
 .if defined(WITHOUT_X11)
 CONFIGURE_ARGS+=--without-x
 PLIST_SUB+=	X11="@comment "
@@ -116,17 +145,6 @@
 PLIST_SUB+=	X11=""
 .endif
 
-.if !defined(WITHOUT_GHOSTSCRIPT)
-USE_GHOSTSCRIPT_RUN=yes
-.endif
-
-.if defined(WITHOUT_PCRE_PORT)
-CONFIGURE_ARGS+=--without-system-pcre
-.else
-LIB_DEPENDS+=	pcre.0:${PORTSDIR}/devel/pcre
-CONFIGURE_ARGS+=--with-system-pcre
-.endif
-
 .if defined(WITH_DVI_MANUALS) && !defined(NOPORTDOCS)
 BUILD_DEPENDS+=	pdflatex:${PORTSDIR}/print/teTeX-base
 ALL_TARGET+=	dvi
@@ -136,28 +154,32 @@
 PLIST_SUB+=	DVI_MANUAL="@comment "
 .endif
 
-.if defined(WITHOUT_PDF_MANUALS) && !defined(NOPORTDOCS)
-PLIST_SUB+=	PDF_MANUAL="@comment "
-.else
-PLIST_SUB+=	PDF_MANUAL=""
-BUILD_DEPENDS+=	pdflatex:${PORTSDIR}/print/teTeX-base
-ALL_TARGET+=	pdf
-INSTALL_TARGET+=	install-pdf
-.endif
-
 .if defined(WITH_INFO_MANUALS) && !defined(NOPORTDOCS)
 ALL_TARGET+=	info
 INFO=		R-FAQ R-admin R-data R-exts R-intro R-lang
 .endif
 
-.if defined(WITH_LETTER_PAPER)
-CONFIGURE_ENV+=	R_PAPERSIZE=letter
+.if defined(WITH_PDF_MANUALS) && !defined(NOPORTDOCS)
+PLIST_SUB+=	PDF_MANUAL=""
+BUILD_DEPENDS+=	pdflatex:${PORTSDIR}/print/teTeX-base
+ALL_TARGET+=	pdf
+INSTALL_TARGET+=	install-pdf
+.else
+PLIST_SUB+=	PDF_MANUAL="@comment "
 .endif
 
 post-patch:
 	@${REINPLACE_CMD} -e 's|(libdir)/pkgconfig|(prefix)/libdata/pkgconfig|g' \
 		${WRKSRC}/src/nmath/standalone/Makefile.in \
 		${WRKSRC}/src/unix/Makefile.in
+	@${REINPLACE_CMD} -e "s|-lpthread|${PTHREAD_LIBS}|g" ${WRKSRC}/configure
+.if defined(WITHOUT_NLS)
+	(cd ${WRKSRC}/src/library/Recommended; \
+	for tarfile in *.tgz *.tar.gz ; do \
+	${TAR} -czf temptgz --exclude='*/po/*' @$$tarfile ; \
+	${MV} temptgz $$tarfile ; \
+	done)
+.endif
 
 regression-test: build
 	@(cd ${WRKSRC}; ${MAKE} check)
diff -ruN R.orig/distinfo R/distinfo
--- R.orig/distinfo	2009-01-07 20:07:42.000000000 -0500
+++ R/distinfo	2009-06-04 06:15:05.000000000 -0400
@@ -1,3 +1,3 @@
-MD5 (R-2.8.1.tar.gz) = acd40621b8942a2464daa2f9cef3273d
-SHA256 (R-2.8.1.tar.gz) = ab488af73ce7a4f2057afcf0e725be96c9ae37f8721143004397b91928ecfa60
-SIZE (R-2.8.1.tar.gz) = 16585380
+MD5 (R-2.9.0.tar.gz) = a5b79a2bc1372136cda4674b5f46d146
+SHA256 (R-2.9.0.tar.gz) = f2de4b710feabf0395ee3503befc69332b78ed6b159e959e93bc086a1a8ad818
+SIZE (R-2.9.0.tar.gz) = 18423754
diff -ruN R.orig/files/patch-configure R/files/patch-configure
--- R.orig/files/patch-configure	1969-12-31 19:00:00.000000000 -0500
+++ R/files/patch-configure	2009-06-04 06:15:05.000000000 -0400
@@ -0,0 +1,12 @@
+#extra linker flags for threaded tk
+--- configure.orig	2009-06-03 19:08:21.000000000 -0400
++++ configure	2009-06-03 19:48:48.000000000 -0400
+@@ -43400,7 +43400,7 @@
+     ## Part 2.  Try finding the tk library.
+     if test -n "${TK_CONFIG}"; then
+       . ${TK_CONFIG}
+-      TCLTK_LIBS="${TCLTK_LIBS} ${TK_LIB_SPEC} ${TK_XLIBSW}"
++      TCLTK_LIBS="${TCLTK_LIBS} ${TK_LIB_SPEC} ${TK_XLIBSW} ${TCL_LD_FLAGS}"
+     else
+ 
+ { echo "$as_me:$LINENO: checking for Tk_Init in -ltk" >&5
diff -ruN R.orig/pkg-plist R/pkg-plist
--- R.orig/pkg-plist	2008-12-14 20:05:52.000000000 -0500
+++ R/pkg-plist	2009-06-04 06:15:05.000000000 -0400
@@ -29,6 +29,7 @@
 lib/R/bin/libtool
 lib/R/bin/mkinstalldirs
 lib/R/bin/pager
+lib/R/bin/rtags
 lib/R/etc/Makeconf
 lib/R/etc/Renviron
 lib/R/etc/ldpaths
@@ -710,6 +711,443 @@
 lib/R/library/MASS/scripts/ch14.R
 lib/R/library/MASS/scripts/ch15.R
 lib/R/library/MASS/scripts/ch16.R
+lib/R/library/Matrix/CONTENTS
+lib/R/library/Matrix/Copyrights
+lib/R/library/Matrix/DESCRIPTION
+lib/R/library/Matrix/Doxyfile
+lib/R/library/Matrix/INDEX
+lib/R/library/Matrix/Meta/Rd.rds
+lib/R/library/Matrix/Meta/data.rds
+lib/R/library/Matrix/Meta/hsearch.rds
+lib/R/library/Matrix/Meta/nsInfo.rds
+lib/R/library/Matrix/Meta/package.rds
+lib/R/library/Matrix/Meta/vignette.rds
+lib/R/library/Matrix/NAMESPACE
+lib/R/library/Matrix/R-ex/BunchKaufman-methods.R
+lib/R/library/Matrix/R-ex/CAex.R
+lib/R/library/Matrix/R-ex/CHMfactor-class.R
+lib/R/library/Matrix/R-ex/Cholesky-class.R
+lib/R/library/Matrix/R-ex/Cholesky.R
+lib/R/library/Matrix/R-ex/CsparseMatrix-class.R
+lib/R/library/Matrix/R-ex/Diagonal.R
+lib/R/library/Matrix/R-ex/Hilbert.R
+lib/R/library/Matrix/R-ex/KNex.R
+lib/R/library/Matrix/R-ex/LU-class.R
+lib/R/library/Matrix/R-ex/Matrix-class.R
+lib/R/library/Matrix/R-ex/Matrix.R
+lib/R/library/Matrix/R-ex/MatrixFactorization-class.R
+lib/R/library/Matrix/R-ex/RsparseMatrix-class.R
+lib/R/library/Matrix/R-ex/Schur-class.R
+lib/R/library/Matrix/R-ex/Schur.R
+lib/R/library/Matrix/R-ex/Subassign-methods.R
+lib/R/library/Matrix/R-ex/TsparseMatrix-class.R
+lib/R/library/Matrix/R-ex/USCounties.R
+lib/R/library/Matrix/R-ex/Xtrct-methods.R
+lib/R/library/Matrix/R-ex/all-methods.R
+lib/R/library/Matrix/R-ex/all.equal-methods.R
+lib/R/library/Matrix/R-ex/atomicVector-class.R
+lib/R/library/Matrix/R-ex/band.R
+lib/R/library/Matrix/R-ex/bandSparse.R
+lib/R/library/Matrix/R-ex/bdiag.R
+lib/R/library/Matrix/R-ex/cBind.R
+lib/R/library/Matrix/R-ex/chol.R
+lib/R/library/Matrix/R-ex/colSums.R
+lib/R/library/Matrix/R-ex/dMatrix-class.R
+lib/R/library/Matrix/R-ex/ddenseMatrix-class.R
+lib/R/library/Matrix/R-ex/ddiMatrix-class.R
+lib/R/library/Matrix/R-ex/denseMatrix-class.R
+lib/R/library/Matrix/R-ex/dgCMatrix-class.R
+lib/R/library/Matrix/R-ex/dgTMatrix-class.R
+lib/R/library/Matrix/R-ex/diagonalMatrix-class.R
+lib/R/library/Matrix/R-ex/dpoMatrix-class.R
+lib/R/library/Matrix/R-ex/drop0.R
+lib/R/library/Matrix/R-ex/dsCMatrix-class.R
+lib/R/library/Matrix/R-ex/dsRMatrix-class.R
+lib/R/library/Matrix/R-ex/dsparseMatrix-class.R
+lib/R/library/Matrix/R-ex/dsyMatrix-class.R
+lib/R/library/Matrix/R-ex/dtCMatrix-class.R
+lib/R/library/Matrix/R-ex/dtRMatrix-class-def.R
+lib/R/library/Matrix/R-ex/dtpMatrix-class.R
+lib/R/library/Matrix/R-ex/dtrMatrix-class.R
+lib/R/library/Matrix/R-ex/expand.R
+lib/R/library/Matrix/R-ex/expm.R
+lib/R/library/Matrix/R-ex/externalFormats.R
+lib/R/library/Matrix/R-ex/facmul.R
+lib/R/library/Matrix/R-ex/forceSymmetric.R
+lib/R/library/Matrix/R-ex/image-methods.R
+lib/R/library/Matrix/R-ex/index-class.R
+lib/R/library/Matrix/R-ex/is.na-methods.R
+lib/R/library/Matrix/R-ex/kronecker-methods.R
+lib/R/library/Matrix/R-ex/ldenseMatrix-class.R
+lib/R/library/Matrix/R-ex/ldiMatrix-class.R
+lib/R/library/Matrix/R-ex/lgeMatrix-class.R
+lib/R/library/Matrix/R-ex/lsparseMatrix-classes.R
+lib/R/library/Matrix/R-ex/lsyMatrix-class.R
+lib/R/library/Matrix/R-ex/ltrMatrix-class.R
+lib/R/library/Matrix/R-ex/lu.R
+lib/R/library/Matrix/R-ex/nMatrix-class.R
+lib/R/library/Matrix/R-ex/ndenseMatrix-class.R
+lib/R/library/Matrix/R-ex/nearPD.R
+lib/R/library/Matrix/R-ex/ngeMatrix-class.R
+lib/R/library/Matrix/R-ex/nnzero.R
+lib/R/library/Matrix/R-ex/norm.R
+lib/R/library/Matrix/R-ex/nsparseMatrix-classes.R
+lib/R/library/Matrix/R-ex/nsyMatrix-class.R
+lib/R/library/Matrix/R-ex/ntrMatrix-class.R
+lib/R/library/Matrix/R-ex/number-class.R
+lib/R/library/Matrix/R-ex/pMatrix-class.R
+lib/R/library/Matrix/R-ex/printSpMatrix.R
+lib/R/library/Matrix/R-ex/rcond.R
+lib/R/library/Matrix/R-ex/replValue-class.R
+lib/R/library/Matrix/R-ex/spMatrix.R
+lib/R/library/Matrix/R-ex/sparseLU-class.R
+lib/R/library/Matrix/R-ex/sparseMatrix-class.R
+lib/R/library/Matrix/R-ex/sparseMatrix.R
+lib/R/library/Matrix/R-ex/sparseQR-class.R
+lib/R/library/Matrix/R-ex/sparseVector-class.R
+lib/R/library/Matrix/R-ex/symmetricMatrix-class.R
+lib/R/library/Matrix/R-ex/symmpart.R
+lib/R/library/Matrix/R-ex/tcrossprod.R
+lib/R/library/Matrix/R-ex/triangularMatrix-class.R
+lib/R/library/Matrix/R-ex/unpack.R
+lib/R/library/Matrix/R-ex/unused-classes.R
+lib/R/library/Matrix/R-ex/xtabs.R
+lib/R/library/Matrix/R/Matrix
+lib/R/library/Matrix/R/Matrix.rdb
+lib/R/library/Matrix/R/Matrix.rdx
+lib/R/library/Matrix/data/CAex.R
+lib/R/library/Matrix/data/KNex.R
+lib/R/library/Matrix/data/USCounties.R
+lib/R/library/Matrix/doc/Announce.txt
+lib/R/library/Matrix/doc/Comparisons.R
+lib/R/library/Matrix/doc/Comparisons.Rnw
+lib/R/library/Matrix/doc/Comparisons.pdf
+lib/R/library/Matrix/doc/DSC2009_abstract.txt
+lib/R/library/Matrix/doc/Design-issues.R
+lib/R/library/Matrix/doc/Design-issues.Rnw
+lib/R/library/Matrix/doc/Design-issues.pdf
+lib/R/library/Matrix/doc/Intro2Matrix.R
+lib/R/library/Matrix/doc/Intro2Matrix.Rnw
+lib/R/library/Matrix/doc/Intro2Matrix.pdf
+lib/R/library/Matrix/doc/Introduction.R
+lib/R/library/Matrix/doc/Introduction.Rnw
+lib/R/library/Matrix/doc/Introduction.pdf
+lib/R/library/Matrix/doc/Matrix.bib
+lib/R/library/Matrix/doc/UFsparse/AMD.txt
+lib/R/library/Matrix/doc/UFsparse/CHOLMOD.txt
+lib/R/library/Matrix/doc/UFsparse/COLAMD.txt
+lib/R/library/Matrix/doc/UFsparse/SPQR.txt
+lib/R/library/Matrix/doc/UFsparse/UFconfig.txt
+lib/R/library/Matrix/doc/UFsparse/UserGuides.txt
+lib/R/library/Matrix/doc/index.html
+lib/R/library/Matrix/doc/myVignette.sty
+lib/R/library/Matrix/doc/sparseModels.R
+lib/R/library/Matrix/doc/sparseModels.Rnw
+lib/R/library/Matrix/doc/sparseModels.pdf
+lib/R/library/Matrix/external/CAex_slots.rda
+lib/R/library/Matrix/external/KNex_slots.rda
+lib/R/library/Matrix/external/USCounties_slots.rda
+lib/R/library/Matrix/external/lund_a.mtx
+lib/R/library/Matrix/external/lund_a.rsa
+lib/R/library/Matrix/external/pores_1.mtx
+lib/R/library/Matrix/external/test3comp.rda
+lib/R/library/Matrix/external/utm300.rua
+lib/R/library/Matrix/help/AnIndex
+lib/R/library/Matrix/help/BunchKaufman-methods
+lib/R/library/Matrix/help/CAex
+lib/R/library/Matrix/help/CHMfactor-class
+lib/R/library/Matrix/help/Cholesky
+lib/R/library/Matrix/help/Cholesky-class
+lib/R/library/Matrix/help/CsparseMatrix-class
+lib/R/library/Matrix/help/Diagonal
+lib/R/library/Matrix/help/Hilbert
+lib/R/library/Matrix/help/KNex
+lib/R/library/Matrix/help/LU-class
+lib/R/library/Matrix/help/Matrix
+lib/R/library/Matrix/help/Matrix-class
+lib/R/library/Matrix/help/MatrixFactorization-class
+lib/R/library/Matrix/help/RsparseMatrix-class
+lib/R/library/Matrix/help/Schur
+lib/R/library/Matrix/help/Schur-class
+lib/R/library/Matrix/help/SparseM-conv
+lib/R/library/Matrix/help/Subassign-methods
+lib/R/library/Matrix/help/TsparseMatrix-class
+lib/R/library/Matrix/help/USCounties
+lib/R/library/Matrix/help/Xtrct-methods
+lib/R/library/Matrix/help/all-methods
+lib/R/library/Matrix/help/all.equal-methods
+lib/R/library/Matrix/help/atomicVector-class
+lib/R/library/Matrix/help/band
+lib/R/library/Matrix/help/bandSparse
+lib/R/library/Matrix/help/bdiag
+lib/R/library/Matrix/help/cBind
+lib/R/library/Matrix/help/chol
+lib/R/library/Matrix/help/colSums
+lib/R/library/Matrix/help/compMatrix-class
+lib/R/library/Matrix/help/dMatrix-class
+lib/R/library/Matrix/help/ddenseMatrix-class
+lib/R/library/Matrix/help/ddiMatrix-class
+lib/R/library/Matrix/help/denseMatrix-class
+lib/R/library/Matrix/help/dgCMatrix-class
+lib/R/library/Matrix/help/dgRMatrix-class
+lib/R/library/Matrix/help/dgTMatrix-class
+lib/R/library/Matrix/help/dgeMatrix-class
+lib/R/library/Matrix/help/diagonalMatrix-class
+lib/R/library/Matrix/help/dpoMatrix-class
+lib/R/library/Matrix/help/drop0
+lib/R/library/Matrix/help/dsCMatrix-class
+lib/R/library/Matrix/help/dsRMatrix-class
+lib/R/library/Matrix/help/dsparseMatrix-class
+lib/R/library/Matrix/help/dsyMatrix-class
+lib/R/library/Matrix/help/dtCMatrix-class
+lib/R/library/Matrix/help/dtRMatrix-class-def
+lib/R/library/Matrix/help/dtpMatrix-class
+lib/R/library/Matrix/help/dtrMatrix-class
+lib/R/library/Matrix/help/expand
+lib/R/library/Matrix/help/expm
+lib/R/library/Matrix/help/externalFormats
+lib/R/library/Matrix/help/facmul
+lib/R/library/Matrix/help/forceSymmetric
+lib/R/library/Matrix/help/generalMatrix-class
+lib/R/library/Matrix/help/image-methods
+lib/R/library/Matrix/help/index-class
+lib/R/library/Matrix/help/is.na-methods
+lib/R/library/Matrix/help/isSymmetric-methods
+lib/R/library/Matrix/help/kronecker-methods
+lib/R/library/Matrix/help/ldenseMatrix-class
+lib/R/library/Matrix/help/ldiMatrix-class
+lib/R/library/Matrix/help/lgeMatrix-class
+lib/R/library/Matrix/help/lsparseMatrix-classes
+lib/R/library/Matrix/help/lsyMatrix-class
+lib/R/library/Matrix/help/ltrMatrix-class
+lib/R/library/Matrix/help/lu
+lib/R/library/Matrix/help/nMatrix-class
+lib/R/library/Matrix/help/ndenseMatrix-class
+lib/R/library/Matrix/help/nearPD
+lib/R/library/Matrix/help/ngeMatrix-class
+lib/R/library/Matrix/help/nnzero
+lib/R/library/Matrix/help/norm
+lib/R/library/Matrix/help/nsparseMatrix-classes
+lib/R/library/Matrix/help/nsyMatrix-class
+lib/R/library/Matrix/help/ntrMatrix-class
+lib/R/library/Matrix/help/number-class
+lib/R/library/Matrix/help/pMatrix-class
+lib/R/library/Matrix/help/printSpMatrix
+lib/R/library/Matrix/help/qr-methods
+lib/R/library/Matrix/help/rcond
+lib/R/library/Matrix/help/replValue-class
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 lib/R/share/licenses/AGPL-3
 lib/R/share/licenses/Artistic-1.0
@@ -8765,23 +9341,25 @@
 lib/R/share/licenses/LGPL-2.1
 lib/R/share/licenses/LGPL-3
 lib/R/share/licenses/license.db
-lib/R/share/locale/de/LC_MESSAGES/R.mo
-lib/R/share/locale/en/LC_MESSAGES/R.mo
-lib/R/share/locale/en@quot/LC_MESSAGES/R.mo
-lib/R/share/locale/en_GB/LC_MESSAGES/R.mo
-lib/R/share/locale/es/LC_MESSAGES/R.mo
-lib/R/share/locale/fr/LC_MESSAGES/R.mo
-lib/R/share/locale/it/LC_MESSAGES/R.mo
-lib/R/share/locale/ja/LC_MESSAGES/R.mo
-lib/R/share/locale/ko/LC_MESSAGES/R.mo
-lib/R/share/locale/pt_BR/LC_MESSAGES/R.mo
-lib/R/share/locale/ru/LC_MESSAGES/R.mo
-lib/R/share/locale/zh_CN/LC_MESSAGES/R.mo
-lib/R/share/locale/zh_TW/LC_MESSAGES/R.mo
+%%NLS%%lib/R/share/locale/de/LC_MESSAGES/R.mo
+%%NLS%%lib/R/share/locale/en/LC_MESSAGES/R.mo
+%%NLS%%lib/R/share/locale/en@quot/LC_MESSAGES/R.mo
+%%NLS%%lib/R/share/locale/en_GB/LC_MESSAGES/R.mo
+%%NLS%%lib/R/share/locale/es/LC_MESSAGES/R.mo
+%%NLS%%lib/R/share/locale/fr/LC_MESSAGES/R.mo
+%%NLS%%lib/R/share/locale/it/LC_MESSAGES/R.mo
+%%NLS%%lib/R/share/locale/ja/LC_MESSAGES/R.mo
+%%NLS%%lib/R/share/locale/ko/LC_MESSAGES/R.mo
+%%NLS%%lib/R/share/locale/pt_BR/LC_MESSAGES/R.mo
+%%NLS%%lib/R/share/locale/ru/LC_MESSAGES/R.mo
+%%NLS%%lib/R/share/locale/zh_CN/LC_MESSAGES/R.mo
+%%NLS%%lib/R/share/locale/zh_TW/LC_MESSAGES/R.mo
 lib/R/share/make/check.mk
+lib/R/share/make/basepkg.mk
+lib/R/share/make/clean.mk
+lib/R/share/make/winshlib.mk
 lib/R/share/make/config.mk
 lib/R/share/make/shlib.mk
-lib/R/share/make/tests.mk
 lib/R/share/make/vars.mk
 lib/R/share/perl/File/Copy/Recursive.pm
 lib/R/share/perl/R/Dcf.pm
@@ -8793,9 +9371,7 @@
 lib/R/share/perl/R/Utils.pm
 lib/R/share/perl/R/Vars.pm
 lib/R/share/perl/Text/DelimMatch.pm
-lib/R/share/perl/build-help-windows.pl
 lib/R/share/perl/build-help.pl
-lib/R/share/perl/massage-Examples.pl
 lib/R/share/sh/dcf.sh
 lib/R/share/sh/echo.sh
 lib/R/share/sh/help-links.sh
@@ -8853,14 +9429,29 @@
 %%DOCSDIR%%/manual/R-intro.html
 %%DOCSDIR%%/manual/R-ints.html
 %%DOCSDIR%%/manual/R-lang.html
-%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-admin.pdf
-%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-data.pdf
-%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-exts.pdf
-%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-FAQ.pdf
-%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-intro.pdf
-%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-ints.pdf
-%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-lang.pdf
-%%PDF_MANUAL%%%%DOCSDIR%%/manual/refman.pdf
+%%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/images/QQ.eps
+%%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/images/ecdf.eps
+%%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/images/fig11.eps
+%%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/images/fig12.eps
+%%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/images/hist.eps
+%%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/images/ice.eps
+%%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/R-FAQ.dvi
+%%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/R-admin.dvi
+%%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/R-data.dvi
+%%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/R-exts.dvi
+%%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/R-intro.dvi
+%%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/R-ints.dvi
+%%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/R-lang.dvi
+%%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/refman.dvi
+%%PORTDOCS%%%%DVI_MANUAL%%@dirrm %%DOCSDIR%%/manual/images
+%%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-admin.pdf
+%%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-data.pdf
+%%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-exts.pdf
+%%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-FAQ.pdf
+%%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-intro.pdf
+%%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-ints.pdf
+%%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-lang.pdf
+%%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/refman.pdf
 @dirrm %%DOCSDIR%%/manual
 @dirrm %%DOCSDIR%%/html/search
 @dirrm %%DOCSDIR%%/html
@@ -8873,33 +9464,33 @@
 @dirrm lib/R/share/perl/File
 @dirrm lib/R/share/perl
 @dirrm lib/R/share/make
-@dirrm lib/R/share/locale/zh_TW/LC_MESSAGES
-@dirrm lib/R/share/locale/zh_TW
-@dirrm lib/R/share/locale/zh_CN/LC_MESSAGES
-@dirrm lib/R/share/locale/zh_CN
-@dirrm lib/R/share/locale/ru/LC_MESSAGES
-@dirrm lib/R/share/locale/ru
-@dirrm lib/R/share/locale/pt_BR/LC_MESSAGES
-@dirrm lib/R/share/locale/pt_BR
-@dirrm lib/R/share/locale/ko/LC_MESSAGES
-@dirrm lib/R/share/locale/ko
-@dirrm lib/R/share/locale/ja/LC_MESSAGES
-@dirrm lib/R/share/locale/ja
-@dirrm lib/R/share/locale/it/LC_MESSAGES
-@dirrm lib/R/share/locale/it
-@dirrm lib/R/share/locale/fr/LC_MESSAGES
-@dirrm lib/R/share/locale/fr
-@dirrm lib/R/share/locale/es/LC_MESSAGES
-@dirrm lib/R/share/locale/es
-@dirrm lib/R/share/locale/en_GB/LC_MESSAGES
-@dirrm lib/R/share/locale/en_GB
-@dirrm lib/R/share/locale/en@quot/LC_MESSAGES
-@dirrm lib/R/share/locale/en@quot
-@dirrm lib/R/share/locale/en/LC_MESSAGES
-@dirrm lib/R/share/locale/en
-@dirrm lib/R/share/locale/de/LC_MESSAGES
-@dirrm lib/R/share/locale/de
-@dirrm lib/R/share/locale
+%%NLS%%@dirrm lib/R/share/locale/zh_TW/LC_MESSAGES
+%%NLS%%@dirrm lib/R/share/locale/zh_TW
+%%NLS%%@dirrm lib/R/share/locale/zh_CN/LC_MESSAGES
+%%NLS%%@dirrm lib/R/share/locale/zh_CN
+%%NLS%%@dirrm lib/R/share/locale/ru/LC_MESSAGES
+%%NLS%%@dirrm lib/R/share/locale/ru
+%%NLS%%@dirrm lib/R/share/locale/pt_BR/LC_MESSAGES
+%%NLS%%@dirrm lib/R/share/locale/pt_BR
+%%NLS%%@dirrm lib/R/share/locale/ko/LC_MESSAGES
+%%NLS%%@dirrm lib/R/share/locale/ko
+%%NLS%%@dirrm lib/R/share/locale/ja/LC_MESSAGES
+%%NLS%%@dirrm lib/R/share/locale/ja
+%%NLS%%@dirrm lib/R/share/locale/it/LC_MESSAGES
+%%NLS%%@dirrm lib/R/share/locale/it
+%%NLS%%@dirrm lib/R/share/locale/fr/LC_MESSAGES
+%%NLS%%@dirrm lib/R/share/locale/fr
+%%NLS%%@dirrm lib/R/share/locale/es/LC_MESSAGES
+%%NLS%%@dirrm lib/R/share/locale/es
+%%NLS%%@dirrm lib/R/share/locale/en_GB/LC_MESSAGES
+%%NLS%%@dirrm lib/R/share/locale/en_GB
+%%NLS%%@dirrm lib/R/share/locale/en@quot/LC_MESSAGES
+%%NLS%%@dirrm lib/R/share/locale/en@quot
+%%NLS%%@dirrm lib/R/share/locale/en/LC_MESSAGES
+%%NLS%%@dirrm lib/R/share/locale/en
+%%NLS%%@dirrm lib/R/share/locale/de/LC_MESSAGES
+%%NLS%%@dirrm lib/R/share/locale/de
+%%NLS%%@dirrm lib/R/share/locale
 @dirrm lib/R/share/licenses
 @dirrm lib/R/share/java
 @dirrm lib/R/share/encodings
@@ -9087,15 +9678,15 @@
 %%NLS%%@dirrm lib/R/library/spatial/po/en@quot/LC_MESSAGES
 %%NLS%%@dirrm lib/R/library/spatial/po/en@quot
 %%NLS%%@dirrm lib/R/library/spatial/po
-%%NLS%%@dirrm lib/R/library/spatial/man
-%%NLS%%@dirrm lib/R/library/spatial/libs
-%%NLS%%@dirrm lib/R/library/spatial/latex
-%%NLS%%@dirrm lib/R/library/spatial/html
-%%NLS%%@dirrm lib/R/library/spatial/help
-%%NLS%%@dirrm lib/R/library/spatial/R-ex
-%%NLS%%@dirrm lib/R/library/spatial/R
-%%NLS%%@dirrm lib/R/library/spatial/Meta
-%%NLS%%@dirrm lib/R/library/spatial
+@dirrm lib/R/library/spatial/man
+@dirrm lib/R/library/spatial/libs
+@dirrm lib/R/library/spatial/latex
+@dirrm lib/R/library/spatial/html
+@dirrm lib/R/library/spatial/help
+@dirrm lib/R/library/spatial/R-ex
+@dirrm lib/R/library/spatial/R
+@dirrm lib/R/library/spatial/Meta
+@dirrm lib/R/library/spatial
 %%NLS%%@dirrm lib/R/library/rpart/po/ru/LC_MESSAGES
 %%NLS%%@dirrm lib/R/library/rpart/po/ru
 %%NLS%%@dirrm lib/R/library/rpart/po/fr/LC_MESSAGES
@@ -9375,6 +9966,20 @@
 @dirrm lib/R/library/base/R
 @dirrm lib/R/library/base/Meta
 @dirrm lib/R/library/base
+@dirrm lib/R/library/Matrix/Meta
+@dirrm lib/R/library/Matrix/R
+@dirrm lib/R/library/Matrix/R-ex
+@dirrm lib/R/library/Matrix/data
+@dirrm lib/R/library/Matrix/doc/UFsparse
+@dirrm lib/R/library/Matrix/doc
+@dirrm lib/R/library/Matrix/external
+@dirrm lib/R/library/Matrix/help
+@dirrm lib/R/library/Matrix/html
+@dirrm lib/R/library/Matrix/include
+@dirrm lib/R/library/Matrix/latex
+@dirrm lib/R/library/Matrix/libs
+@dirrm lib/R/library/Matrix/man
+@dirrm lib/R/library/Matrix
 @dirrm lib/R/library/MASS/scripts
 %%NLS%%@dirrm lib/R/library/MASS/po/fr/LC_MESSAGES
 %%NLS%%@dirrm lib/R/library/MASS/po/fr


>Release-Note:
>Audit-Trail:
>Unformatted:



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