ports/129063: Update math/R to version 2.8.0

Pedro F. Giffuni giffunip at tutopia.com
Sat Nov 22 04:20:02 UTC 2008 

>Number:         129063
>Category:       ports
>Synopsis:       Update math/R to version 2.8.0
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          update
>Submitter-Id:   current-users
>Arrival-Date:   Sat Nov 22 04:20:01 UTC 2008
>Closed-Date:
>Last-Modified:
>Originator:     Pedro F. Giffuni
>Release:        7.1-BETA2
>Organization:
>Environment:
FreeBSD kakumen.cable.net.co 7.1-BETA2 FreeBSD 7.1-BETA2 #0: Sun Oct 12 20:59:28 UTC 2008     root at driscoll.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC  amd64

>Description:
- Update to latest release with new features.
>How-To-Repeat:

>Fix:
diff -ruN R.orig/Makefile R/Makefile
--- R.orig/Makefile	2008-11-21 21:07:10.000000000 -0500
+++ R/Makefile	2008-11-21 21:08:34.000000000 -0500
@@ -7,7 +7,7 @@
 #
 
 PORTNAME=	R
-PORTVERSION=	2.7.2
+PORTVERSION=	2.8.0
 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/ \
diff -ruN R.orig/distinfo R/distinfo
--- R.orig/distinfo	2008-11-21 21:07:10.000000000 -0500
+++ R/distinfo	2008-11-21 21:10:50.000000000 -0500
@@ -1,3 +1,3 @@
-MD5 (R-2.7.2.tar.gz) = 6122945e9301825b97a506151b3cefde
-SHA256 (R-2.7.2.tar.gz) = 7184c1f85fafce518e6dbccb5a64ba47a62d8694c7019da0e1c1e83ff98c3ff4
-SIZE (R-2.7.2.tar.gz) = 16466658
+MD5 (R-2.8.0.tar.gz) = 5213c9644aec984278b669df1a63a2ce
+SHA256 (R-2.8.0.tar.gz) = 3f125987ed988ccc73234da4c0daee8c79eac81aff66e10d9caeb9616d77c19d
+SIZE (R-2.8.0.tar.gz) = 16558443
diff -ruN R.orig/pkg-plist R/pkg-plist
--- R.orig/pkg-plist	2008-11-21 21:07:10.000000000 -0500
+++ R/pkg-plist	2008-11-21 23:08:12.000000000 -0500
@@ -68,9 +68,7 @@
 lib/R/include/R_ext/stats_stubs.h
 lib/R/include/Rconfig.h
 lib/R/include/Rdefines.h
-lib/R/include/Rdevices.h
 lib/R/include/Rembedded.h
-lib/R/include/Rgraphics.h
 lib/R/include/Rinterface.h
 lib/R/include/Rinternals.h
 lib/R/include/Rmath.h
@@ -874,6 +872,7 @@
 lib/R/library/base/R-ex/groupGeneric.R
 lib/R/library/base/R-ex/gzcon.R
 lib/R/library/base/R-ex/iconv.R
+lib/R/library/base/R-ex/icuSetCollate.R
 lib/R/library/base/R-ex/identical.R
 lib/R/library/base/R-ex/ifelse.R
 lib/R/library/base/R-ex/integer.R
@@ -963,6 +962,7 @@
 lib/R/library/base/R-ex/rank.R
 lib/R/library/base/R-ex/rapply.R
 lib/R/library/base/R-ex/raw.R
+lib/R/library/base/R-ex/rawConnection.R
 lib/R/library/base/R-ex/rawConversion.R
 lib/R/library/base/R-ex/readBin.R
 lib/R/library/base/R-ex/readChar.R
@@ -1247,6 +1247,7 @@
 lib/R/library/base/help/gzcon
 lib/R/library/base/help/hexmode
 lib/R/library/base/help/iconv
+lib/R/library/base/help/icuSetCollate
 lib/R/library/base/help/identical
 lib/R/library/base/help/identity
 lib/R/library/base/help/ifelse
@@ -1260,6 +1261,7 @@
 lib/R/library/base/help/is.object
 lib/R/library/base/help/is.recursive
 lib/R/library/base/help/is.single
+lib/R/library/base/help/is.unsorted
 lib/R/library/base/help/isR
 lib/R/library/base/help/isS4
 lib/R/library/base/help/isSymmetric
@@ -1347,6 +1349,7 @@
 lib/R/library/base/help/rank
 lib/R/library/base/help/rapply
 lib/R/library/base/help/raw
+lib/R/library/base/help/rawConnection
 lib/R/library/base/help/rawConversion
 lib/R/library/base/help/readBin
 lib/R/library/base/help/readChar
@@ -1376,6 +1379,7 @@
 lib/R/library/base/help/seq.POSIXt
 lib/R/library/base/help/sequence
 lib/R/library/base/help/serialize
+lib/R/library/base/help/setTimeLimit
 lib/R/library/base/help/sets
 lib/R/library/base/help/shQuote
 lib/R/library/base/help/showConnections
@@ -1444,6 +1448,7 @@
 lib/R/library/base/help/with
 lib/R/library/base/help/write
 lib/R/library/base/help/writeLines
+lib/R/library/base/help/xtfrm
 lib/R/library/base/help/zMachine
 lib/R/library/base/help/zMethods
 lib/R/library/base/help/zScript
@@ -1637,6 +1642,7 @@
 lib/R/library/base/html/gzcon.html
 lib/R/library/base/html/hexmode.html
 lib/R/library/base/html/iconv.html
+lib/R/library/base/html/icuSetCollate.html
 lib/R/library/base/html/identical.html
 lib/R/library/base/html/identity.html
 lib/R/library/base/html/ifelse.html
@@ -1650,6 +1656,7 @@
 lib/R/library/base/html/is.object.html
 lib/R/library/base/html/is.recursive.html
 lib/R/library/base/html/is.single.html
+lib/R/library/base/html/is.unsorted.html
 lib/R/library/base/html/isR.html
 lib/R/library/base/html/isS4.html
 lib/R/library/base/html/isSymmetric.html
@@ -1737,6 +1744,7 @@
 lib/R/library/base/html/rank.html
 lib/R/library/base/html/rapply.html
 lib/R/library/base/html/raw.html
+lib/R/library/base/html/rawConnection.html
 lib/R/library/base/html/rawConversion.html
 lib/R/library/base/html/readBin.html
 lib/R/library/base/html/readChar.html
@@ -1766,6 +1774,7 @@
 lib/R/library/base/html/seq.html
 lib/R/library/base/html/sequence.html
 lib/R/library/base/html/serialize.html
+lib/R/library/base/html/setTimeLimit.html
 lib/R/library/base/html/sets.html
 lib/R/library/base/html/shQuote.html
 lib/R/library/base/html/showConnections.html
@@ -1834,6 +1843,7 @@
 lib/R/library/base/html/with.html
 lib/R/library/base/html/write.html
 lib/R/library/base/html/writeLines.html
+lib/R/library/base/html/xtfrm.html
 lib/R/library/base/html/zMachine.html
 lib/R/library/base/html/zMethods.html
 lib/R/library/base/html/zScript.html
@@ -2026,6 +2036,7 @@
 lib/R/library/base/latex/gzcon.tex
 lib/R/library/base/latex/hexmode.tex
 lib/R/library/base/latex/iconv.tex
+lib/R/library/base/latex/icuSetCollate.tex
 lib/R/library/base/latex/identical.tex
 lib/R/library/base/latex/identity.tex
 lib/R/library/base/latex/ifelse.tex
@@ -2039,6 +2050,7 @@
 lib/R/library/base/latex/is.object.tex
 lib/R/library/base/latex/is.recursive.tex
 lib/R/library/base/latex/is.single.tex
+lib/R/library/base/latex/is.unsorted.tex
 lib/R/library/base/latex/isR.tex
 lib/R/library/base/latex/isS4.tex
 lib/R/library/base/latex/isSymmetric.tex
@@ -2126,6 +2138,7 @@
 lib/R/library/base/latex/rank.tex
 lib/R/library/base/latex/rapply.tex
 lib/R/library/base/latex/raw.tex
+lib/R/library/base/latex/rawConnection.tex
 lib/R/library/base/latex/rawConversion.tex
 lib/R/library/base/latex/readBin.tex
 lib/R/library/base/latex/readChar.tex
@@ -2155,6 +2168,7 @@
 lib/R/library/base/latex/seq.tex
 lib/R/library/base/latex/sequence.tex
 lib/R/library/base/latex/serialize.tex
+lib/R/library/base/latex/setTimeLimit.tex
 lib/R/library/base/latex/sets.tex
 lib/R/library/base/latex/shQuote.tex
 lib/R/library/base/latex/showConnections.tex
@@ -2223,6 +2237,7 @@
 lib/R/library/base/latex/with.tex
 lib/R/library/base/latex/write.tex
 lib/R/library/base/latex/writeLines.tex
+lib/R/library/base/latex/xtfrm.tex
 lib/R/library/base/latex/zMachine.tex
 lib/R/library/base/latex/zMethods.tex
 lib/R/library/base/latex/zScript.tex
@@ -2933,6 +2948,7 @@
 lib/R/library/datasets/R-ex/mtcars.R
 lib/R/library/datasets/R-ex/nhtemp.R
 lib/R/library/datasets/R-ex/nottem.R
+lib/R/library/datasets/R-ex/occupationalStatus.R
 lib/R/library/datasets/R-ex/precip.R
 lib/R/library/datasets/R-ex/presidents.R
 lib/R/library/datasets/R-ex/pressure.R
@@ -3019,6 +3035,7 @@
 lib/R/library/datasets/help/mtcars
 lib/R/library/datasets/help/nhtemp
 lib/R/library/datasets/help/nottem
+lib/R/library/datasets/help/occupationalStatus
 lib/R/library/datasets/help/precip
 lib/R/library/datasets/help/presidents
 lib/R/library/datasets/help/pressure
@@ -3105,6 +3122,7 @@
 lib/R/library/datasets/html/mtcars.html
 lib/R/library/datasets/html/nhtemp.html
 lib/R/library/datasets/html/nottem.html
+lib/R/library/datasets/html/occupationalStatus.html
 lib/R/library/datasets/html/precip.html
 lib/R/library/datasets/html/presidents.html
 lib/R/library/datasets/html/pressure.html
@@ -3190,6 +3208,7 @@
 lib/R/library/datasets/latex/mtcars.tex
 lib/R/library/datasets/latex/nhtemp.tex
 lib/R/library/datasets/latex/nottem.tex
+lib/R/library/datasets/latex/occupationalStatus.tex
 lib/R/library/datasets/latex/precip.tex
 lib/R/library/datasets/latex/presidents.tex
 lib/R/library/datasets/latex/pressure.tex
@@ -3978,6 +3997,7 @@
 lib/R/library/grid/R-ex/grid.locator.R
 lib/R/library/grid/R-ex/grid.ls.R
 lib/R/library/grid/R-ex/grid.move.to.R
+lib/R/library/grid/R-ex/grid.null.R
 lib/R/library/grid/R-ex/grid.plot.and.legend.R
 lib/R/library/grid/R-ex/grid.polygon.R
 lib/R/library/grid/R-ex/grid.record.R
@@ -4074,6 +4094,7 @@
 lib/R/library/grid/help/grid.ls
 lib/R/library/grid/help/grid.move.to
 lib/R/library/grid/help/grid.newpage
+lib/R/library/grid/help/grid.null
 lib/R/library/grid/help/grid.pack
 lib/R/library/grid/help/grid.place
 lib/R/library/grid/help/grid.plot.and.legend
@@ -4148,6 +4169,7 @@
 lib/R/library/grid/html/grid.ls.html
 lib/R/library/grid/html/grid.move.to.html
 lib/R/library/grid/html/grid.newpage.html
+lib/R/library/grid/html/grid.null.html
 lib/R/library/grid/html/grid.pack.html
 lib/R/library/grid/html/grid.place.html
 lib/R/library/grid/html/grid.plot.and.legend.html
@@ -4221,6 +4243,7 @@
 lib/R/library/grid/latex/grid.ls.tex
 lib/R/library/grid/latex/grid.move.to.tex
 lib/R/library/grid/latex/grid.newpage.tex
+lib/R/library/grid/latex/grid.null.tex
 lib/R/library/grid/latex/grid.pack.tex
 lib/R/library/grid/latex/grid.place.tex
 lib/R/library/grid/latex/grid.plot.and.legend.tex
@@ -4525,11 +4548,14 @@
 lib/R/library/methods/R-ex/NextMethod.R
 lib/R/library/methods/R-ex/RClassUtils.R
 lib/R/library/methods/R-ex/RMethodUtils.R
+lib/R/library/methods/R-ex/S3Part.R
 lib/R/library/methods/R-ex/S4groupGeneric.R
 lib/R/library/methods/R-ex/StructureClasses.R
 lib/R/library/methods/R-ex/as.R
+lib/R/library/methods/R-ex/callGeneric.R
 lib/R/library/methods/R-ex/canCoerce.R
 lib/R/library/methods/R-ex/cbind2.R
+lib/R/library/methods/R-ex/dotsMethods.R
 lib/R/library/methods/R-ex/findMethods.R
 lib/R/library/methods/R-ex/getClass.R
 lib/R/library/methods/R-ex/getMethod.R
@@ -4542,7 +4568,6 @@
 lib/R/library/methods/R-ex/new.R
 lib/R/library/methods/R-ex/promptClass.R
 lib/R/library/methods/R-ex/representation.R
-lib/R/library/methods/R-ex/seemsS4Object.R
 lib/R/library/methods/R-ex/setClass.R
 lib/R/library/methods/R-ex/setClassUnion.R
 lib/R/library/methods/R-ex/setGeneric.R
@@ -4574,15 +4599,19 @@
 lib/R/library/methods/help/ObjectsWithPackage-class
 lib/R/library/methods/help/RClassUtils
 lib/R/library/methods/help/RMethodUtils
+lib/R/library/methods/help/S3Part
 lib/R/library/methods/help/S4groupGeneric
 lib/R/library/methods/help/SClassExtension-class
 lib/R/library/methods/help/Session
 lib/R/library/methods/help/StructureClasses
 lib/R/library/methods/help/TraceClasses
 lib/R/library/methods/help/as
+lib/R/library/methods/help/callGeneric
 lib/R/library/methods/help/canCoerce
 lib/R/library/methods/help/cbind2
 lib/R/library/methods/help/classRepresentation-class
+lib/R/library/methods/help/dotsMethods
+lib/R/library/methods/help/findClass
 lib/R/library/methods/help/findMethods
 lib/R/library/methods/help/fixPrevious
 lib/R/library/methods/help/genericFunction-class
@@ -4597,14 +4626,12 @@
 lib/R/library/methods/help/languageEl
 lib/R/library/methods/help/method.skeleton
 lib/R/library/methods/help/methodUtilities
-lib/R/library/methods/help/methods-deprecated
+lib/R/library/methods/help/methods-defunct
 lib/R/library/methods/help/methods-package
 lib/R/library/methods/help/new
-lib/R/library/methods/help/oldGet
 lib/R/library/methods/help/promptClass
 lib/R/library/methods/help/promptMethods
 lib/R/library/methods/help/representation
-lib/R/library/methods/help/seemsS4Object
 lib/R/library/methods/help/setClass
 lib/R/library/methods/help/setClassUnion
 lib/R/library/methods/help/setGeneric
@@ -4637,15 +4664,19 @@
 lib/R/library/methods/html/ObjectsWithPackage-class.html
 lib/R/library/methods/html/RClassUtils.html
 lib/R/library/methods/html/RMethodUtils.html
+lib/R/library/methods/html/S3Part.html
 lib/R/library/methods/html/S4groupGeneric.html
 lib/R/library/methods/html/SClassExtension-class.html
 lib/R/library/methods/html/Session.html
 lib/R/library/methods/html/StructureClasses.html
 lib/R/library/methods/html/TraceClasses.html
 lib/R/library/methods/html/as.html
+lib/R/library/methods/html/callGeneric.html
 lib/R/library/methods/html/canCoerce.html
 lib/R/library/methods/html/cbind2.html
 lib/R/library/methods/html/classRepresentation-class.html
+lib/R/library/methods/html/dotsMethods.html
+lib/R/library/methods/html/findClass.html
 lib/R/library/methods/html/findMethods.html
 lib/R/library/methods/html/fixPrevious.html
 lib/R/library/methods/html/genericFunction-class.html
@@ -4660,14 +4691,12 @@
 lib/R/library/methods/html/languageEl.html
 lib/R/library/methods/html/method.skeleton.html
 lib/R/library/methods/html/methodUtilities.html
-lib/R/library/methods/html/methods-deprecated.html
+lib/R/library/methods/html/methods-defunct.html
 lib/R/library/methods/html/methods-package.html
 lib/R/library/methods/html/new.html
-lib/R/library/methods/html/oldGet.html
 lib/R/library/methods/html/promptClass.html
 lib/R/library/methods/html/promptMethods.html
 lib/R/library/methods/html/representation.html
-lib/R/library/methods/html/seemsS4Object.html
 lib/R/library/methods/html/setClass.html
 lib/R/library/methods/html/setClassUnion.html
 lib/R/library/methods/html/setGeneric.html
@@ -4699,15 +4728,19 @@
 lib/R/library/methods/latex/ObjectsWithPackage-class.tex
 lib/R/library/methods/latex/RClassUtils.tex
 lib/R/library/methods/latex/RMethodUtils.tex
+lib/R/library/methods/latex/S3Part.tex
 lib/R/library/methods/latex/S4groupGeneric.tex
 lib/R/library/methods/latex/SClassExtension-class.tex
 lib/R/library/methods/latex/Session.tex
 lib/R/library/methods/latex/StructureClasses.tex
 lib/R/library/methods/latex/TraceClasses.tex
 lib/R/library/methods/latex/as.tex
+lib/R/library/methods/latex/callGeneric.tex
 lib/R/library/methods/latex/canCoerce.tex
 lib/R/library/methods/latex/cbind2.tex
 lib/R/library/methods/latex/classRepresentation-class.tex
+lib/R/library/methods/latex/dotsMethods.tex
+lib/R/library/methods/latex/findClass.tex
 lib/R/library/methods/latex/findMethods.tex
 lib/R/library/methods/latex/fixPrevious.tex
 lib/R/library/methods/latex/genericFunction-class.tex
@@ -4722,14 +4755,12 @@
 lib/R/library/methods/latex/languageEl.tex
 lib/R/library/methods/latex/method.skeleton.tex
 lib/R/library/methods/latex/methodUtilities.tex
-lib/R/library/methods/latex/methods-deprecated.tex
+lib/R/library/methods/latex/methods-defunct.tex
 lib/R/library/methods/latex/methods-package.tex
 lib/R/library/methods/latex/new.tex
-lib/R/library/methods/latex/oldGet.tex
 lib/R/library/methods/latex/promptClass.tex
 lib/R/library/methods/latex/promptMethods.tex
 lib/R/library/methods/latex/representation.tex
-lib/R/library/methods/latex/seemsS4Object.tex
 lib/R/library/methods/latex/setClass.tex
 lib/R/library/methods/latex/setClassUnion.tex
 lib/R/library/methods/latex/setGeneric.tex
@@ -8359,6 +8390,7 @@
 lib/R/library/utils/R-ex/prompt.R
 lib/R/library/utils/R-ex/promptData.R
 lib/R/library/utils/R-ex/promptPackage.R
+lib/R/library/utils/R-ex/read.DIF.R
 lib/R/library/utils/R-ex/read.fortran.R
 lib/R/library/utils/R-ex/read.fwf.R
 lib/R/library/utils/R-ex/read.socket.R
@@ -8435,6 +8467,7 @@
 lib/R/library/utils/help/glob2rx
 lib/R/library/utils/help/head
 lib/R/library/utils/help/help
+lib/R/library/utils/help/help.request
 lib/R/library/utils/help/help.search
 lib/R/library/utils/help/help.start
 lib/R/library/utils/help/index.search
@@ -8542,6 +8575,7 @@
 lib/R/library/utils/html/glob2rx.html
 lib/R/library/utils/html/head.html
 lib/R/library/utils/html/help.html
+lib/R/library/utils/html/help.request.html
 lib/R/library/utils/html/help.search.html
 lib/R/library/utils/html/help.start.html
 lib/R/library/utils/html/index.search.html
@@ -8648,6 +8682,7 @@
 lib/R/library/utils/latex/getS3method.tex
 lib/R/library/utils/latex/glob2rx.tex
 lib/R/library/utils/latex/head.tex
+lib/R/library/utils/latex/help.request.tex
 lib/R/library/utils/latex/help.search.tex
 lib/R/library/utils/latex/help.start.tex
 lib/R/library/utils/latex/help.tex
@@ -8703,6 +8738,8 @@
 lib/R/library/utils/latex/write.table.tex
 lib/R/library/utils/latex/zip.file.extract.tex
 lib/R/library/utils/man/utils.Rd.gz
+lib/R/library/utils/misc/exDIF.csv
+lib/R/library/utils/misc/exDIF.dif
 %%NLS%%lib/R/library/utils/po/en at quot/LC_MESSAGES/R-utils.mo
 %%NLS%%lib/R/library/utils/po/de/LC_MESSAGES/R-utils.mo
 %%NLS%%lib/R/library/utils/po/fr/LC_MESSAGES/R-utils.mo
@@ -8899,6 +8936,7 @@
 %%NLS%%@dirrm lib/R/library/utils/po/en at quot/LC_MESSAGES
 %%NLS%%@dirrm lib/R/library/utils/po/en at quot
 %%NLS%%@dirrm lib/R/library/utils/po
+ at dirrm lib/R/library/utils/misc
 @dirrm lib/R/library/utils/man
 @dirrm lib/R/library/utils/latex
 @dirrm lib/R/library/utils/html


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