14 files changed, 44 insertions, 1355 deletions

diff --git a/math/R-cran-RSvgDevice/Makefile b/math/R-cran-RSvgDevice/Makefile
index 271a73cfac9b..49ce86f4d0fd 100644
--- a/math/R-cran-RSvgDevice/Makefile
+++ b/math/R-cran-RSvgDevice/Makefile
@@ -7,7 +7,7 @@
 
 PORTNAME=	RSvgDevice
 PORTVERSION=	0.6.4.1
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math
 PKGNAMEPREFIX=	R-cran-
 DISTNAME=	${PORTNAME}_${PORTVERSION}
diff --git a/math/R-cran-RSvgDevice/pkg-plist b/math/R-cran-RSvgDevice/pkg-plist
index 6674eeaf0ed1..352a2863e58d 100644
--- a/math/R-cran-RSvgDevice/pkg-plist
+++ b/math/R-cran-RSvgDevice/pkg-plist
@@ -1,21 +1,19 @@
-%%R_MOD_DIR%%/CONTENTS
 %%R_MOD_DIR%%/DESCRIPTION
 %%R_MOD_DIR%%/INDEX
 %%R_MOD_DIR%%/Meta/Rd.rds
 %%R_MOD_DIR%%/Meta/hsearch.rds
+%%R_MOD_DIR%%/Meta/links.rds
 %%R_MOD_DIR%%/Meta/package.rds
-%%R_MOD_DIR%%/R-ex/RSvgDevice.R
 %%R_MOD_DIR%%/R/RSvgDevice
 %%R_MOD_DIR%%/R/RSvgDevice.rdb
 %%R_MOD_DIR%%/R/RSvgDevice.rdx
 %%R_MOD_DIR%%/help/AnIndex
-%%R_MOD_DIR%%/help/RSvgDevice
+%%R_MOD_DIR%%/help/paths.rds
+%%R_MOD_DIR%%/help/RSvgDevice.rdb
+%%R_MOD_DIR%%/help/RSvgDevice.rdx
+%%R_MOD_DIR%%/help/aliases.rds
 %%R_MOD_DIR%%/html/00Index.html
-%%R_MOD_DIR%%/html/RSvgDevice.html
-%%R_MOD_DIR%%/latex/RSvgDevice.tex
 %%R_MOD_DIR%%/libs/RSvgDevice.so
-%%R_MOD_DIR%%/man/RSvgDevice.Rd.gz
-@dirrm %%R_MOD_DIR%%/man
 @dirrm %%R_MOD_DIR%%/libs
 @dirrm %%R_MOD_DIR%%/latex
 @dirrm %%R_MOD_DIR%%/html
diff --git a/math/R-cran-Zelig/Makefile b/math/R-cran-Zelig/Makefile
index a6674876decb..4196bb6121b0 100644
--- a/math/R-cran-Zelig/Makefile
+++ b/math/R-cran-Zelig/Makefile
@@ -7,7 +7,7 @@
 
 PORTNAME=	Zelig
 PORTVERSION=	3.4.3
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math
 PKGNAMEPREFIX=	R-cran-
 DISTNAME=	${PORTNAME}_3.4-3
diff --git a/math/R-cran-Zelig/pkg-plist b/math/R-cran-Zelig/pkg-plist
index 49121badcec8..d992ee15a078 100644
--- a/math/R-cran-Zelig/pkg-plist
+++ b/math/R-cran-Zelig/pkg-plist
@@ -1,4 +1,3 @@
-%%R_MOD_DIR%%/CONTENTS
 %%R_MOD_DIR%%/COPYING
 %%R_MOD_DIR%%/DESCRIPTION
 %%R_MOD_DIR%%/INDEX
@@ -7,6 +6,7 @@
 %%R_MOD_DIR%%/Meta/data.rds
 %%R_MOD_DIR%%/Meta/demo.rds
 %%R_MOD_DIR%%/Meta/hsearch.rds
+%%R_MOD_DIR%%/Meta/links.rds
 %%R_MOD_DIR%%/Meta/nsInfo.rds
 %%R_MOD_DIR%%/Meta/package.rds
 %%R_MOD_DIR%%/Meta/vignette.rds
@@ -14,27 +14,6 @@
 %%R_MOD_DIR%%/R/Zelig
 %%R_MOD_DIR%%/R/Zelig.rdb
 %%R_MOD_DIR%%/R/Zelig.rdx
-%%R_MOD_DIR%%/R-ex/current.packages.R
-%%R_MOD_DIR%%/R-ex/dims.R
-%%R_MOD_DIR%%/R-ex/friendship.R
-%%R_MOD_DIR%%/R-ex/gsource.R
-%%R_MOD_DIR%%/R-ex/mi.R
-%%R_MOD_DIR%%/R-ex/model.frame.multiple.R
-%%R_MOD_DIR%%/R-ex/model.matrix.multiple.R
-%%R_MOD_DIR%%/R-ex/network.R
-%%R_MOD_DIR%%/R-ex/parse.formula.R
-%%R_MOD_DIR%%/R-ex/parse.par.R
-%%R_MOD_DIR%%/R-ex/plot.ci.R
-%%R_MOD_DIR%%/R-ex/plot.surv.R
-%%R_MOD_DIR%%/R-ex/repl.R
-%%R_MOD_DIR%%/R-ex/rocplot.R
-%%R_MOD_DIR%%/R-ex/set.start.R
-%%R_MOD_DIR%%/R-ex/setx.R
-%%R_MOD_DIR%%/R-ex/ternaryplot.R
-%%R_MOD_DIR%%/R-ex/user.prompt.R
-%%R_MOD_DIR%%/R-ex/zeligDepStatus.R
-%%R_MOD_DIR%%/R-ex/zeligDepUpdate.R
-%%R_MOD_DIR%%/R-ex/zeligVDC.R
 %%R_MOD_DIR%%/data/MatchIt.url.tab
 %%R_MOD_DIR%%/data/PErisk.txt
 %%R_MOD_DIR%%/data/SupremeCourt.txt
@@ -694,185 +673,11 @@
 %%R_MOD_DIR%%/doc/zeligmodels.html
 %%R_MOD_DIR%%/doc/zinput.tex
 %%R_MOD_DIR%%/help/AnIndex
-%%R_MOD_DIR%%/help/MatchIt.url
-%%R_MOD_DIR%%/help/PErisk
-%%R_MOD_DIR%%/help/SupremeCourt
-%%R_MOD_DIR%%/help/Weimar
-%%R_MOD_DIR%%/help/Zelig
-%%R_MOD_DIR%%/help/Zelig-package
-%%R_MOD_DIR%%/help/Zelig.url
-%%R_MOD_DIR%%/help/approval
-%%R_MOD_DIR%%/help/bivariate
-%%R_MOD_DIR%%/help/coalition
-%%R_MOD_DIR%%/help/coalition2
-%%R_MOD_DIR%%/help/current.packages
-%%R_MOD_DIR%%/help/dims
-%%R_MOD_DIR%%/help/eidat
-%%R_MOD_DIR%%/help/free1
-%%R_MOD_DIR%%/help/free2
-%%R_MOD_DIR%%/help/friendship
-%%R_MOD_DIR%%/help/grunfeld
-%%R_MOD_DIR%%/help/gsource
-%%R_MOD_DIR%%/help/help.zelig
-%%R_MOD_DIR%%/help/hoff
-%%R_MOD_DIR%%/help/homerun
-%%R_MOD_DIR%%/help/immigration
-%%R_MOD_DIR%%/help/klein
-%%R_MOD_DIR%%/help/kmenta
-%%R_MOD_DIR%%/help/macro
-%%R_MOD_DIR%%/help/match.data
-%%R_MOD_DIR%%/help/mexico
-%%R_MOD_DIR%%/help/mi
-%%R_MOD_DIR%%/help/mid
-%%R_MOD_DIR%%/help/model.end
-%%R_MOD_DIR%%/help/model.frame.multiple
-%%R_MOD_DIR%%/help/model.matrix.multiple
-%%R_MOD_DIR%%/help/network
-%%R_MOD_DIR%%/help/newpainters
-%%R_MOD_DIR%%/help/parse.formula
-%%R_MOD_DIR%%/help/parse.par
-%%R_MOD_DIR%%/help/plot.ci
-%%R_MOD_DIR%%/help/plot.surv
-%%R_MOD_DIR%%/help/plot.zelig
-%%R_MOD_DIR%%/help/put.start
-%%R_MOD_DIR%%/help/repl
-%%R_MOD_DIR%%/help/rocplot
-%%R_MOD_DIR%%/help/sanction
-%%R_MOD_DIR%%/help/set.start
-%%R_MOD_DIR%%/help/setx
-%%R_MOD_DIR%%/help/sim
-%%R_MOD_DIR%%/help/sna.ex
-%%R_MOD_DIR%%/help/summary.zelig
-%%R_MOD_DIR%%/help/swiss
-%%R_MOD_DIR%%/help/ternaryplot
-%%R_MOD_DIR%%/help/ternarypoints
-%%R_MOD_DIR%%/help/tobin
-%%R_MOD_DIR%%/help/turnout
-%%R_MOD_DIR%%/help/user.prompt
-%%R_MOD_DIR%%/help/voteincome
-%%R_MOD_DIR%%/help/zeligDepStatus
-%%R_MOD_DIR%%/help/zeligDepUpdate
-%%R_MOD_DIR%%/help/zeligVDC
+%%R_MOD_DIR%%/help/Zelig.rdb
+%%R_MOD_DIR%%/help/Zelig.rdx
+%%R_MOD_DIR%%/help/aliases.rds
+%%R_MOD_DIR%%/help/paths.rds
 %%R_MOD_DIR%%/html/00Index.html
-%%R_MOD_DIR%%/html/MatchIt.url.html
-%%R_MOD_DIR%%/html/PErisk.html
-%%R_MOD_DIR%%/html/SupremeCourt.html
-%%R_MOD_DIR%%/html/Weimar.html
-%%R_MOD_DIR%%/html/Zelig-package.html
-%%R_MOD_DIR%%/html/Zelig.html
-%%R_MOD_DIR%%/html/Zelig.url.html
-%%R_MOD_DIR%%/html/approval.html
-%%R_MOD_DIR%%/html/bivariate.html
-%%R_MOD_DIR%%/html/coalition.html
-%%R_MOD_DIR%%/html/coalition2.html
-%%R_MOD_DIR%%/html/current.packages.html
-%%R_MOD_DIR%%/html/dims.html
-%%R_MOD_DIR%%/html/eidat.html
-%%R_MOD_DIR%%/html/free1.html
-%%R_MOD_DIR%%/html/free2.html
-%%R_MOD_DIR%%/html/friendship.html
-%%R_MOD_DIR%%/html/grunfeld.html
-%%R_MOD_DIR%%/html/gsource.html
-%%R_MOD_DIR%%/html/help.zelig.html
-%%R_MOD_DIR%%/html/hoff.html
-%%R_MOD_DIR%%/html/homerun.html
-%%R_MOD_DIR%%/html/immigration.html
-%%R_MOD_DIR%%/html/klein.html
-%%R_MOD_DIR%%/html/kmenta.html
-%%R_MOD_DIR%%/html/macro.html
-%%R_MOD_DIR%%/html/match.data.html
-%%R_MOD_DIR%%/html/mexico.html
-%%R_MOD_DIR%%/html/mi.html
-%%R_MOD_DIR%%/html/mid.html
-%%R_MOD_DIR%%/html/model.end.html
-%%R_MOD_DIR%%/html/model.frame.multiple.html
-%%R_MOD_DIR%%/html/model.matrix.multiple.html
-%%R_MOD_DIR%%/html/network.html
-%%R_MOD_DIR%%/html/newpainters.html
-%%R_MOD_DIR%%/html/parse.formula.html
-%%R_MOD_DIR%%/html/parse.par.html
-%%R_MOD_DIR%%/html/plot.ci.html
-%%R_MOD_DIR%%/html/plot.surv.html
-%%R_MOD_DIR%%/html/plot.zelig.html
-%%R_MOD_DIR%%/html/put.start.html
-%%R_MOD_DIR%%/html/repl.html
-%%R_MOD_DIR%%/html/rocplot.html
-%%R_MOD_DIR%%/html/sanction.html
-%%R_MOD_DIR%%/html/set.start.html
-%%R_MOD_DIR%%/html/setx.html
-%%R_MOD_DIR%%/html/sim.html
-%%R_MOD_DIR%%/html/sna.ex.html
-%%R_MOD_DIR%%/html/summary.zelig.html
-%%R_MOD_DIR%%/html/swiss.html
-%%R_MOD_DIR%%/html/ternaryplot.html
-%%R_MOD_DIR%%/html/ternarypoints.html
-%%R_MOD_DIR%%/html/tobin.html
-%%R_MOD_DIR%%/html/turnout.html
-%%R_MOD_DIR%%/html/user.prompt.html
-%%R_MOD_DIR%%/html/voteincome.html
-%%R_MOD_DIR%%/html/zeligDepStatus.html
-%%R_MOD_DIR%%/html/zeligDepUpdate.html
-%%R_MOD_DIR%%/html/zeligVDC.html
-%%R_MOD_DIR%%/latex/MatchIt.url.tex
-%%R_MOD_DIR%%/latex/PErisk.tex
-%%R_MOD_DIR%%/latex/SupremeCourt.tex
-%%R_MOD_DIR%%/latex/Weimar.tex
-%%R_MOD_DIR%%/latex/Zelig-package.tex
-%%R_MOD_DIR%%/latex/Zelig.tex
-%%R_MOD_DIR%%/latex/Zelig.url.tex
-%%R_MOD_DIR%%/latex/approval.tex
-%%R_MOD_DIR%%/latex/bivariate.tex
-%%R_MOD_DIR%%/latex/coalition.tex
-%%R_MOD_DIR%%/latex/coalition2.tex
-%%R_MOD_DIR%%/latex/current.packages.tex
-%%R_MOD_DIR%%/latex/dims.tex
-%%R_MOD_DIR%%/latex/eidat.tex
-%%R_MOD_DIR%%/latex/free1.tex
-%%R_MOD_DIR%%/latex/free2.tex
-%%R_MOD_DIR%%/latex/friendship.tex
-%%R_MOD_DIR%%/latex/grunfeld.tex
-%%R_MOD_DIR%%/latex/gsource.tex
-%%R_MOD_DIR%%/latex/help.zelig.tex
-%%R_MOD_DIR%%/latex/hoff.tex
-%%R_MOD_DIR%%/latex/homerun.tex
-%%R_MOD_DIR%%/latex/immigration.tex
-%%R_MOD_DIR%%/latex/klein.tex
-%%R_MOD_DIR%%/latex/kmenta.tex
-%%R_MOD_DIR%%/latex/macro.tex
-%%R_MOD_DIR%%/latex/match.data.tex
-%%R_MOD_DIR%%/latex/mexico.tex
-%%R_MOD_DIR%%/latex/mi.tex
-%%R_MOD_DIR%%/latex/mid.tex
-%%R_MOD_DIR%%/latex/model.end.tex
-%%R_MOD_DIR%%/latex/model.frame.multiple.tex
-%%R_MOD_DIR%%/latex/model.matrix.multiple.tex
-%%R_MOD_DIR%%/latex/network.tex
-%%R_MOD_DIR%%/latex/newpainters.tex
-%%R_MOD_DIR%%/latex/parse.formula.tex
-%%R_MOD_DIR%%/latex/parse.par.tex
-%%R_MOD_DIR%%/latex/plot.ci.tex
-%%R_MOD_DIR%%/latex/plot.surv.tex
-%%R_MOD_DIR%%/latex/plot.zelig.tex
-%%R_MOD_DIR%%/latex/put.start.tex
-%%R_MOD_DIR%%/latex/repl.tex
-%%R_MOD_DIR%%/latex/rocplot.tex
-%%R_MOD_DIR%%/latex/sanction.tex
-%%R_MOD_DIR%%/latex/set.start.tex
-%%R_MOD_DIR%%/latex/setx.tex
-%%R_MOD_DIR%%/latex/sim.tex
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-%%R_MOD_DIR%%/latex/zeligDepUpdate.tex
-%%R_MOD_DIR%%/latex/zeligVDC.tex
-%%R_MOD_DIR%%/man/Zelig.Rd.gz
 %%R_MOD_DIR%%/zideal/zvcServer.R
 @dirrm %%R_MOD_DIR%%/Meta
 @dirrm %%R_MOD_DIR%%/R
diff --git a/math/R-cran-car/Makefile b/math/R-cran-car/Makefile
index 8c6e1443e132..468d127ce463 100644
--- a/math/R-cran-car/Makefile
+++ b/math/R-cran-car/Makefile
@@ -7,7 +7,7 @@
 
 PORTNAME=	car
 PORTVERSION=	1.2.13
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math
 PKGNAMEPREFIX=	R-cran-
 DISTNAME=	${PORTNAME}_1.2-13
diff --git a/math/R-cran-car/pkg-plist b/math/R-cran-car/pkg-plist
index e6d404209814..0b334b3fc2d5 100644
--- a/math/R-cran-car/pkg-plist
+++ b/math/R-cran-car/pkg-plist
@@ -1,298 +1,25 @@
 %%R_MOD_DIR%%/CHANGES
-%%R_MOD_DIR%%/CONTENTS
 %%R_MOD_DIR%%/DESCRIPTION
 %%R_MOD_DIR%%/INDEX
 %%R_MOD_DIR%%/Meta/Rd.rds
 %%R_MOD_DIR%%/Meta/data.rds
 %%R_MOD_DIR%%/Meta/hsearch.rds
+%%R_MOD_DIR%%/Meta/links.rds
 %%R_MOD_DIR%%/Meta/nsInfo.rds
 %%R_MOD_DIR%%/Meta/package.rds
+%%R_MOD_DIR%%/help/AnIndex
+%%R_MOD_DIR%%/help/paths.rds
+%%R_MOD_DIR%%/help/car.rdb
+%%R_MOD_DIR%%/help/car.rdx
+%%R_MOD_DIR%%/help/aliases.rds
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-%%R_MOD_DIR%%/R-ex/Ask.R
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--- a/math/R-cran-gpclib/pkg-plist
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@@ -1,46 +1,30 @@
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-%%R_MOD_DIR%%/latex/sm.script.tex
-%%R_MOD_DIR%%/latex/sm.sigma.tex
-%%R_MOD_DIR%%/latex/sm.sigma2.compare.tex
-%%R_MOD_DIR%%/latex/sm.sphere.tex
-%%R_MOD_DIR%%/latex/sm.surface3d.tex
-%%R_MOD_DIR%%/latex/sm.survival.tex
-%%R_MOD_DIR%%/latex/sm.tex
-%%R_MOD_DIR%%/latex/sm.ts.pdf.tex
-%%R_MOD_DIR%%/latex/sm.variogram.tex
-%%R_MOD_DIR%%/man/sm.Rd.gz
 %%R_MOD_DIR%%/scripts/air_band.q
 %%R_MOD_DIR%%/scripts/air_boot.q
 %%R_MOD_DIR%%/scripts/air_cont.q
@@ -289,12 +153,9 @@
 %%R_MOD_DIR%%/smdata/worm.doc
 @dirrm %%R_MOD_DIR%%/Meta
 @dirrm %%R_MOD_DIR%%/R
-@dirrm %%R_MOD_DIR%%/R-ex
 @dirrm %%R_MOD_DIR%%/data
 @dirrm %%R_MOD_DIR%%/help
 @dirrm %%R_MOD_DIR%%/html
-@dirrm %%R_MOD_DIR%%/latex
-@dirrm %%R_MOD_DIR%%/man
 @dirrm %%R_MOD_DIR%%/scripts
 @dirrm %%R_MOD_DIR%%/smdata
 @dirrm %%R_MOD_DIR%%
diff --git a/math/R-cran-sp/Makefile b/math/R-cran-sp/Makefile
index 146415b1f5e6..14a9084fcaef 100644
--- a/math/R-cran-sp/Makefile
+++ b/math/R-cran-sp/Makefile
@@ -7,7 +7,7 @@
 
 PORTNAME=	sp
 PORTVERSION=	0.9.37
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math
 PKGNAMEPREFIX=	R-cran-
 DISTNAME=	${PORTNAME}_0.9-37
diff --git a/math/R-cran-sp/pkg-plist b/math/R-cran-sp/pkg-plist
index f8ec62a68c27..ff8f9515f394 100644
--- a/math/R-cran-sp/pkg-plist
+++ b/math/R-cran-sp/pkg-plist
@@ -4,6 +4,7 @@ lib/R/library/sp/Meta/package.rds
 lib/R/library/sp/Meta/Rd.rds
 lib/R/library/sp/Meta/hsearch.rds
 lib/R/library/sp/Meta/data.rds
+lib/R/library/sp/Meta/links.rds
 lib/R/library/sp/Meta/vignette.rds
 lib/R/library/sp/Meta/demo.rds
 lib/R/library/sp/Meta/nsInfo.rds
@@ -25,236 +26,13 @@ lib/R/library/sp/doc/sp.R
 lib/R/library/sp/doc/index.html
 lib/R/library/sp/ChangeLog
 lib/R/library/sp/CITATION
-lib/R/library/sp/man/sp.Rd.gz
 lib/R/library/sp/help/AnIndex
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-lib/R/library/sp/help/Rlogo
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-lib/R/library/sp/help/SpatialGridDataFrame-class
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-lib/R/library/sp/help/SpatialPolygonsDataFrame-class
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-lib/R/library/sp/help/as.SpatialPolygons.PolygonsList
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-lib/R/library/sp/help/bbox
-lib/R/library/sp/help/bpy.colors
-lib/R/library/sp/help/bubble
-lib/R/library/sp/help/char2dms
-lib/R/library/sp/help/coordinates-methods
-lib/R/library/sp/help/coordinates
-lib/R/library/sp/help/coordnames-methods
-lib/R/library/sp/help/degaxis
-lib/R/library/sp/help/dimensions
-lib/R/library/sp/help/gridded-methods
-lib/R/library/sp/help/gridlines
-lib/R/library/sp/help/image
-lib/R/library/sp/help/is.projected
-lib/R/library/sp/help/mapasp
-lib/R/library/sp/help/meuse
-lib/R/library/sp/help/meuse.grid
-lib/R/library/sp/help/meuse.grid_ll
-lib/R/library/sp/help/meuse.riv
-lib/R/library/sp/help/nowrapSpatialLines
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-lib/R/library/sp/help/spplot
-lib/R/library/sp/help/spsample
-lib/R/library/sp/help/stack
-lib/R/library/sp/help/zerodist
+lib/R/library/sp/help/aliases.rds
+lib/R/library/sp/help/sp.rdx
+lib/R/library/sp/help/sp.rdb
+lib/R/library/sp/help/paths.rds
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-lib/R/library/sp/html/bpy.colors.html
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-lib/R/library/sp/html/coordinates.html
-lib/R/library/sp/html/coordnames-methods.html
-lib/R/library/sp/html/degaxis.html
-lib/R/library/sp/html/dimensions.html
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-lib/R/library/sp/html/spplot.html
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-lib/R/library/sp/latex/spplot.tex
-lib/R/library/sp/latex/spsample.tex
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-lib/R/library/sp/R-ex/SpatialPixelsDataFrame-class.R
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-lib/R/library/sp/R-ex/gridlines.R
-lib/R/library/sp/R-ex/image.R
-lib/R/library/sp/R-ex/meuse.R
-lib/R/library/sp/R-ex/meuse.grid.R
-lib/R/library/sp/R-ex/meuse.grid_ll.R
-lib/R/library/sp/R-ex/meuse.riv.R
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-lib/R/library/sp/R-ex/overlay.R
-lib/R/library/sp/R-ex/point.in.polygon.R
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-lib/R/library/sp/R-ex/stack.R
-lib/R/library/sp/R-ex/zerodist.R
 lib/R/library/sp/INDEX
-lib/R/library/sp/CONTENTS
 @dirrm lib/R/library/sp/Meta
 @dirrm lib/R/library/sp/libs
 @dirrm lib/R/library/sp/R
@@ -262,9 +40,6 @@ lib/R/library/sp/CONTENTS
 @dirrm lib/R/library/sp/demo
 @dirrm lib/R/library/sp/doc
 @dirrm lib/R/library/sp/external
-@dirrm lib/R/library/sp/man
 @dirrm lib/R/library/sp/help
 @dirrm lib/R/library/sp/html
-@dirrm lib/R/library/sp/latex
-@dirrm lib/R/library/sp/R-ex
 @dirrm lib/R/library/sp