r: updated to work with rstudio-1.3

3 files changed, 128 insertions, 6 deletions

diff --git a/r/.footprint b/r/.footprint
index f6aea0041..f7fc5a617 100644
--- a/r/.footprint
+++ b/r/.footprint
@@ -88,6 +88,38 @@ drwxr-xr-x	root/root	usr/lib/R/bin/exec/
 -rwxr-xr-x	root/root	usr/lib/R/bin/mkinstalldirs
 -rwxr-xr-x	root/root	usr/lib/R/bin/pager
 -rwxr-xr-x	root/root	usr/lib/R/bin/rtags
+drwxr-xr-x	root/root	usr/lib/R/doc/
+-rw-r--r--	root/root	usr/lib/R/doc/BioC_mirrors.csv
+-rw-r--r--	root/root	usr/lib/R/doc/COPYRIGHTS
+-rw-r--r--	root/root	usr/lib/R/doc/CRAN_mirrors.csv
+-rw-r--r--	root/root	usr/lib/R/doc/FAQ
+-rw-r--r--	root/root	usr/lib/R/doc/KEYWORDS
+-rw-r--r--	root/root	usr/lib/R/doc/KEYWORDS.db
+-rw-r--r--	root/root	usr/lib/R/doc/RESOURCES
+drwxr-xr-x	root/root	usr/lib/R/doc/html/
+-rw-r--r--	root/root	usr/lib/R/doc/html/R.css
+-rw-r--r--	root/root	usr/lib/R/doc/html/Rlogo.pdf
+-rw-r--r--	root/root	usr/lib/R/doc/html/Rlogo.svg
+-rw-r--r--	root/root	usr/lib/R/doc/html/Search.html
+-rw-r--r--	root/root	usr/lib/R/doc/html/SearchOn.html
+-rw-r--r--	root/root	usr/lib/R/doc/html/about.html
+-rw-r--r--	root/root	usr/lib/R/doc/html/favicon.ico
+-rw-r--r--	root/root	usr/lib/R/doc/html/index.html
+-rw-r--r--	root/root	usr/lib/R/doc/html/left.jpg
+-rw-r--r--	root/root	usr/lib/R/doc/html/logo.jpg
+-rw-r--r--	root/root	usr/lib/R/doc/html/packages-head-utf8.html
+-rw-r--r--	root/root	usr/lib/R/doc/html/packages.html
+-rw-r--r--	root/root	usr/lib/R/doc/html/resources.html
+-rw-r--r--	root/root	usr/lib/R/doc/html/right.jpg
+-rw-r--r--	root/root	usr/lib/R/doc/html/up.jpg
+drwxr-xr-x	root/root	usr/lib/R/doc/manual/
+drwxr-xr-x	root/root	usr/lib/R/doc/manual/images/
+-rw-r--r--	root/root	usr/lib/R/doc/manual/images/QQ.png
+-rw-r--r--	root/root	usr/lib/R/doc/manual/images/ecdf.png
+-rw-r--r--	root/root	usr/lib/R/doc/manual/images/fig11.png
+-rw-r--r--	root/root	usr/lib/R/doc/manual/images/fig12.png
+-rw-r--r--	root/root	usr/lib/R/doc/manual/images/hist.png
+-rw-r--r--	root/root	usr/lib/R/doc/manual/images/ice.png
 drwxr-xr-x	root/root	usr/lib/R/etc/
 lrwxrwxrwx	root/root	usr/lib/R/etc/Makeconf -> /etc/R/Makeconf
 lrwxrwxrwx	root/root	usr/lib/R/etc/Renviron -> /etc/R/Renviron
@@ -230,6 +262,31 @@ drwxr-xr-x	root/root	usr/lib/R/library/Matrix/data/
 -rw-r--r--	root/root	usr/lib/R/library/Matrix/data/CAex.R
 -rw-r--r--	root/root	usr/lib/R/library/Matrix/data/KNex.R
 -rw-r--r--	root/root	usr/lib/R/library/Matrix/data/USCounties.R
+drwxr-xr-x	root/root	usr/lib/R/library/Matrix/doc/
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/Announce.txt
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/Comparisons.R
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/Comparisons.Rnw
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/Comparisons.pdf
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/Design-issues.R
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/Design-issues.Rnw
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/Design-issues.pdf
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/Intro2Matrix.R
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/Intro2Matrix.Rnw
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/Intro2Matrix.pdf
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/Introduction.R
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/Introduction.Rnw
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/Introduction.pdf
+drwxr-xr-x	root/root	usr/lib/R/library/Matrix/doc/SuiteSparse/
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/SuiteSparse/AMD.txt
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/SuiteSparse/CHOLMOD.txt
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/SuiteSparse/COLAMD.txt
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/SuiteSparse/SPQR.txt
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/SuiteSparse/SuiteSparse_config.txt
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/SuiteSparse/UserGuides.txt
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/index.html
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/sparseModels.R
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/sparseModels.Rnw
+-rw-r--r--	root/root	usr/lib/R/library/Matrix/doc/sparseModels.pdf
 drwxr-xr-x	root/root	usr/lib/R/library/Matrix/external/
 -rw-r--r--	root/root	usr/lib/R/library/Matrix/external/CAex_slots.rda
 -rw-r--r--	root/root	usr/lib/R/library/Matrix/external/KNex_slots.rda
@@ -784,6 +841,22 @@ drwxr-xr-x	root/root	usr/lib/R/library/grid/R/
 -rw-r--r--	root/root	usr/lib/R/library/grid/R/grid
 -rw-r--r--	root/root	usr/lib/R/library/grid/R/grid.rdb
 -rw-r--r--	root/root	usr/lib/R/library/grid/R/grid.rdx
+drwxr-xr-x	root/root	usr/lib/R/library/grid/doc/
+-rw-r--r--	root/root	usr/lib/R/library/grid/doc/DivByZero.txt
+-rw-r--r--	root/root	usr/lib/R/library/grid/doc/changes.txt
+-rw-r--r--	root/root	usr/lib/R/library/grid/doc/displaylist.pdf
+-rw-r--r--	root/root	usr/lib/R/library/grid/doc/frame.pdf
+-rw-r--r--	root/root	usr/lib/R/library/grid/doc/grid.pdf
+-rw-r--r--	root/root	usr/lib/R/library/grid/doc/grobs.pdf
+-rw-r--r--	root/root	usr/lib/R/library/grid/doc/interactive.pdf
+-rw-r--r--	root/root	usr/lib/R/library/grid/doc/locndimn.pdf
+-rw-r--r--	root/root	usr/lib/R/library/grid/doc/moveline.pdf
+-rw-r--r--	root/root	usr/lib/R/library/grid/doc/nonfinite.pdf
+-rw-r--r--	root/root	usr/lib/R/library/grid/doc/plotexample.pdf
+-rw-r--r--	root/root	usr/lib/R/library/grid/doc/rotated.pdf
+-rw-r--r--	root/root	usr/lib/R/library/grid/doc/saveload.pdf
+-rw-r--r--	root/root	usr/lib/R/library/grid/doc/sharing.pdf
+-rw-r--r--	root/root	usr/lib/R/library/grid/doc/viewports.pdf
 drwxr-xr-x	root/root	usr/lib/R/library/grid/help/
 -rw-r--r--	root/root	usr/lib/R/library/grid/help/AnIndex
 -rw-r--r--	root/root	usr/lib/R/library/grid/help/aliases.rds
@@ -1052,6 +1125,8 @@ drwxr-xr-x	root/root	usr/lib/R/library/parallel/R/
 -rw-r--r--	root/root	usr/lib/R/library/parallel/R/parallel
 -rw-r--r--	root/root	usr/lib/R/library/parallel/R/parallel.rdb
 -rw-r--r--	root/root	usr/lib/R/library/parallel/R/parallel.rdx
+drwxr-xr-x	root/root	usr/lib/R/library/parallel/doc/
+-rw-r--r--	root/root	usr/lib/R/library/parallel/doc/parallel.pdf
 drwxr-xr-x	root/root	usr/lib/R/library/parallel/help/
 -rw-r--r--	root/root	usr/lib/R/library/parallel/help/AnIndex
 -rw-r--r--	root/root	usr/lib/R/library/parallel/help/aliases.rds
@@ -1084,6 +1159,14 @@ drwxr-xr-x	root/root	usr/lib/R/library/rpart/data/
 -rw-r--r--	root/root	usr/lib/R/library/rpart/data/Rdata.rdb
 -rw-r--r--	root/root	usr/lib/R/library/rpart/data/Rdata.rds
 -rw-r--r--	root/root	usr/lib/R/library/rpart/data/Rdata.rdx
+drwxr-xr-x	root/root	usr/lib/R/library/rpart/doc/
+-rw-r--r--	root/root	usr/lib/R/library/rpart/doc/index.html
+-rw-r--r--	root/root	usr/lib/R/library/rpart/doc/longintro.R
+-rw-r--r--	root/root	usr/lib/R/library/rpart/doc/longintro.Rnw
+-rw-r--r--	root/root	usr/lib/R/library/rpart/doc/longintro.pdf
+-rw-r--r--	root/root	usr/lib/R/library/rpart/doc/usercode.R
+-rw-r--r--	root/root	usr/lib/R/library/rpart/doc/usercode.Rnw
+-rw-r--r--	root/root	usr/lib/R/library/rpart/doc/usercode.pdf
 drwxr-xr-x	root/root	usr/lib/R/library/rpart/help/
 -rw-r--r--	root/root	usr/lib/R/library/rpart/help/AnIndex
 -rw-r--r--	root/root	usr/lib/R/library/rpart/help/aliases.rds
@@ -1298,6 +1381,42 @@ drwxr-xr-x	root/root	usr/lib/R/library/survival/data/
 -rw-r--r--	root/root	usr/lib/R/library/survival/data/Rdata.rdb
 -rw-r--r--	root/root	usr/lib/R/library/survival/data/Rdata.rds
 -rw-r--r--	root/root	usr/lib/R/library/survival/data/Rdata.rdx
+drwxr-xr-x	root/root	usr/lib/R/library/survival/doc/
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/adjcurve.R
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/adjcurve.Rnw
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/adjcurve.pdf
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/approximate.R
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/approximate.Rnw
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/approximate.pdf
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/compete.R
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/compete.Rnw
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/compete.pdf
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/concordance.R
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/concordance.Rnw
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/concordance.pdf
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/index.html
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/multi.Rnw
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/multi.pdf
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/other.Rnw
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/other.pdf
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/population.R
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/population.Rnw
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/population.pdf
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/splines.R
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/splines.Rnw
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/splines.pdf
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/survival.R
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/survival.Rnw
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/survival.pdf
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/tiedtimes.R
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/tiedtimes.Rnw
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/tiedtimes.pdf
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/timedep.R
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/timedep.Rnw
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/timedep.pdf
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/validate.R
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/validate.Rnw
+-rw-r--r--	root/root	usr/lib/R/library/survival/doc/validate.pdf
 drwxr-xr-x	root/root	usr/lib/R/library/survival/help/
 -rw-r--r--	root/root	usr/lib/R/library/survival/help/AnIndex
 -rw-r--r--	root/root	usr/lib/R/library/survival/help/aliases.rds
@@ -1717,6 +1836,8 @@ drwxr-xr-x	root/root	usr/lib/R/library/utils/R/
 drwxr-xr-x	root/root	usr/lib/R/library/utils/Sweave/
 -rw-r--r--	root/root	usr/lib/R/library/utils/Sweave/Sweave-test-1.Rnw
 -rw-r--r--	root/root	usr/lib/R/library/utils/Sweave/example-1.Rnw
+drwxr-xr-x	root/root	usr/lib/R/library/utils/doc/
+-rw-r--r--	root/root	usr/lib/R/library/utils/doc/Sweave.pdf
 drwxr-xr-x	root/root	usr/lib/R/library/utils/help/
 -rw-r--r--	root/root	usr/lib/R/library/utils/help/AnIndex
 -rw-r--r--	root/root	usr/lib/R/library/utils/help/aliases.rds
diff --git a/r/.signature b/r/.signature
index 83489a575..ba795ecfd 100644
--- a/r/.signature
+++ b/r/.signature
@@ -1,7 +1,7 @@
 untrusted comment: verify with /etc/ports/contrib.pub
-RWSagIOpLGJF3zHplZ3ryKpyRZ2aqBMkPIHTi2TI4EgzuG/GQNeSELFAlrElElWbSLdGx/WwTlIP7GCaYTZ0IUjt1IpXFDkGswI=
-SHA256 (Pkgfile) = 6b9bc9527c44c5121803e8bcf2c47c45c0c982d3a572e8f87692fb9e41c8539f
-SHA256 (.footprint) = 4255b79956909b6fec37491dafb5141385b1c982ec378877f2d0caaee8a3e756
+RWSagIOpLGJF39ChFI6ln8ii4/SEj2l9kbUxw5wqPK33iZSXHa+XCVxffb9MUTOKDWUy3IKP+qBl82kS8mPtjnNk6qQls2gQxws=
+SHA256 (Pkgfile) = 82f55f0ff4b924f629df27efb3ccd6e372daeff269313db8fd1af7f43481c1c6
+SHA256 (.footprint) = e2b6dd2da40317845871f0a1672fb65facf0ab579a4ac0df039d409b261a8c8c
 SHA256 (R-4.0.0.tar.gz) = 06beb0291b569978484eb0dcb5d2339665ec745737bdfb4e873e7a5a75492940
 SHA256 (r.desktop) = 25b01ea93fa704884b65ba002d44d4e99725bd826997e8c73b6467df9f23c798
 SHA256 (r.png) = 465b623f15d8144fb30b52791047a22302c275d51f749d8732454e4496c1a989
diff --git a/r/Pkgfile b/r/Pkgfile
index 3aa5ee5c2..bb7f440a0 100644
--- a/r/Pkgfile
+++ b/r/Pkgfile
@@ -6,7 +6,7 @@
 
 name=r
 version=4.0.0
-release=1
+release=2
 source=(https://cran.r-project.org/src/base/R-4/R-$version.tar.gz
   r.desktop r.png R.conf
   R-3.4.1-parallel.patch R-3.4.1-rmath-shared.patch
@@ -92,9 +92,10 @@ build() {
     -iname '*THANKS*' -o \
     -iname '*NEWS*' -o \
     -iname '*LICENSE*' -o \
-    -iname 'doc' -o \
     -iname '*CHANGELOG*' \
     \) -exec rm -r '{}' \+ || true
-    #doh! don't remove INSTALL or you won't be able to install R packages
+    ## doh! don't remove INSTALL or you won't be able to install R packages
     #-iname '*INSTALL*' -o \
+    ## rstudio now depends on finding docs that R provides..
+    #-iname 'doc' -o \
 }