[Vegan-commits] r2990 - in pkg/vegan: . R inst/doc man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Feb 25 13:09:52 CET 2016
Author: jarioksa
Date: 2016-02-25 13:09:51 +0100 (Thu, 25 Feb 2016)
New Revision: 2990
Added:
pkg/vegan/vignettes/FAQ-vegan.Rmd
pkg/vegan/vignettes/partitioning.Rnw
pkg/vegan/vignettes/varpart23.pdf
pkg/vegan/vignettes/varpart4.pdf
Removed:
pkg/vegan/inst/doc/partitioning.pdf
pkg/vegan/vignettes/.install_extras
pkg/vegan/vignettes/FAQ-vegan.texi
pkg/vegan/vignettes/Makefile
Modified:
pkg/vegan/DESCRIPTION
pkg/vegan/NAMESPACE
pkg/vegan/R/vegandocs.R
pkg/vegan/man/vegandocs.Rd
Log:
Merge branch 'cran-2.3' into r-forge-svn-local
Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION 2016-02-23 14:47:03 UTC (rev 2989)
+++ pkg/vegan/DESCRIPTION 2016-02-25 12:09:51 UTC (rev 2990)
@@ -6,9 +6,10 @@
Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos,
M. Henry H. Stevens, Helene Wagner
Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>
-Depends: permute (>= 0.8-0), lattice, R (>= 2.15.0)
-Suggests: parallel, tcltk
+Depends: permute (>= 0.8-0), lattice, R (>= 3.0.0)
+Suggests: parallel, tcltk, knitr
Imports: MASS, cluster, mgcv
+VignetteBuilder: utils, knitr
Description: Ordination methods, diversity analysis and other
functions for community and vegetation ecologists.
License: GPL-2
Modified: pkg/vegan/NAMESPACE
===================================================================
--- pkg/vegan/NAMESPACE 2016-02-23 14:47:03 UTC (rev 2989)
+++ pkg/vegan/NAMESPACE 2016-02-25 12:09:51 UTC (rev 2990)
@@ -73,7 +73,8 @@
import(stats)
import(graphics)
import(permute)
-importFrom(utils, browseURL, combn, flush.console, head, object.size, tail, str)
+importFrom(utils, news, vignette, combn, flush.console, head, object.size,
+ tail, str)
importFrom(tools, Rd2txt, startDynamicHelp)
import(grDevices) ## too many functions to be listed separately
import(lattice)
Modified: pkg/vegan/R/vegandocs.R
===================================================================
--- pkg/vegan/R/vegandocs.R 2016-02-23 14:47:03 UTC (rev 2989)
+++ pkg/vegan/R/vegandocs.R 2016-02-25 12:09:51 UTC (rev 2990)
@@ -1,29 +1,18 @@
`vegandocs` <-
- function (doc = c("NEWS", "ONEWS", "FAQ-vegan.pdf",
- "intro-vegan.pdf", "diversity-vegan.pdf",
- "decision-vegan.pdf", "partitioning.pdf", "permutations.pdf"))
+ function (doc = c("NEWS", "ONEWS", "FAQ-vegan",
+ "intro-vegan", "diversity-vegan",
+ "decision-vegan", "partitioning", "permutations"))
{
doc <- match.arg(doc)
- if (length(grep(".pdf", doc)) > 0) {
- if (doc == "permutations.pdf")
- doc <- file.path(system.file(package="permute"), "doc", doc)
- else
- doc <- file.path(system.file(package="vegan"), "doc", doc)
- if (.Platform$OS.type == "windows")
- shell.exec(doc)
- else system(paste(getOption("pdfviewer"), doc, "&"))
- } else if (doc == "NEWS") {
- ## Try html
- helptype <- getOption("help_type")
- if (length(helptype) && helptype == "html") {
- browseURL(paste("file://",
- system.file(package="vegan", "doc", "NEWS.html"),
- sep=""))
- } else {
- file.show(Rd2txt(file.path(system.file(package="vegan"),
- "NEWS.Rd"), tempfile()))
- }
- } else {
+ if (doc == "NEWS") {
+ .Deprecated('news(package="vegan")')
+ news(package = "vegan")
+ } else if (doc %in% vignette(package="vegan")$results[, "Item"]) {
+ .Deprecated('browseVignettes("vegan")')
+ vignette(doc, package = "vegan")
+ } else if (doc == "permutations") {
+ .Deprecated('browseVignettes("permute")')
+ vignette(doc, package = "permute")
+ } else # last resort
file.show(system.file(package="vegan", doc))
- }
}
Deleted: pkg/vegan/inst/doc/partitioning.pdf
===================================================================
--- pkg/vegan/inst/doc/partitioning.pdf 2016-02-23 14:47:03 UTC (rev 2989)
+++ pkg/vegan/inst/doc/partitioning.pdf 2016-02-25 12:09:51 UTC (rev 2990)
@@ -1,984 +0,0 @@
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[TRUNCATED]
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