[Bioc-devel] not including vignette in R CMD check

[Martin Morgan]

On 06/20/2012 12:46 PM, Kasper Daniel Hansen wrote:
> I have a package (to be submitted) with two "vignettes".
>
> One is a user guide with quick examples, and should be checked as part
> of R CMD check.
>
> The other contains a runable longer analysis and I would like to
> exclude it from the daily R CMD build due to length and resource
> demands.  But it is in principle still runable on a bigger system.  I
> want to include the Rnw file and I want the pdf to be indexed.
>
> What is the preferred way for doing this, these days?  I know Wolfgang
> has an old solution in tilingArray, but I was wondering if there is a
> better way now.

Hi Kapser -- two suggestions

The first is a variant of Wolfgang's approach -- include the Rnw files 
for big and small, and the pdf file for big in vignettes/. Both Rnw 
files have \VignetteIndexEntry.

$ tree vig
vig
├── DESCRIPTION
├── NAMESPACE
└── vignettes
     ├── big.pdf
     ├── big.Rnw
     ├── Makefile
     └── small.Rnw

Write a Makefile that compiles only small

$ cat vig/vignettes/Makefile
all: small.pdf

%.tex: %.Rnw
	"$(R_HOME)/bin/R" CMD Sweave $^

%.pdf: %.tex
	texi2dvi --pdf --clean $^

clean:
	rm -f *tex

(evaluate from the command line, e.g., for testing, with R CMD make). 
Build the package with R CMD build vig, and inspect the result

$ tar tzf vig_1.0.tar.gz
vig/
vig/inst/
vig/inst/doc/
vig/inst/doc/small.Rnw
vig/inst/doc/big.pdf
vig/inst/doc/small.pdf
vig/inst/doc/big.Rnw
vig/vignettes/
vig/vignettes/Makefile
vig/vignettes/small.Rnw
vig/vignettes/big.Rnw
vig/NAMESPACE
vig/DESCRIPTION

big and small are both indexed, e.g., by vignette(package="vig") or 
browseVignettes() or on package html help page; the .R source is 
available for both big and small.

A second approach is to manually create an inst/doc/index.html, which is 
then available on the package html help page (though vignettes aren't 
discoverable through other means, like vignette() / browseVignette()).

Martin

>
> Kasper
>
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