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

Some comments

1) with my testing it appears that both Sweave files (big.Rnw and
small.Rnw) are run, but I could be wrong.
2) the clean target clearly is against the recommendations in R-exts

Unfortunately, the paragraph in R-exts on all of this is rather opaque
and seems weird.  For example "Whenever a Makefile is found, then R
CMD build will try to run make after the Sweave runs. The first target
in the Makefile should take care of both creation of PDF files and
cleaning up afterwards (including after Sweave), i.e., delete all
files that shall not appear in the final package archive." implies
that even the presence of a Makefile cannot prevent Sweave from
processing source files.

Anyway, reading the section carefully reveals "By default R CMD build
will run Sweave on all files in Sweave format in vignettes, or if that
does not exist, inst/doc (but not in sub-directories)."  This implies
that if both /vignettes and /inst/doc exists, Sweave is only run on
the files in /vignettes.

So my solution is simply to place small.Rnw in /vignettes and big.Rnw
and big.pdf in /inst/doc.

On my Mac it seems to work in the sense that vignettes() lists both of
them and if I use

   >  help.start()

and go to
   packages ->  PACKAGE_NAME->   overview of user guides and vignettes
I see both of them

(as an aside, it has been a long time since I used help.start but I
see that there is a "User Manuals" on the front page that lists all
the vignettes of the Recommended/Base packages, but not any other
package I have installed ... seems weird to me ...???)

Thanks,
Kasper


On Thu, Jun 21, 2012 at 10:08 AM, Martin Morgan<mtmorgan at fhcrc.org>  wrote:

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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