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

[Martin Morgan]

On 06/21/2012 08:42 PM, Kasper Daniel Hansen wrote:
> 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.

OK, sorry for my misleading advice and thanks for clearing this up. Martin

>
> 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
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>>
>> --
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M1 B861
>> Phone: (206) 667-2793


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793