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

[Kasper Daniel Hansen]

On Fri, Jun 22, 2012 at 12:07 AM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 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

Well, I was also convinced the Makefile would work.  Very weird that
Sweave gets run even if the Makefile is present, and hard to detect.
I only found out because I wanted to move the "rm -f" line up to be
part of the %.pdf target and suddenly I started seeing both big.tex
and small.tex.

Also weird that when you inspect the source build tarball, it contains
the vignette directory and also a copy of the source files in
inst/doc, so it has both vignettes/small.Rnw and inst/doc/small.Rnw.
Apparently the vignettes dir does not really get installed, but is
still present.  As an aside, the tangled R code (small.R) is generated
at install time.

Anyway, I have my solution,
Kasper

>> 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