[Bioc-devel] R-3.0.2 and vignettes that should not be built

[Ramon Diaz-Uriarte]

kasperdanielhansen at gmail.com writes:


Dear Kasper,


> A package source would be good so I can do some testing.  Or post what

It is in BioC, but I can send you my sources if you want. Anyway ...

> happens if you leave out inst/doc/big.Rnw (but keep inst/doc/big.pdf).  I
> would assume (see below) that this keeps the pdf.


you are right. I should have tried that! Removing the .Rnw leaves the pdf in
place. (Of course, that is still not what we want)


>
> R-exts still mentions that Rnw's are only processed in either /vignettes or
> /inst/doc, not both (which is what you describe).  

Well, the Rnw under /inst/doc are not processed in the usual sense: they are not
Sweaved and texed. But their presence seems to lead to the PDF being deleted.

> It also says: "In addition to the help files in Rd format, R packages allow
> the inclusion of documents in arbitrary other formats. The standard location
> for these is subdirectory inst/doc of a source package, the contents will be
> copied to subdirectory docwhen the package is installed."
>

Right, I forgot to copy that; that is why I assumed that anything under
/inst/doc would just be copied if /vignettes exists.


> So this looks undocumented behaviour, I would say.  Probably due to the
> fact that you have both Rnw and pdf there, which - as I read the
> documentation - should be allowable.
>

Yes.


Best,


R.

> Best,
> Kasper
>
>
> On Tue, Sep 17, 2013 at 8:50 AM, Kasper Daniel Hansen <
> kasperdanielhansen at gmail.com> wrote:
>
>> As you describe this, this seems to be a change from the previously
>> documented (in R-exts) behaviour in R.  Let us review the "new"
>> documentation and then we probably need to take it up with R-devel, but
>> before doing so, experience suggests that doing our "homework" is
>> beneficial.  Is the package publicly available somewhere?  That may be
>> useful for other people.
>>
>> Kasper
>>
>>
>> On Tue, Sep 17, 2013 at 7:09 AM, Ramon Diaz-Uriarte <rdiaz02 at gmail.com>wrote:
>>
>>>
>>>
>>> Dear All,
>>>
>>> Suppose a package contains a vignette that is built quickly
>>> (small.Rnw) and another that takes a long time (big.Rnw).
>>> We want to provide both the source and the PDF for both, but on routine
>>> CMD build we only want to build the short one (the PDF for the long one
>>> having been pre-generated).
>>>
>>>
>>> This issue has come up before in this list and I think one suggested
>>> solution (see thread started by Kasper Daniel Hansen on 2012-06-12:
>>> https://stat.ethz.ch/pipermail/bioc-devel/2012-June/003446.html) was
>>> to:
>>>
>>> - place small.Rnw (and small.bib) under /vignettes
>>> - place big.Rnw AND big.pdf under /inst/doc
>>>
>>> When we execute(d) (as BioC does)
>>>
>>> R CMD build --keep-empty-dirs --no-resave-data source
>>>
>>> the PDF for small would be created (and placed under /inst/doc in
>>> source.tar.gz) and big.* would also be placed under /inst/doc. This has
>>> worked just fine for me up to now.
>>>
>>>
>>> Now, however, with R-3.0.2 (downloaded this morning; svn rev 63937), the
>>> build does not place big.pdf under /inst/doc in the tar.gz. Thus,
>>> we get a warning when we run CMD check
>>>
>>>
>>> Package vignette without corresponding PDF/HTML:
>>>    ‘big.Rnw’
>>>
>>>
>>> What is the recommended way of dealing with this? Should this question be
>>> moved to R-devel (I asked here because an identical question was dealt
>>> with in this list).
>>>
>>> Best,
>>>
>>>
>>> R.
>>>
>>>
>>> --
>>> Ramon Diaz-Uriarte
>>> Department of Biochemistry, Lab B-25
>>> Facultad de Medicina
>>> Universidad Autónoma de Madrid
>>> Arzobispo Morcillo, 4
>>> 28029 Madrid
>>> Spain
>>>
>>> Phone: +34-91-497-2412
>>>
>>> Email: rdiaz02 at gmail.com
>>>        ramon.diaz at iib.uam.es
>>>
>>> http://ligarto.org/rdiaz
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>>


-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina 
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdiaz02 at gmail.com
       ramon.diaz at iib.uam.es

http://ligarto.org/rdiaz