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

Tue Sep 17 16:22:18 CEST 2013

kasperdanielhansen at gmail.com writes:

> I have reported this on R-devel.  I think it is a bug or at least
> unintended behavior.
>

Yes, just saw it. Thanks.

> If this does not get resolved, I would put the Rnw file inside /inst/Rnws
> or some other directory.  You don't (I assume) really care about the Rnw

Good idea; that would work.

Best,

R.

> file being installed, but you care about the PDF being present to the user.
>
> Best,
> Kasper
>
>
>
>
> On Tue, Sep 17, 2013 at 9:56 AM, Ramon Diaz-Uriarte <rdiaz02 at gmail.com>wrote:
>
>>
>> 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
>>
>>
>>

-- 
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