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

[Ramon Diaz-Uriarte]

Dear Kasper,


kasperdanielhansen at gmail.com writes:

> 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

I've done that homework to the best of my knowledge and specifically I've read
the R-exts of the version I downloaded this morning. But I still cannot
understand what should happen. For instance:

"The preferred location for the sources is the subdirectory vignettes of the
source package, but pro tem for compatibility with the layout before R 2.14.0,
vignette sources will be looked for in inst/doc if subdirectory vignettes does
not exist"

or

"By default R CMD build will run Sweave on all Sweave vignette source files in
vignettes, or pro tem if that does not exist, inst/doc (but not in
sub-directories)"


and

"When R CMD build builds the vignettes, it copies these and the vignette sources
from directory vignettes to inst/doc."

But I do not see any explicit statement about what happens if both /inst/doc and
/vignettes exist and inst/doc has a PDF.

In the past it seems that, when /vignettes existed, the sources and built pdfs
were copied to /inst/doc, and that /inst/doc (which might also have contained
other PDFs) was what ended up in the tar.gz. Now, it seems, the PDF of the
non-built vignetted (the one in /inst/doc) does not make it to /inst/doc in the
tar.gz.


> beneficial.  Is the package publicly available somewhere?  That may be
> useful for other people.
>

Sure, it is ADaCGH2 in BioC:

http://www.bioconductor.org/packages/2.13/bioc/html/ADaCGH2.html


Best,


R.


> 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