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

Tue Sep 17 16:07:49 CEST 2013

Dear Kasper,

kasperdanielhansen at gmail.com writes:

> Small complaints about the package: I am on OS X and first I have to deal
> with the default of typedev on OS X to be the Cairo package which I don't

Actually, I started using Cairo because ADaCGH2 ought to be able to run in
headless servers without X11 and Cairo seems suited for that ("Files are created
without the dependence on X11"). I also think I remember that some colleagues
that have Macs reported problems with graphics that were removed when using
Cairo (because of the creation of pngs under forking and/or MPI). 

> have installed and then I need to install threeparttable in Tex
> installation.  There is a lot to be said for minimal vignettes.

Sure. But it was the best way I could find to include footnotes in tables.

>
> Anyway, seems like the pdf gets included when the longexamples Rnw file
> gets removed.
>

Yes, but we often want BOTH the pdf and the Rnw (so users have access to the
original code).

> Finally: sure you need the index.html in inst/doc?
>

I do not need it, but if I don't include it, my recollection is that the
index.html that was automatically generated did not include links to the PDF,
source, and code of the two vignettes (which I think is due to the long.Rnw not
having been processed).

Best,

R.

> Kasper
>
>
> On Tue, Sep 17, 2013 at 9:26 AM, Ramon Diaz-Uriarte <rdiaz02 at gmail.com>wrote:
>
>>
>> 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
>>
>>
>>

-- 
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