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

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

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

Kasper


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

>
> Dear Kasper,
>
>
> kasperdanielhansen@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@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@gmail.com
> >>        ramon.diaz@iib.uam.es
> >>
> >> http://ligarto.org/rdiaz
> >>
> >> _______________________________________________
> >> Bioc-devel@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@gmail.com
>        ramon.diaz@iib.uam.es
>
> http://ligarto.org/rdiaz
>
>
>

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