I have reported this on R-devel. I think it is a bug or at least unintended behavior.
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 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 <rdia...@gmail.com>wrote: > > kasperdanielhan...@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 < > > kasperdanielhan...@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 <rdia...@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: rdia...@gmail.com > >>> ramon.d...@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: rdia...@gmail.com > ramon.d...@iib.uam.es > > http://ligarto.org/rdiaz > > > [[alternative HTML version deleted]]
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