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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
