Dear Kasper,
kasperdanielhan...@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 <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
