It is stated in R-exts that Sweave files (.Rnw) are either processed in /vignettes or /inst/doc, not both. Furthermore, it is stated that external manuals and other files in /inst/doc will be installed.
This behaviour has been used to deal with the situation where a package has two "vignettes", one that is easily processed and one that has a long running time. This could be done by having /vignettes/small.Rnw /inst/doc/big.pdf with obvious notation. Now, big.pdf is really produced by a Sweave document, so what we really have is /vignettes/small.Rnw /inst/doc/big.pdf /inst/doc/big.Rnw This used to work, in the sense that the tarball produced by R CMD build produced /inst/doc/small.Rnw /inst/doc/small.pdf /inst/doc/big.pdf /inst/doc/big.Rnw Recently (R-3.0.2 beta, specifically "R version 3.0.2 beta (2013-09-16 r63937)"), the final tarball only has /inst/doc/small.Rnw /inst/doc/small.pdf /inst/doc/big.Rnw If we remove /inst/doc/big.Rnw the pdf gets included. So it seems that the presence of /inst/doc/big.Rnw prevents the pdf from being included. This seems to me to be unwanted behaviour, since R-exts 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." However, it is also clear that Sweave docs are "special". Still, I believe the past behaviour was better and more in line with what I infer as the intended behaviour. An example is the ADaCGH2 package in Bioconductor which I am not involved with. I include a cc to the maintainer who reported this on bioc-devel. Best, Kasper [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel