processing of /vignettes and /inst/doc
On 17/09/2013 9:56 AM, Kasper Daniel Hansen wrote:
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.
The long run intention is that vignettes will be in the vignettes directory, and nowhere else. Files in inst/doc will be installed, but they are not vignettes, they are just documentation files. This has been documented for a long time, but it hasn't been enforced. The new change is that vignettes will be produced at build time, by the package maintainer, not by the user, at INSTALL time. Version 3.0.2 is intended to handle tar.gz files built under earlier versions of R according to the old rules, and also tarballs built under the new system. So how your example below is handled depends on which version built the tarball. I'll assume everything is being done with 3.0.2 beta.
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
Since this package has a vignettes directory, it's assumed that that is where the vignettes are. So the current version doesn't see inst/doc/big.Rnw as a vignette.
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
That looks like a bug, in that inst/doc/big.pdf should still have been included as a non-vignette documentation file. I'll look into that.
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."
That statement should be correct, hence current behaviour is a bug. Duncan Murdoch
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]]
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