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
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