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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