[Rd] removing files on windows as part of vignette building

[Kasper Daniel Hansen]

This is about the Bioconductor package Genominator.

As part of the vignette building process, we create two sizable
sqlite3 databases, in the vignette directory (inst/doc).  When we
build the source tarball, these databases are deleted, but when a
Windows binary is being made on the Bioconductor build servers the
file(s) are not removed (as far as I read the documentation/code they
ought to be).  If I try to remove them explicitly, by including a
Makefile with a target

clean:
          rm -rf Rplots.pdf my.db pmy.db

(there are two databases), it fails with the error message

 rm: cannot remove `Rplots.pdf': Device or resource busy
rm: cannot remove `my.db': Device or resource busy
rm: cannot remove `pmy.db': Device or resource busy
make: *** [all] Error 1
Error in tools::buildVignettes(dir = ".") : running 'make' failed
Execution halted

Note that
(1) This did not happen under R-2.11
(2) It does not happen under Linux or OS X.

I believe this is a general phenomenon of no cleanup on windows.  If I
look at the affy package from Bioconductor, the windows binary has a
file
  doc/Rplots.pdf
that is not present inside inst/doc in the source tarball.

I have not been able to find a package on CRAN with a vignette with
plots in it, that did also include the pdf version of the vignette or
where Rplots.pdf was not also included in the source tarball, so this
may be an issue specific to the Bioconductor build system.

I guess an alternative to creating the database inside inst/doc is to
use a tempfile.  Comments?

Kasper