[Bioc-devel] Bioconductor Package Builder and _R_CHECK_FORCE_SUGGESTS_

[Dan Tenenbaum]

On Thu, May 16, 2013 at 10:53 PM, Renaud Gaujoux
<renaud at mancala.cbio.uct.ac.za> wrote:
> Hi,
>
> I am trying to submit a package to Bioconductor with a Suggests dependency
> to RcppOctave, which is not available on Windows or Mac, and available on
> Linux only if octave is installed (RcppOctave is mine as well but getting
> working on other platforms than Linux is not yet on the agenda). All builds
> go fine but checks are not performed due to this missing dependency. This
> can be solved using _R_CHECK_FORCE_SUGGESTS_ = false, which is what is used
> on CRAN, at least for Windows and Mac.
>
> Is there a recommended way around this?
> I know I could "hide" the dependency using require('RcppOctave',
> character.only = TRUE), but I am wondering if there is a
> Bioconducotr-chekc-specific solution to still keep the dependency listed in
> the DESCRIPTION file.
>

What we have done in situations like this is to (mis-)use the
Enhances: field. R CMD check will not fail if a package in Enhances is
not present.

We do not want to set _R_CHECK_FORCE_SUGGESTS_=false globally, because
on our build system, in 99% of cases, we want to make sure that all
Suggested packages really are present.

We could conceivably set _R_CHECK_FORCE_SUGGESTS_=false when specific
packages are checked, but that functionality does not exist yet.

BTW, it looks like RcppOctave is not building on Mac because Octave is
not installed on the Mac build machine a CRAN (though there may be
other problems):

http://www.r-project.org/nosvn/R.check/r-release-macosx-x86_64/RcppOctave-00install.html

If you do use the Enhances approach, you'll of course have to make
sure that any code in your vignette or unit tests that use RcppOctave
will need to be run only if require(RcppOctave).

Thanks,
Dan



> Thank you.
>
> Bests,
> Renaud
>
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>
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