[Bioc-devel] warnings from R CMD check on Win32 about object files in src/

[Seth Falcon]

Martin Maechler <maechler at stat.math.ethz.ch> writes:
> For "day to day" work, I live with the warning
>
>     >> * checking if this is a source package ... WARNING
>     >> Subdirectory 'msbase/src' contains object files.
>
> very well. But it *is* reasonable to give a warning: If these
> object files were compiled on a different architecture,
> or---more realistically---with different version of the C
> compiler, or ... (you name it),

Agreed.  I think I've determined why this is giving us grief:

R CMD INSTALL, when called on a package source directory, leaves
object files in the src/ subdirectory.

R CMD build cleans the src directory as does R CMD check if the check
process needs to build stuff (otherwise it reports a warning).

As I understand it, the recommended way to build binary packages on
Windows is:

R CMD INSTALL --build

and *not* R CMD build --binary

Since we use INSTALL on a package source directory during our
automated build process, we are left with a dirty src/ directory and
receive our warning.

Q1: Is R CMD INSTALL --build still prefered to R CMD build --binary?

If we are stuck with R CMD INSTALL --build, then an option for R CMD
check like --clean-src would be helpful.

Thoughts?  Further suggestions?

Best,

+ seth