[Bioc-devel] questions about windows build execute permissions and R version dependency

Martin Morgan martin.morgan at roswellpark.org
Thu Mar 23 09:26:00 CET 2017

On 03/22/2017 11:08 PM, Alicia Schep wrote:
> Hi,
> I have a two questions about the bioconductor build and BiocCheck process
> when submitting packages.
> 1) My submitted package ('motifmatchr') returns the following warning on
> the Windows computer:
> Warning: file 'motifmatchr/cleanup' did not have execute permissions: corrected
> How can this warning be averted?  How to give the file permission? I tried
> fixing this issue by making the file executable on my computer-- on GitHub
> it shows up as marked as "Executable File". This did not prevent the
> warning though.

It seems like you've done the right thing and R is mistaken. It's also 
irrelevant, since you have a cleanup.win file that supersedes cleanup. 
Ignore the warning.

> 2) The same package also gives a warning in BiocCheck related to the
> version of R required in DESCRIPTION.  As the package is currently hosted
> on GitHub and tested against the current release of R using travis, I would
> like the github version to have a dependency of only R 3.3 rather than R
> 3.4. Is it possible to have a different dependency for the R version on
> GitHub versus on Bioconductor?

Certainly anything is possible, e.g., creating a release branch on 
github with a different dependency, but again I'd suggest evaluating 
whether the warning is relevant in your situation, and if not ignoring it.

 From the Bioconductor perspective, the fact that your package builds on 
travis under an earlier version of R is unknown, so the assertion that 
it only requires R-3.3 is not supportable -- the warning tries to bring 
your version requirements into line with what we know to be true. Of 
course the assertion that it depends on a version of R > 3.4 is also not 


> Appreciate any guidance on these question.  Thanks,
> Alicia
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