[Bioc-devel] ViennaRNA and Biopython in R package

[Martin Morgan]

On 08/21/2017 06:39 PM, carl fakhry wrote:
> Hi Martin,
> 
> 
> I wrote an R package which has functions that invoke system commands. Part of the system commands which I am using is calls to the ViennaRNA package (https://www.tbi.univie.ac.at/RNA/#)  and calls to python which requires a specific python library, Biopython. Both of these packages are very commonly used in the bioinformatics world.
> 
> 
> The R package can install properly without installing ViennaRNA or Biopython. However, to use the package the user would need to install them to have the R package work properly. What should I do in this case? Should I make an extra vignette which details the installation process?

Hi Carl --

Actually, if the R package is only useful with the relevant software, 
then I think it should fail to load, with an informative error message 
(implment .onLoad <- ... in R/zzz.R, for instance).

While a vignette is 'nice', I think an INSTALL file in the top-level 
directory is more appropriate (one will often be trying to convince a 
sys admin to install this additional software, and they appreciate plain 
text); your error message could point  to that (e.g., on bioconductor, 
at 
http://bioconductor.org/packages/release/bioc/install/ChemmineOB/INSTALL).

You need to carefully justify the use of non-R software, in particular a 
lot of Biopython functionality is readily available in Bioconductor, so 
it wouldn't make sense to add a fragile interface and additional system 
dependencies to duplicate available functionality.

It is also important that the software, including INSTALL instructions, 
follow very standard protocols on Windows, Mac, and Linux platforms -- 
the Bioconductor build system in particular needs to be configured to 
work with all packages using system dependencies, and some combinations 
will be very difficult for us to implement or maintain.

You'll also need to verify, more so than a typical Bioconductor package, 
that your software works across platforms. Things like paths, temporary 
directories, and encodings are all likely to be particularly problematic.

And don't forget to verify that the licenses of these software packages 
are consistent with your own license, and do not impose odd 
restrictions, e.g., for academic use only, that would make the R package 
unsuitable for Bioconductor.

Martin

> 
> 
> Thanks,
> 
> Carl
> 
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