[Bioc-devel] Size limits of packages when including other executables

[Dan Tenenbaum]

On Thu, Jun 6, 2013 at 1:48 AM, Thomas Dybdal Pedersen
<thomasp85 at gmail.com> wrote:
> Hi
>
> I'm developing a wrapper for the peptide-identification tool MS GF+. The algorithm is developed in Java and the .jar file has a size around 20 mb.
>
> For the ease of the user, I think it would make sense to pack the java code together with the wrapper (this has been cleared with the MS GF+ developer), and would have the added benefit of securing version compatibility. This, on the other hand, stretches the size limits imposed in the guidelines by several factors…
>
> What is the opinion on this? Is the size limits set in stone or can they be lifted for certain cases besides annotation packages?
>

We generally do frown on this, you're right, but if you're sure all
the classes in the JAR are necessary, then we'll allow it.

What's more important than getting buy-in from the developer of the
Java code is finding out what license the Java code is written under,
making sure that is compatible with the license of the R package, and
acknowledging the Java license as well as the R license in your
package. See the licensing section of the "Writing R Extensions"
manual for more information. Note that some licenses require that all
source code be either in the package, or that a link be provided that
points to it; this would apply to your jar file (which presumably
contains only .class files and no Java source).

Dan


> best
>
> Thomas Pedersen, PhD student at DTU, Denmark
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