[Bioc-devel] Help with creating first Bioconductor package

[Laurent Gatto]

Dear January,

On 14 November 2014 10:51, January Weiner wrote:

> Dear all,
>
> I am building my first Bioconductor package and, before wasting
> everyone's time with a faulty submission, I would like to clarify
> certain things.
>
> 1) The package seems to fulfill the requirements of the Bioconductor
> Package Guidelines and passes all checks except one "consideration":
>
> CONSIDER: Indenting lines with a multiple of 4 spaces;
>
> I love to indent my code with 2 spaces, is it a problem? Or do I have
> to reformat all code before release? This is doable, but it would
> complicate my workflow and if I am allowed to avoid it, I will. I see
> that not all Bioconductor packages stick to this formatting (many even
> use tabs instead of spaces).

I don't think this is a reason for rejection, as long as all other
aspects of the formatting are fine (for instance miles-long lines). 

> 2) Another problem I have is the testing package on other platforms. I
> do not have a Windows machine to test my package. Could someone help
> me and test my package (build, check and BiocCheck) on Windows and
> MacOS? Otherwise -- how do you check your packages? You keep an up to
> date R development environment on three platforms?

As mentioned by Julian, you could use http://win-builder.r-project.org/
for Windows. But I don't think you are expected to check it on all
platforms before submission. If your package contains straightforward R
code, there is no reason to anticipate issues on other platforms.

> 3) Finally, I would love to have someone to go through my package and
> tell me what they think. I'm not sure to what extent the reviewing
> process is technical (like on CRAN), or whether the actual content of
> the package is evaluated as well. The package is small, it is
> basically one or two functions that I need in my work and could not
> find anywhere else -- it boils down to using Mann-Whitney for GO
> enrichment tests on sorted lists of genes, coupled to an algorithm
> that works like the "conditional=TRUE" option in hyperGtest. I have
> been using this for a while in my work and it does exactly what I
> wanted it to do.

The review will not centre on any scientific aspects of the code, but
will focus on technical and documentation aspects and inter-operability
within the Bioconductor environment, as per package preparation and
submission guidelines:

  http://bioconductor.org/developers/package-submission/
  http://bioconductor.org/developers/package-guidelines/

Hope this helps.

Best wishes,

Laurent

> Thank you so much,
>
> j.