[Bioc-devel] Help with creating first Bioconductor package

Tim Triche, Jr. tim.triche at gmail.com
Fri Nov 14 17:50:18 CET 2014

feel free to put the code up on GitHub if you want comments prior to review
(e.g. "vignette won't compile", "dependencies are screwed up", "S3 objects
as far as the eye can see", etc.)

Statistics is the grammar of science.
Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science>

On Fri, Nov 14, 2014 at 2:51 AM, January Weiner <january.weiner at gmail.com>

> 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).
> 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?
> 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.
> Thank you so much,
> j.
> --
> -------- January Weiner --------------------------------------
> http://logfc.wordpress.com
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