[Bioc-devel] Help with creating first Bioconductor package

Dan Tenenbaum dtenenba at fredhutch.org
Fri Nov 14 18:15:17 CET 2014

----- Original Message -----
> From: "January Weiner" <january.weiner at gmail.com>
> To: bioc-devel at r-project.org
> Sent: Friday, November 14, 2014 2:51:11 AM
> Subject: [Bioc-devel] Help with creating first Bioconductor package
> 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).

Note that it just says CONSIDER. So you do not _have_ to do anything. 
Pay more attention to things that are RECOMMENDED, and definitely fix
anything that says REQUIRED.


> 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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