[Bioc-devel] Help with creating first Bioconductor package

Martin Morgan mtmorgan at fredhutch.org
Fri Nov 14 19:43:03 CET 2014

On 11/14/2014 02:51 AM, 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).
> 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 Julian mentioned, the package gets automatically built across platforms when 
you submit it to Bioconductor; you're then free to iterate on the submission 
process until the tractable issues are addressed. Many developers submit their 
package in this way multiple times, and both sides (the developer, and the bioc 
core team) benefit. Eventually you'll either have green across all platforms 
(like on the build report http://bioconductor.org/checkResults/3.1/bioc-LATEST/) 
or you'll be stymied, someone from the Bioc team will be assigned to review your 
package, and they'll get you through the rest.

You'll want to develop your package on Bioc- and R-devel, as this is the 
environment in which your package will be introduced to the Bioc community.

I think the r-project win-builder is really intended to support CRAN-bound 
packages, so I'm not sure that it's appropriate to use that service.

It's our intention to pilot a new approach to training -- an hour-long google 
'hangout' with presentation then Q & A -- using new package submission as our 
test case; we're likely to offer the hangout in early December.


> 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.

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