[Bioc-devel] Help with creating first Bioconductor package

January Weiner january.weiner at gmail.com
Fri Nov 14 11:51:11 CET 2014

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,


-------- January Weiner --------------------------------------

More information about the Bioc-devel mailing list