[Bioc-devel] Help with creating first Bioconductor package
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.