[Bioc-devel] Submitting two strongly related packages (software + data)

Dan Tenenbaum dtenenba at fhcrc.org
Wed Nov 6 01:26:30 CET 2013

Hi Nicolas,

----- Original Message -----
> From: "Nicolas De Jay" <nicolas.dejay at mail.mcgill.ca>
> To: bioc-devel at r-project.org
> Sent: Tuesday, November 5, 2013 4:02:20 PM
> Subject: [Bioc-devel] Submitting two strongly related packages (software +	data)
> Hi,
> I have never used a mailing list before so do not hesitate to let me
> know
> if I'm doing something wrong.
> I have been growingly increasingly fond of the Bioconductor project
> and
> along with a small intend on submitting a package.  We have tried to
> follow
> package guidelines as much as possible and noticed a size limit on
> software
> packages (4MB).  The example data sets will greatly exceed that quota
> (~150MB) so we figured we'd package the data separately (e.g. minfi
> and
> minfiData).  In that case, what is the right order for submitting the
> packages?  Of course, the data package will be completely documented
> first
> so should we
> 1. submit the data package, then the software package? (You will have
> to
> take our word that the software package is coming up.)
> 2. submit the software package, then the data package? (The software
> depends on the data though for the vignette!)
> 3. submit both at the same time.

Submit both at the same time, to the same issue in our tracker. This makes it easier for us to know that the packages go together.

> Also, is there a way to test for Bioconductor compliance like the
> --as-cran
> option of the R CMD check command?

Not really. Part of "Bicoonductor compliance" is a subjective human looking at the package and that can't be automated.
Reading our guidelines carefully should minimize these problems.
However, once you submit a package it will automatically be built and checked on all platforms which may turn up some issues.


> Thank you for your help.  I'm looking forward to becoming an active
> developer in the Bioconductor community.
> ---
> *Nicolas De Jay *
> M.Sc. Student
> Department of Human Genetics
> Montreal Children's Hospital Research Institute, McGill University
> Health
> Centre
> 4060 Ste Catherine West, PT-239
> Montreal, QC H3Z2Z3, Canada
> T: (514) 412-4440 | E: nicolas.dejay at mail.mcgill.ca
> 	[[alternative HTML version deleted]]
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