[Bioc-devel] Package size limitation
tguennel at vcu.edu
Fri Aug 1 19:39:07 CEST 2008
Thanks everyone, I found what I needed!
Department of Biostatistics
Virginia Commonwealth University
Theater Row 3035F
From: Patrick Aboyoun [mailto:paboyoun at fhcrc.org]
Sent: Friday, August 01, 2008 12:27 PM
To: Kasper Daniel Hansen
Cc: Tobias Guennel; bioc-devel at stat.math.ethz.ch
Subject: Re: [Bioc-devel] Package size limitation
To elaborate on Kasper's well-stated points, the Bioconductor project
has separate repositories for software, experiment data, and annotation
BioC software: http://bioconductor.org/packages/release/bioc/
BioC experiment data:
BioC annotation metadata:
The main criterion for an experiment data package is that it should be
novel in some way to make it useful for other software developers to
utilize it when illustrating concepts in their software package. More
often than not, including a subset of your data in your software package
will suffice. One common misconception by new package developers is that
examples in the man pages and the vignettes need to be 100% "real". The
main goal of vignettes and man pages is to illustrate concepts rather
than reveal scientific findings. You are encouraged to provide
references to scientific papers that demonstrate the latter within your
software's documentation, but typically end-users want your package to
have a small storage footprint on their machine and have the examples
run in a short time frame.
If you are not sure how to handle your particular situation, when the
Bioconductor team previews and reviews your package, we will help you
through any tricky decisions. Good luck with your package submission and
thanks for your interest in the Bioconductor project!
Kasper Daniel Hansen wrote:
> I believe the right way to do this is the following
> 1) Make an AffyBatch containing only a few probesets to use for your
> examples. Include this in the package
> 2) Submit a package containing your experiment
> 3) Use the package above in a vignette.
> But I am sure someone else will chime in.
> On Jul 31, 2008, at 8:22 PM, Tobias Guennel wrote:
>> Dear all,
>> I'm writing my first R package that I want to submit to Bioconductor
>> implementing an algorithm for detecting differentially expressed
>> genes that
>> is not available in R yet.
>> The example data set is an AffyBatch object that contains 6 read in
>> files, which were used in the paper introducing the algorithm and are
>> suitable to show the application of the package. Unfortunately,
>> the data example increases the size of the compressed package to 6MB.
>> Is there a way to drastically reduce the size of an Affybatch object
>> or are
>> there other options that can reduce the file size?
>> Thanks for your help,
>> Tobias Guennel
>> Research Assistant
>> Department of Biostatistics
>> Virginia Commonwealth University
>> Theater Row 3035F
>> Bioc-devel at stat.math.ethz.ch mailing list
> Bioc-devel at stat.math.ethz.ch mailing list
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