[Bioc-devel] Package size limitation

Patrick Aboyoun paboyoun at fhcrc.org
Fri Aug 1 18:27:00 CEST 2008

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.
> Kasper
> 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 
>> *.CEL
>> files, which were used in the paper introducing the algorithm and are 
>> most
>> suitable to show the application of the package. Unfortunately, 
>> including
>> 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
>> 804-828-2527
>> _______________________________________________
>> Bioc-devel at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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