[Bioc-devel] Interfacing libraries not part of Bioconductor

rcaloger raffaele.calogero at gmail.com
Thu Mar 5 10:47:18 CET 2009

I am the maintainer of oneChannelGUI, a graphical inteface to various 
Bioconductor packages.
I am putting some effort in increasing the capability of oneChannelGUI 
in the analysis of exon-arrays.
Recently Xing et al . have published a nice paper on a new tool for exon 
arrays analysis (MADS: a new and improved method for analysis of 
differential alternative splicing by exon-tiling microarrays. RNA. 2008 
This tool was subsequently embedded in the JETTA software 
http://gluegrant1.stanford.edu/~junhee/JETTA/ , which is also available 
as R package for win/mac/linux platforms.
I am working on interfacing this libray in oneChannelGUI, however I need 
some advice regarding the insertion in Biocondutor of libraries that are 
not part of it.
Since in one of my function I call jetta library, I need to declare it 
in the suggested packages in the DESCRIPTION file of oneChannelGUI.
In my function I have implemented a routine that download and install 
from the http://gluegrant1.stanford.edu/~junhee/JETTA/ web page the 
specific platform package.
Therefore the users interested to use jetta could handle it.
However, if I will load the package on the devel repository of 
Bioconductor, the presence in the suggested packages of jetta will 
produce a warning.  How can  I handle this problem?
Is this acceptable by Bioconductor?
Is there any way to avoid the warning?
e.g. ask to the Biocore team to install the jetta lib on the repository. 
Is this feasible?

I am open to any suggestion



Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
tel.   ++39 0116705417
Lab.   ++39 0116705408
Fax    ++39 0119038639
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
www:   http://www.bioinformatica.unito.it
Info: http://publicationslist.org/raffaele.calogero

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