[Bioc-devel] Interfacing libraries not part of Bioconductor

rcaloger raffaele.calogero at gmail.com
Fri Mar 6 10:52:29 CET 2009

Dear Patrick,
I asked to the developer of jetta suggesting to join Bioconductor, but I 
did not get any answer, yet.
I am sending this email as cc to jetta developer.
Many thanks

Patrick Aboyoun ha scritto:
> Raffaele,
> In order to minimize the problems for the end-users and the build 
> system, the ideal situation would be to have JETTA as part of the 
> Bioconductor project. Have you talked with the JETTA authors to see if 
> they would be interested in joining the Bioconductor community? This 
> could help increase the exposure of their software as well as minimize 
> their long-term effort of maintaining a distribution site and testing 
> system.
> Patrick
> rcaloger wrote:
>> Hi,
>> 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 Aug;14(8):1470-9).
>> 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
>> Cheers
>> Raffaele


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
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Mobile ++39 3333827080
email: raffaele.calogero at unito.it
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Info: http://publicationslist.org/raffaele.calogero

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