[Bioc-devel] Interfacing libraries not part of Bioconductor

Patrick Aboyoun paboyoun at fhcrc.org
Fri Mar 6 18:02:52 CET 2009

True enough, but those packages are on CRAN. The jetta package is "off 
the grid" so an R user has a harder time finding and installing it than 
if it were in Bioconductor or on CRAN.

Thanks for contacting the jetta folks. If it doesn't work out, you can 
always write if (require(jetta)) statements so your package will still 
build and pass check without it.


Vincent Carey wrote:
> Note that the Bioconductor MLInterfaces package creates interfaces to many
> packages that are not part of
> Bioconductor.  Some interface calls will fail if a given package is not
> installed.
> On Thu, Mar 5, 2009 at 4:47 AM, rcaloger <raffaele.calogero at gmail.com>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/<http://gluegrant1.stanford.edu/%7Ejunhee/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/<http://gluegrant1.stanford.edu/%7Ejunhee/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
>> Lab.   ++39 0116705408
>> Fax    ++39 0119038639
>> Mobile ++39 3333827080
>> email: raffaele.calogero at unito.it
>>      raffaele[dot]calogero[at]gmail[dot]com
>> www:   http://www.bioinformatica.unito.it
>> Info: http://publicationslist.org/raffaele.calogero
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