[Bioc-devel] Interfacing libraries not part of Bioconductor
raffaele.calogero at gmail.com
Sat Mar 7 00:40:47 CET 2009
Many thanks for the info!
I will use the if (require(jetta)) till jetta will be part of
Patrick Aboyoun ha scritto:
> 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
>> packages that are not part of
>> Bioconductor. Some interface calls will fail if a given package is not
>> On Thu, Mar 5, 2009 at 4:47 AM, rcaloger
>> <raffaele.calogero at gmail.com>wrote:
>>> 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
>>> 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
>>> which is also available as R package for win/mac/linux platforms.
>>> I am working on interfacing this libray in oneChannelGUI, however I
>>> 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
>>> 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
>>> Bioc-devel at stat.math.ethz.ch mailing list
>> [[alternative HTML version deleted]]
>> Bioc-devel at stat.math.ethz.ch mailing list
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
tel. ++39 0116705417
Lab. ++39 0116705408
Fax ++39 0119038639
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
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