Vince,
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.
Raffaele,
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.
Patrick
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