[Bioc-devel] Interfacing libraries not part of Bioconductor

[rcaloger]

Many thanks for the info!
I will use the if (require(jetta))    till jetta will be part of 
Bioconductor
Cheers
Raffaele
Patrick Aboyoun ha scritto:
> 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
>>>
>>> _______________________________________________
>>> Bioc-devel at stat.math.ethz.ch mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>     
>>
>>     [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>   
>


-- 

----------------------------------------
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