[BioC] gcrma using deprecated package

[Marc Carlson]

Hi Ton,

This is just a courtesy message to indicate that the matchprobes package
(in the form that we know it) is going away.  It is mostly a message to
package authors who depend on matchprobes, and  also the direct users of
matchprobes to let them know where the functionality from the
matchprobes package is migrating away to.  If you are not using
matchprobes directly, there should be little to no impact on you.


  Marc



Zhijin Wu wrote:
> I believe you can still use it for now. IT does mean that I should
> revise the code to keep up with the changes though.
>
> Thanks,
> Jean Wu
> Rullmann, J.A.C. (Ton) wrote:
>> We recently installed R 2.9.0 and Bioconductor 2.4.1.
>> When I run "gcrma" I get the following message:
>>
>>   [begin message]
>> Computing affinitiesLoading required package: matchprobes
>>
>> *** Deprecation warning ***
>> The matchprobes package is deprecated and will not be supported
>> anymore starting with Bioconductor 2.4. Please switch to using the
>> Biostrings package for efficient string manipulations. If you need
>> to build a probe package, please see the makeProbePackage vignette
>> in the AnnotationDbi package.
>>   [end message]
>>
>> Is there a problem with the installation, and if so, what should be
>> done to fix it?
>>
>> Thanks!
>>
>> Ton Rullmann
>> Senior Research Scientist
>> Project Leader Systems Biology
>> Dept. Molecular Design and Informatics
>> T: +31 412 661423
>> F: +31 412 662539
>> ton.rullmann at spcorp.com
>>
>> Schering-Plough
>> RK 2309
>> PO Box 20
>> 5340 BH Oss, The Netherlands
>> www.schering-plough.com
>>
>>
>>
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>
>