[BioC] gcrma using deprecated package

[Rullmann, J.A.C. (Ton)]

Hi,
Thanks for your answers, Jean and Marc.
I have now discovered that the source of the "problem" is not gcrma
directly, but the fact that I had an older version of hgu133plus2probe
in my private R library directory. It probably got there because gcrma
downloads the probe package when you have not loaded it before calling
gcrma, even if the probe package is available on the local system.

In this case there probably wasn't any harm. It would be nice though if
R or BioC could detect when you are using a package version in your
private library for which there is a newer version available in the
system-wide library location.

Thanks
Ton

Ton Rullmann
T: +31 412 661423
ton.rullmann at spcorp.com


-----Original Message-----
From: Zhijin Wu [mailto:zwu at stat.brown.edu] 
Sent: Wednesday, 26 August, 2009 16:57
To: Rullmann, J.A.C. (Ton)
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] gcrma using deprecated package

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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-- 
------------------------------------
Zhijin (Jean) Wu
Assistant Professor of Biostatistics
Brown University, Box G-S121
Providence, RI  02912

Tel: 401 863 1230
Fax: 401 863 9182
http://www.stat.brown.edu/zwu


This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited --- Please immediately and permanently delete.