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 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.

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 > > > > 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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- ------------------------------------ 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

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@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 > > > > 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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- ------------------------------------ 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.