Dear Mayte, Could you please let me know which versions of goTools, GO and hgu133a you are using so that I could try to reproduce the error? Regards, Agnes -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Mayte Suarez-Farinas Sent: Monday, May 09, 2005 11:30 AM To: bioconductor@stat.math.ethz.ch Subject: [BioC] GO Tools Hi. I was trying to use goTools library and I got the following error with with my data and with the example in the documentation. data(probeID) ontoCompare(affylist, probeType="hgu133a", plot=TRUE) [1] "Starting ontoCompare..." Error in get("GO:0003674", env = GOMFCHILDREN) : recursive default argument reference I work with unix version 2.0.1 and I update last week all biocondoctor level packages ... R.version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 2 minor 0.1 year 2004 month 11 day 15 language R Mayte S. Farinas _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

Hi Agnes, thanks for your reply. Here it is: goTools: 1.0.6 GO: 1.7.0 hgu133a: 1.7.0 On Mon, 9 May 2005, Paquet, Agnes wrote: > Dear Mayte, > > Could you please let me know which versions of goTools, GO and hgu133a > you are using so that I could try to reproduce the error? > > Regards, > > Agnes > > > > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Mayte > Suarez-Farinas > Sent: Monday, May 09, 2005 11:30 AM > To: bioconductor@stat.math.ethz.ch > Subject: [BioC] GO Tools > > > Hi. > I was trying to use goTools library and I got the following error > with > with my data and with the example in the documentation. > > data(probeID) > ontoCompare(affylist, probeType="hgu133a", plot=TRUE) > [1] "Starting ontoCompare..." > Error in get("GO:0003674", env = GOMFCHILDREN) : > recursive default argument reference > > I work with unix version 2.0.1 and I update last week all biocondoctor > level packages ... > > R.version > _ > platform i686-pc-linux-gnu > arch i686 > os linux-gnu > system i686, linux-gnu > status > major 2 > minor 0.1 > year 2004 > month 11 > day 15 > language R > > Mayte S. Farinas > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > -- Mayte Suarez Farinas The Rockefeller University 1230 York Avenue, Box 212 New York, NY 10021 phone: 1-212-327-8186 fax: 1-212-327-7422

Hi Mayte, I am using exactly the same versions under Windows (R2.0.1 and R2.1.0), but I can't reproduce the error. This example was also tested on different platforms for the new Bioconductor release and there wasn't any problem. I don't have access to a Unix machine so I will unfortunately not be able to perform more testing to solve your problem. Perhaps you could try to reinstall GO and goTools from different builds and see if this helps... Best, Agnes -----Original Message----- From: Mayte Suarez-Farinas [mailto:mayte@babel.rockefeller.edu] Sent: Monday, May 09, 2005 4:14 PM To: Paquet, Agnes Cc: bioconductor@stat.math.ethz.ch Subject: RE: [BioC] GO Tools Hi Agnes, thanks for your reply. Here it is: goTools: 1.0.6 GO: 1.7.0 hgu133a: 1.7.0 On Mon, 9 May 2005, Paquet, Agnes wrote: > Dear Mayte, > > Could you please let me know which versions of goTools, GO and hgu133a > you are using so that I could try to reproduce the error? > > Regards, > > Agnes > > > > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Mayte > Suarez-Farinas > Sent: Monday, May 09, 2005 11:30 AM > To: bioconductor@stat.math.ethz.ch > Subject: [BioC] GO Tools > > > Hi. > I was trying to use goTools library and I got the following error > with > with my data and with the example in the documentation. > > data(probeID) > ontoCompare(affylist, probeType="hgu133a", plot=TRUE) > [1] "Starting ontoCompare..." > Error in get("GO:0003674", env = GOMFCHILDREN) : > recursive default argument reference > > I work with unix version 2.0.1 and I update last week all biocondoctor > level packages ... > > R.version > _ > platform i686-pc-linux-gnu > arch i686 > os linux-gnu > system i686, linux-gnu > status > major 2 > minor 0.1 > year 2004 > month 11 > day 15 > language R > > Mayte S. Farinas > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > -- Mayte Suarez Farinas The Rockefeller University 1230 York Avenue, Box 212 New York, NY 10021 phone: 1-212-327-8186 fax: 1-212-327-7422