Hi - I'm getting the following error when I try to do rma on loaded CEL data: > datafiles <- ReadAffy() > procinfo <- rma(datafiles) Note: You did not specify a download type. Using a default value of: Win32 This will be fine for almost all users Error in FUN(X[[1]], ...) : No direct or inherited method for function "pkgVersion" for this call For some reason it's not creating the procinfo object that I want it to create. Any ideas? Thx, -paul

On Sat, Dec 20, 2003 at 01:48:31AM -0500, Paul Grosu wrote: > > Hi - > > I'm getting the following error when I try to do rma on loaded CEL data: > > > datafiles <- ReadAffy() > > procinfo <- rma(datafiles) > Note: You did not specify a download type. Using a default value of: Win32 > This will be fine for almost all users > > Error in FUN(X[[1]], ...) : No direct or inherited method for function > "pkgVersion" for this call > > For some reason it's not creating the procinfo object that I want it to > create. Any ideas? > > Thx, > -paul > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >From R outputs you copied, it seems that you are using a windows version of R. You might want to specifify which version of R and of the packages you are using... Apparently the trouble comes from an attempt to download something, which makes the cdfenvs and the autoload mecanism (relying on reposTools) good suspects. Without version numbers for R, affy and reposTools, I can't guess further. Hoping it helps, L. -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent

Cool! What ended up happening was that I wiped my R and reinstalled it from scratch. Later I learned that I can use debug or trace to find out what might be the problem. Thx, -paul -----Original Message----- From: Laurent Gautier [mailto:laurent@cbs.dtu.dk] Sent: Monday, December 22, 2003 4:33 AM To: Paul Grosu Cc: 'bioconductor@stat.math.ethz.ch' Subject: Re: [BioC] simple error On Sat, Dec 20, 2003 at 01:48:31AM -0500, Paul Grosu wrote: > > Hi - > > I'm getting the following error when I try to do rma on loaded CEL data: > > > datafiles <- ReadAffy() > > procinfo <- rma(datafiles) > Note: You did not specify a download type. Using a default value of: Win32 > This will be fine for almost all users > > Error in FUN(X[[1]], ...) : No direct or inherited method for function > "pkgVersion" for this call > > For some reason it's not creating the procinfo object that I want it to > create. Any ideas? > > Thx, > -paul > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >From R outputs you copied, it seems that you are using a windows version of R. You might want to specifify which version of R and of the packages you are using... Apparently the trouble comes from an attempt to download something, which makes the cdfenvs and the autoload mecanism (relying on reposTools) good suspects. Without version numbers for R, affy and reposTools, I can't guess further. Hoping it helps, L. -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent