Thanks, Dr. Gentleman! ...Tao ----- Original Message ---- From: Robert Gentleman <rgentlem@fhcrc.org> To: "Shi, Tao" <shidaxia at="" yahoo.com=""> Cc: bioconductor at stat.math.ethz.ch Sent: Tuesday, January 31, 2006 11:52:17 AM Subject: Re: [BioC] conflict between ROC and Hmisc or Design? Yes, it seems that Hmisc defines a function named contents and that interferes with the one in Biobase. A work around, load Biobase first, a fixed version of Biobase will appear on the devel arm shortly. Robert Shi, Tao wrote: > Hi list, > > I found that I can't load 'ROC' after 'Hmisc' or 'Design' have been loaded. It works the other way around. Do you know why? From the error message, it seems the problem is in 'Biobase'.... > > thanks, > > ...Tao > > > >>library(Hmisc) > > Hmisc library by Frank E Harrell Jr > > Type library(help='Hmisc'), ?Overview, or ?Hmisc.Overview') > to see overall documentation. > > NOTE:Hmisc no longer redefines [.factor to drop unused levels when > subsetting. To get the old behavior of Hmisc type dropUnusedLevels(). > > Attaching package: 'Hmisc' > > > The following object(s) are masked from package:stats : > > ecdf > > >>library(ROC) > > Loading required package: Biobase > Loading required package: tools > Error in setMethod("contents", "environment", function(object, all.names) { : > no existing definition for function 'contents' > Error: .onLoad failed in 'loadNamespace' for 'Biobase' > > > ========================================== > Another R session: > >>library(ROC) > > Loading required package: Biobase > Loading required package: tools > Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. > >>package.version("ROC") > > [1] "1.1.1" > >>package.version("Hmisc") > > [1] "3.0-7" > >>package.version("Design") > > [1] "2.0-12" > >>package.version("Biobase") > > [1] "1.5.12" > >>R.Version() > > $platform > [1] "i386-pc-mingw32" > > $arch > [1] "i386" > > $os > [1] "mingw32" > > $system > [1] "i386, mingw32" > > $status > [1] "" > > $major > [1] "2" > > $minor > [1] "1.1" > > $year > [1] "2005" > > $month > [1] "06" > > $day > [1] "20" > > $language > [1] "R" > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

Vince, I tried with R2.2.1, ROC 1.4.0 (1.5.1 only works for R2.3.0 which I couldn't find), Biobase 1.9.2, and Hmisc 3.0.10, the problem stays. The problem is not crucial for me, since I can always load ROC first. I'm just curious. I'll wait for the new version out, then. Thanks, ...Tao ----- Original Message ---- From: Vincent Carey 525-2265 <stvjc@channing.harvard.edu> To: "Shi, Tao" <shidaxia at="" yahoo.com=""> Cc: bioconductor at stat.math.ethz.ch Sent: Tuesday, January 31, 2006 11:46:13 AM Subject: Re: [BioC] conflict between ROC and Hmisc or Design? I cannot reproduce this problem relative to Hmisc. Note that ROC is now at version 1.5.1 and you are using ROC 1.1.1 ; Biobase is at 1.9.2, you are using 1.5.12. So updating your versions of these packages may solve the problem. --- Vince Carey, PhD Assoc. Prof Med (Biostatistics) Harvard Medical School Channing Laboratory - ph 6175252265 fa 6177311541 181 Longwood Ave Boston MA 02115 USA stvjc at channing.harvard.edu On Tue, 31 Jan 2006, Shi, Tao wrote: > Hi list, > > I found that I can't load 'ROC' after 'Hmisc' or 'Design' have been loaded. It works the other way around. Do you know why? From the error message, it seems the problem is in 'Biobase'.... > > thanks, > ...