[BioC] conflict between ROC and Hmisc or Design?

[Robert Gentleman]

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"
> 
> 
> 
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-- 
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