[BioC] Cannot install GO & KEGG

[Robert Gentleman]

Hi Ashwin,
 They have been deprecated for some time. Use GO.db and KEGG.db.


Ashwin Kumar wrote:
> Hello group,
> 
>                        I have a problem in my bioconductor ,,  I cannot
> install specific packages such as GO & KEGG, other ones like
> gPlots,affydata,limma etc  are installed with no issues I am pasting the
> workspace for my installation procedure along with the error. If anyone
> could advice a solution it will be very helpfull for my work here....
> 
> 
>> source("http://bioconductor.org/biocLite.R")
> Warning messages:
> 1: In safeSource() : Redefining ‘biocinstall’
> 2: In safeSource() : Redefining ‘biocinstallPkgGroups’
> 3: In safeSource() : Redefining ‘biocinstallRepos’
>> biocLite("KEGG")
> Running biocinstall version 2.4.10 with R version 2.9.0
> Your version of R requires version 2.4 of Bioconductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>   argument 'lib' is missing: using
> '/home/mlscub1/R/i486-pc-linux-gnu-library/2.9'
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
>   package ‘KEGG’ is not available
> 
> 
> 
> 
> 
> Thanfully
> A.Ashwin
> MLSC
> Manipal Univeersity
> INDIA
> 
> 	[[alternative HTML version deleted]]
> 
> 
> 
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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, M1-B514
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org