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]]

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]] > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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