[BioC] Biobase/BioBase capitalization user errors in Windows

James Wettenhall wettenhall at wehi.edu.au
Thu May 29 14:04:52 MEST 2003


Hi,

Thanks very much to all Bioconductor developers for version 1.2!

Often I can't remember the capitalization in Bioconductor 
package names, so after running getBioC() to get Bioconductor 
1.2, I accidentally typed:
library(BioBase) 
instead of 
library(Biobase).  
This is obviously Operating System dependent, but in Windows 2000, 
R 1.7.0, getPkgVigs and .First.lib gave some rather unfriendly 
errors, e.g. "packages: Biobase are not installed" :

Perhaps one way to get around this is to change the following 
line in Biobase's getPkgVigs :
        rows <- match(package, pkgs)
to :
        rows <- match(tolower(package),tolower(pkgs))

Regards,
James

> library(BioBase)
Welcome to Bioconductor 
         Vignettes contain introductory material.  To view, 
         simply type: openVignette() 
         For details on reading vignettes, see
         the openVignette help page.
Creating a new generic function for "summary" in package 
reposTools 

Synching your local package management information ...
Error in getPkgVigs(pkgName) : packages: Biobase are not 
installed
Error in library(BioBase) : .First.lib failed
> library(Biobase)
Welcome to Bioconductor 
         Vignettes contain introductory material.  To view, 
         simply type: openVignette() 
         For details on reading vignettes, see
         the openVignette help page.



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