[BioC] Bioconductor and R_LIBS

Steve Taylor stephen.taylor at molecular-sciences.ox.ac.uk
Thu Mar 31 09:45:09 CEST 2005


We have recently installed R 2.0.1 on Solaris 9 (sparc) and downloaded 
the latest set of BioConductor packages.

BioConductor is used by several people here on our Solaris machine and 
we are finding during testing of the system after installation that 
there are warning messages appearing when trying to use certain 
libraries due to insufficient privileges.

I had read that it is possible to point to a personal library directory 
by setting the environment variable R_LIBS. Even when I do this, when 
loading a library it still appears to be trying to write to the system 

For example:

 > .libPaths()
[1] "/home/cbrg/validate/myRlibs"    "/package/R/2.0.1/lib/R/library"
 > library(affy)
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.
Loading required package: reposTools
Warning messages:
1: Incorrect permissions to edit package database, 
/package/R/2.0.1/lib/R/library/liblisting.Rda in: 
save.locLib(locLibList, curLib)
2: Incorrect permissions to edit package database, 
/package/R/2.0.1/lib/R/library/liblisting.Rda in: 
save.locLib(locLibList, curLib)

In this case, this doesn't stop the user using the affy package (in fact 
this seems to be an issue with reposTools) but the warnings are  a 
little disconcerting.

Apologies if this is more of an R question but I wondered if anyone else 
had encountered this and if there is a solution to fix it?

Thanks and Regards,

Steve Taylor
Computational Biology Research Group
University of Oxford

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