[BioC] can't instal MetaData package "mouse4302"

Seth Falcon sfalcon at fhcrc.org
Thu Mar 3 16:28:09 CET 2005

Hi Gordon,

We've discovered a wide-spread issue with how the Windows metaData 
packages were built that makes the data very difficult to access.

We are working on a fix and should have corrected packages posted soon.

The Source packages, for Linux, are still available.  From the 
transcript you sent, it would be helpful to know the value of the 
environment variable R_LIBS as well as the library package path, which 
you can get like this from inside R:

path = .libPaths()

This function returns invisibly, so you have to capture its return 
value in a variable in order to see it.

On Mar 3, 2005, at 1:58 AM, Gordon Smyth wrote:
> > library(reposTools)
> Loading required package: tools
> Warning messages:
> 1: Incorrect permissions to edit package database, 
> /usr/local/lib/R/library/liblisting.Rda in: save.locLib(locLibList, 
> curLib)
> 2: Incorrect permissions to edit package database, 
> /usr/local/lib/R/library/liblisting.Rda in: save.locLib(locLibList, 
> curLib)

The above message indicates a permission problem with where you are 
installing your packages to.

> [1] "Attempting to download mouse4302 from 
> http://www.bioconductor.org/data/metaData/"
> [1] "Download complete."
> [1] "Installing mouse4302"
> * Installing *source* package 'mouse4302' ...
> ** R
> ** data
> ** preparing package for lazy loading
> Error in .find.package("mouse4302") : none of the packages were found
> Execution halted
> ERROR: lazy loading failed for package 'mouse4302'
> From URL:  http://www.bioconductor.org/data/metaData/
>         mouse4302 version 1.6.8

I've seen this error when the library path I was installing packages 
into was not the default R system path and I had not set  and 
"exported" R_LIBS to my non-default path before running R.  See the 
documentation for install.packages where there is a brief note about 

Hope that helps,

+ seth

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