[Bioc-devel] package cannot be loaded

[Martin Morgan]

On 02/24/2012 07:14 AM, Mueller, Arne wrote:
> Hello,
>
> I'm relatively new to bioconductor development, and I've a problem with an error R CMD check spits out:
>
> R CMD check Gviz
>
> BiocInstaller version 1.3.7, ?biocLite for help
> * using log directory ‘/Users/muellar2/workspace-indigo/Gviz.Rcheck’
> * using R Under development (unstable) (2012-02-22 r58461)
> * using platform: x86_64-apple-darwin10.8.0 (64-bit)
> * using session charset: UTF-8
> * checking for file ‘Gviz/DESCRIPTION’ ... OK
> * this is package ‘Gviz’ version ‘0.99.0’
> * checking package namespace information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking if there is a namespace ... OK
> * checking for executable files ... OK
> * checking whether package ‘Gviz’ can be installed ... OK
> * checking installed package size ... OK
> * checking package directory ... OK
> * checking for portable file names ... OK
> * checking for sufficient/correct file permissions ... OK
> * checking DESCRIPTION meta-information ... OK
> * checking top-level files ... OK
> * checking index information ... OK
> * checking package subdirectories ... OK
> * checking R files for non-ASCII characters ... OK
> * checking R files for syntax errors ... OK
> * checking whether the package can be loaded ... ERROR
> Loading this package had a fatal error status code 1
> Loading log:
> Loading required package: grid
> Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) :
>    there is no package called ‘Biobase’
> Error: package/namespace load failed for ‘Gviz’
> Execution halted
>
> I can build and install the Gviz package as well as loading it in an
interactive R-session (and grid and Biobase, too). Any idea how to
figure out where the problem is?

My guess is either that you are using a different R, or that in your 
interactive session you have (implicitly?) source'd a startup file 
(.Rprofile, .RData, ..., see ?Startup) that is not source'd at the 
command line. If you are using the same R, then starting with R 
--vanilla would be more like installation at the command line; I'd look 
to the definition of .libPaths().

Martin

>
>   Thanks a lot for your help,
>
>   Arne
>
>
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>
>
>
>
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