[Bioc-devel] package cannot be loaded

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

  Thanks a lot for your help,

  Arne


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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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