[Bioc-devel] package cannot be loaded

[Mueller, Arne]

Hello - thanks for the hint, it did source the .Rprofile!

  Arne


On 2/24/12 5:45 PM, "Martin Morgan" <mtmorgan at fhcrc.org> wrote:

>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 Œ/Users/muellar2/workspace-indigo/Gviz.Rcheck¹
>> * 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 ŒGviz/DESCRIPTION¹ ... OK
>> * this is package ŒGviz¹ version Œ0.99.0¹
>> * 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 ŒGviz¹ 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 ŒBiobase¹
>> Error: package/namespace load failed for ŒGviz¹
>> 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
>>
>>
>> 	[[alternative HTML version deleted]]
>>
>>
>>
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
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