[Bioc-devel] namespace 'GenomeInfoDb' is not available

[Martin Morgan]

On 04/29/2015 08:10 PM, Chenglin Liu wrote:
> Dear all,
>
>
>
> I am trying to develop a new package. Everything goes fine on Linux and Mac.
> However, when I do
>
>
>
> R CMD Check on Windows, there are a lot of warnings about
>
> "namespace 'GenomeInfoDb' is not available and has been replaced by
> .GlobalEnv when processing object ''.
>
> Could anyone can help me about that?
>
>
>
> Thank you in advance.
>
>
>
> Installing package prior to check...
>
>
> install for i386
>
> * installing *source* package 'OperaMate' ...
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''

I think this means that you have a serialized item (e.g., an R object in the 
data/ folder) that includes a reference to the GenomeInfoDb name space (e.g., a 
Seqinfo() instance, perhaps associated with a GRanges?) but the version of R you 
are using does not have the GenomeInfoDb package installed. Perhaps this 
situation arises because your DESCRIPTION file is missing Imports: GenomeInfoDb 
(or perhaps Depends: GenomeInfoDb) ?

If this does not help, then perhaps you can provide the content of your 
DESCRIPTION file?

Martin Morgan



> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
>
> install for x64
>
> * installing *source* package 'OperaMate' ...
> ** testing if installed package can be loaded
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> Warning: namespace 'GenomeInfoDb' is not available and has been replaced
> by .GlobalEnv when processing object ''
> * MD5 sums
> packaged installation of 'OperaMate' as OperaMate_0.99.5.zip
> * DONE (OperaMate)
>
>
>
>
>
>
>
> Ashley
>
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


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