[Bioc-devel] NAMESPACE woes

Seth Falcon sfalcon at fhcrc.org
Wed Sep 13 03:14:05 CEST 2006

Hi Paul,

Paul Shannon <pshannon at systemsbiology.org> writes:
> * checking whether the name space can be loaded with stated dependencies ... WARNING
>    >>>   Error in eval(expr, envir, enclos) : could not find function
>    >>> "setClass" Error: unable to load R code in package 'Ruuid'
>          Execution halted
>          A namespace must be able to be loaded with just the base
> namespace loaded: otherwise if the namespace gets loaded by a saved
> object, the session will be unable to start.
>          Probably some imports need to be declared in the NAMESPACE
> file.

For now for _this_ particular warning message related to Ruuid, I
think the thing to do is to ignore it for now.  

AFAICT, the warning is coming from Ruuid and will appear in any
package that has a (possibly indirect) dependency on Ruuid.  The issue
is related to creating S4 instances in C code and how this plays with
one of the checks where the package is loaded with the default set of
packages set to NULL. 

This is a rather bogus test for just about any BioC package in the
sense that if you do not have methods loaded, not much good will

> My NAMESPACE file looks like this: import(Ruuid, graph)

Do you actually use Ruuid or just graph?  I'm hoping to remove graph's
dependence on Ruuid tomorrow which should make things better...


+ seth

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