[Bioc-devel] NAMESPACE woes [was Re: Update on upcoming BioC 1.9 release]

Paul Shannon pshannon at systemsbiology.org
Wed Sep 13 02:45:36 CEST 2006

I'm trying to fix the 'check' errors in my 1.9 bioc gaggle package.
Perhaps someone can help with me with my confusion.

   - I installed R 2.4.0.alpha on linux
   - I install the gaggle's prerequisites (Ruuid 1.10.0, graph 1.10.6, rJava 0.4-9)
   - I run R CMD check gaggle_1.1.6.tar.gz, and got the following warning:

       * checking whether the package can be loaded with stated dependencies ... OK
       * 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.

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

Since Ruuid has no prerequisites of its own, I am puzzled by the check failure, and the
(possibly misleading) error message:

      unable to load R code in package 'Ruuid'

For what it's worth, I have had problems (and proably will -still- have them) with
NAMESPACE and rJava.   rJava doesn't use NAMESPACES itself, and the new R seems
to require NAMESPACES all the way down.

I'll be very grateful if anyone can help me out.

Thanks -

 - Paul

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