[Bioc-devel] check failure: prerequisit package does not use NAMESPACE

Paul Shannon pshannon at systemsbiology.org
Fri Sep 15 00:52:55 CEST 2006

Hi Seth,

  > I admint to being pro-NAMESPACE, but are you sure you can't work
  > around this?  You should have rJava in Depends and not mention it
  > in your NAMESPACE file.

If there's a way to work around it, I haven't been able to find it.
Here's what happens if rJava is in the DESCRIPTION 

  Depends: R (>= 2.4.0), rJava (>= 0.4), graph (>= 1.11.5)

but not in the NAMESPACE


   * checking whether the name space can be loaded with stated dependencies ... WARNING
   Loading required package: methods
   First.lib -- libname: /users/pshannon/tmp/r/2006-09-14/gaggle.Rcheck pkgname: gaggle
   initializing gaggle package 1.1.7
   path to jar: /users/pshannon/tmp/r/2006-09-14/gaggle.Rcheck/gaggle/jars/gaggleRShell.jar
         script:  gaggle.R $Revision: 882 $   $Date: 2006-08-30 14:57:21 -0700 (Wed, 30 Aug 2006) $
   Error in fun(...) : could not find function ".jinit"
   Error: .onLoad failed in 'loadNamespace' for 'gaggle'
   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.

Sorry for all this fuss...

 - Paul

More information about the Bioc-devel mailing list