Re: [Bioc-devel] best practice: dependencies of dependencies / no visible global function definition

2015-06-24 Thread Martin Morgan
On 06/24/2015 10:42 AM, Michael Lawrence wrote: In order for R to find those symbols reliably, you need to import those functions into your NAMESPACE, and therefore you should ensure yes that the Biobase package is listed on the Depends line of your DESCRIPTION. Your package directly depends

Re: [Bioc-devel] best practice: dependencies of dependencies / no visible global function definition

2015-06-24 Thread Michael Lawrence
In order for R to find those symbols reliably, you need to import those functions into your NAMESPACE, and therefore you should ensure that the Biobase package is listed on the Depends line of your DESCRIPTION. Your package directly depends on Biobase, so there's no redundancy by having it listed i

[Bioc-devel] best practice: dependencies of dependencies / no visible global function definition

2015-06-24 Thread Ludwig Geistlinger
I'm surely not the first asking this question. But as I did not find a clear answer to that (e.g. in the 'Writing R extensions' manual or in the diverse posts on this), I risk asking it again. As an example: I'm dealing a lot with ExpressionSets (from Biobase) and GeneSet[Collection]s (from GSEAB