[Bioc-devel] Docker granularity: containers for individual R packages, running on a normal R installation?

[Wolfgang Huber]

Dear Sean
I understand the second point. As for .Call not being the right paradigm, then maybe some other method invocation mechanism? In essence, my question is whether someone already has figured out whether new virtualisation tools can help avoid some of the tradtional Makeovers/configure pain.
Wolfgang 






> On Apr 14, 2015, at 13:52 GMT+2, Sean Davis <seandavi at gmail.com> wrote:
> 
> Hi, Wolfgang.
> 
> One way to think of docker is as a very efficient, self-contained virtual machine.  The operative term is "self-contained".  The docker containers resemble real machines from the inside and the outside.  These machines can expose ports and can mount file systems, but something like .Call would need to use a network protocol, basically.  So, I think the direct answer to your question is "no".  
> 
> That said, there is no reason that a docker container containing all complex system dependencies for the Bioc build system, for example, couldn't be created with a minimal R installation.  Such a system could then become the basis for further installations, perhaps even package-specific ones (though those would need to include all R package dependencies, also).  R would need to run INSIDE the container, though, to get the benefits of the installed complex dependencies.
> 
> I imagine Dan or others might have other thoughts to contribute.  
> 
> Sean
> 
> 
> On Tue, Apr 14, 2015 at 7:23 AM, Wolfgang Huber <whuber at embl.de> wrote:
> Is it possible to ship individual R packages (that e.g. contain complex, tricky to compile C/C++ libraries or other system resources) as Docker containers (or analogous) so that they would still run under a “normal”, system-installed R. Or, is it possible to provide a Docker container that contains such complex system dependencies such that a normal R package can access it e.g. via .Call ?
> 
> (This question exposes my significant ignorance on the topic, I’m still asking it for the potential benefit of a potential answer.)
> 
> Wolfgang
> 
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