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

[Michael Lawrence]

That's why virtual runtimes, like Java, were invented.

On Tue, Apr 14, 2015 at 1:17 PM, Wolfgang Huber <whuber at embl.de> wrote:

> 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
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

	[[alternative HTML version deleted]]