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

Sean Davis seandavi at gmail.com
Tue Apr 14 13:52:55 CEST 2015

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.


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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> Bioc-devel at r-project.org mailing list
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