[Bioc-devel] Dependencies in Bioconductor dockers

Dan Tenenbaum dtenenba at fredhutch.org
Fri Aug 28 20:42:19 CEST 2015

----- Original Message -----
> From: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
> To: "Laurent Gatto" <lg390 at cam.ac.uk>
> Cc: "bioC-devel" <bioc-devel at stat.math.ethz.ch>
> Sent: Wednesday, August 26, 2015 2:36:08 PM
> Subject: Re: [Bioc-devel] Dependencies in Bioconductor dockers
> This might be especially nice if we use the docker containers for R
> check.

In this case, you would be checking your own package, right, so the docker image cannot know in advance what the Suggests dependencies of your package are.

[More below].

> On Wed, Aug 26, 2015 at 10:56 PM, Laurent Gatto <lg390 at cam.ac.uk>
> wrote:
> >
> > Dear all,
> >
> > As far as I can see, the Suggests dependencies of a package are not
> > included in the docker containers. Would you consider adding these?
> > It
> > would be nice to be able to run all examples and vignette code of
> > the
> > packages available in a container.

Adding the Suggests dependencies of all packages installed on the image is going to make the image much bigger. This request comes soon after other requests to reduce the size of the images. We should probably have a wider discussion and decide exactly what type of docker images we want to have. 

Use cases that have been mentioned are:

  - an image for building/checking with travis (sounds similar to Kasper's request above). 
    For this one in particular, small size is important as Travis has to build its environment 
    from scratch every time, and loading large images takes too long. 
  - an image that has the Suggests dependencies of all installed packages installed. 

We might want to pick a different way to decide what packages are installed on a given image. 
Currently we install all packages with a given biocView (Sequencing for example) and this leads to
very large images (sequencing = ~7.5GB).


> >
> > Best wishes,
> >
> > Laurent
> >
> > _______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
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