[Bioc-devel] Dependencies in Bioconductor dockers

[Dan Tenenbaum]

----- Original Message -----
> From: "Laurent Gatto" <lg390 at cam.ac.uk>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>, "bioC-devel" <bioc-devel at stat.math.ethz.ch>, "Laurent
> Gatto" <lg390 at cam.ac.uk>
> Sent: Friday, August 28, 2015 2:28:29 PM
> Subject: Re: [Bioc-devel] Dependencies in Bioconductor dockers
> 
> 
> On 28 August 2015 20:42, Dan Tenenbaum wrote:
> 
> > ----- 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
> >> CMD
> >> 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).
> 
> Thank you for these clarifications, Dan.
> 
> If there is interest in having full/complete containers in addition
> to
> requiring light ones, would it make sense to distribute both? Would
> that
> be much overhead?
> 

I think it definitely makes sense to distribute the light containers. (and even then, I want to see how small a 'light' container is--one that contains R, LaTeX, and every system dependency that we know about)
I am a little hesitant to make the existing bloated containers even bigger by adding all the Suggests dependencies. That's why I said we might want to revisit the way we decide what packages are on a given container. Right now we use biocViews (Microarray, Sequencing, Proteomics, FlowCytometry) but that results in huge containers containing many packages that people arguably don't use that much but just happen to have the correct biocView. Of course it does have the benefit of being a somewhat democratic method.

Dan


Dan

> Laurent
> 
> > Dan
> >
> >> >
> >> > Best wishes,
> >> >
> >> > Laurent
> >> >
> >> > _______________________________________________
> >> > Bioc-devel at r-project.org mailing list
> >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> >
> >> 
> >> 	[[alternative HTML version deleted]]
> >> 
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> >> 
> 
> 
>