[Bioc-devel] Dependencies in Bioconductor dockers

[Laurent Gatto]

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?

Laurent

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