On 28 August 2015 20:42, Dan Tenenbaum wrote: > ----- Original Message ----- >> From: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com> >> To: "Laurent Gatto" <lg...@cam.ac.uk> >> Cc: "bioC-devel" <bioc-de...@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 <lg...@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 >> > >> > _______________________________________________ >> > Bioc-devel@r-project.org mailing list >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
