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Bioconductor / bioc_docker

[DEPRECATED] Docker containers for Bioconductor
https://github.com/bioconductor/bioconductor_docker
Artistic License 2.0
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Update for Release 3.9 #84

Open sneumann opened 5 years ago

sneumann commented 5 years ago

Hi, rocker/rstudio:3.6.0 appeared yesterday. For release we need a branch R3.6.0_Bioc3.9 The 3.8 release branch was missing the _ (minor cosmetic itch).

Configuration happens in https://github.com/Bioconductor/bioc_docker/blob/master/config.yml It would be great to cleanup some of the comments and make them more explicit, e.g. should always be false to should always be false in release, or 'true half the year->true during devel cycle may to october` (or was it the other devel cycle ?) and remove outdated comments (rstudio-daily does not exist anymore ?).

Check if we still want to support use_numbered_branch, which is used in https://github.com/Bioconductor/bioc_docker/blob/master/src/base/Dockerfile.in#L72 to (optionally) install an R from sources. This does help during the weeks where rstudio:devel reports the next R version, which has (and will) cause the bioc docker to fail during april, unless the biocVersion hack is used in our Dockerfile(s). But it would be a very special case, as we can't be sure our R compilation is consistent with what rocker uses, so I suggest to stick with the rocker R version in our images always.

Yours, Steffen

lshep commented 5 years ago

I will make some time in the upcoming weeks to clean up the notes in the config file as well as clean up the base/core installation scripts. For now moving through the pull request change so the dockers can start building the correct images/versions