Conflicting definitions of "devel"/"release" between actual Bioconductor and bioconductor_docker

Question

Conflicting definitions of "devel"/"release" between actual Bioconductor and bioconductor_docker

bschilder opened this issue 3 years ago · 12 comments

Unless I'm missing something, there appears to be a lag between when Bioconductor changes the previous devel to become the current release (3.14 as of today), and when the bioconductor/bioconductor_docker container is updated (it currently lists 3.14 as the devel and 3.13 as the release, which is no longer true).
https://hub.docker.com/layers/bioconductor/bioconductor_docker/devel/images/sha256-5edc02a68f1bbee9db21950b95c133aaab97e15781d3cc1690fed41b3689c2d2?context=explore

This causes (GitHub Action) workflows that depend on harmonized devel/release naming schemes across Bioconductor and bioconductor_docker to break.

How long of a delay is there between when a new version of Bioconductor is released and when this bioconductor_docker is updated? Is this something that is currently automated?

GHA workflow

Example GHA workflow output

Answer 1 · 2021-10-27T22:49:25.000Z

This seems to be a recurring issue that could potentially be addressed with automated updates to bioconductor_docker every time a new version of Bioconductor is released:
#29
#17
#8

Answer 2 · 2021-10-28T16:42:57.000Z

Yes, we check the docker image once the release is done to make sure everything is working as expected.

Reasons:

We currently do not have automated tests for our docker images. We run some manual tests.
We make sure all the packages are being installed without issues (other than those reported on the build system)

Usually, it's just the day after the release, i.e today by end of day or early tomorrow.

Answer 3 · 2021-10-28T20:35:41.000Z

Thanks so much for the info and the quick reply @nturaga! See here #29 for some potential ideas.

Answer 4 · 2021-10-30T11:47:43.000Z

Hi reading above, should a docker image for RELEASE_3_14 be available here now https://hub.docker.com/r/bioconductor/bioconductor_docker/tags ?

Can only see RELEASE_3_13 and devel which uses 3.15. Be great to get 3.14 for a workshop we have on Monday, actions currently failing due to having no 3.14 Docker available https://github.com/tidytranscriptomics-workshops/rpharma2021_tidytranscriptomics/actions

Answer 5 · 2021-10-31T14:39:14.000Z

It's available now. Please check.

Answer 6 · 2021-10-31T16:04:16.000Z

@mblue9 Let me know if it worked?

Answer 7 · 2021-10-31T16:19:34.000Z

Trying it now & looks like it's working. Thanks a lot @nturaga !!

Answer 8 · 2023-01-06T16:53:55.000Z

Hi Brian, @bschilder
Regarding your note here: https://github.com/marketplace/actions/rworkflows Acknowledgements > Details
"Often" is an overstatement. The devel container does take a day or two to get updated immediately after the release. Our updates are increasingly automated thanks to Alex @almahmoud
Throughout the rest of the six month period, the devel container corresponds to the devel version of Bioconductor.

Answer 9 · 2023-01-06T16:59:28.000Z

Hi Brian, @bschilder Regarding your note here: https://github.com/marketplace/actions/rworkflows Acknowledgements > Details "Often" is an overstatement. The devel container does take a day or two to get updated immediately after the release. Our updates are increasingly automated thanks to Alex @almahmoud Throughout the rest of the six month period, the devel container corresponds to the devel version of Bioconductor.

I was referring to the lag after updates, but I can clarify in the description. Great to hear improvements in automation and checking are happening! Thanks for the continued efforts.

Answer 10 · 2023-01-06T17:33:07.000Z

Thanks for the clarification.
The lag is due to the release events schedule and the actual time it takes to update them. The containers get updated post-release.

Answer 11 · 2023-01-07T12:01:23.000Z

The lag is due to the release events schedule and the actual time it takes to update them. The containers get updated post-release.

The note now reads:

NOTE: Whenever a new version of Bioconductor is released,
the bioconductor/bioconductor_docker container will often lag behind the actual Bioconductor releases
for up to several days, due to the time it takes to update the container.
This means that sometimes "devel" in Bioconductor/bioconductor_docker is actually referring to the "release"
version of Bioconductor. See this Issue
for details.

Does that seem accurate to you @LiNk-NY ?

Answer 12 · 2023-01-09T14:55:23.000Z

Looks good. The second to last sentence might going into too much detail but you could say that during that period, devel still refers to the previous release's devel which is the current release version (if this info is necessary).