[Bioc-devel] bioconductor/metabolomics Docker image available
Hi Steffen,
On 07/27/2016 09:11 AM, Dan Tenenbaum wrote:
----- Original Message -----
From: "Steffen Neumann" <sneumann at ipb-halle.de> To: "Dan Tenenbaum" <dtenenba at fredhutch.org> Cc: "bioc-devel" <bioc-devel at r-project.org> Sent: Wednesday, July 27, 2016 5:02:22 AM Subject: bioconductor/metabolomics Docker image available Hi Dan and BioC community! I now cleaned up my Bioconductor/bioc_docker and opened a pull request to add a Metabolomics Bioconductor [1]. This works on our Jenkins installation, where I regularly build the devel_metabolomics [2] and release [3] images. The image for the previous devel version (BioC-3.3) does build, but the image for the old release version (BioC-3.2) does not, due to the mzR issue on new gcc we talked about a few months ago. If you want, I can send a second pull request and modify bioc_docker/config.yml to use the current versions 3.3 for release, and 3.4 for devel.
Yes, please do this.
As you're probably aware, many of the containers were failing to build due (in part) to outdated versions. Dan updated config.yml yesterday and we are monitoring the builds of the other containers. Can you please merge your branch with master and update your pull request (i.e., no changes needed to config.yml )? Thanks. Valerie
A more general question, what is the current docker strategy for Bioconductor. Are they build/tested on a regular basis ?
Built daily, but not tested.
Are failure reported to package maintainers, or should they ?
Failure is not reported to anyone, it probably should be.
Should the docker images be part of the regular checkResults report ?
I think they should be in a separate report, but perhaps one that lives under /checkResults. Dan
Yours, Steffen [1] https://github.com/Bioconductor/bioc_docker/pull/4 [2] http://phenomenal-h2020.eu/jenkins/job/bioc_docker_devel_metabolomics/ [3] http://phenomenal-h2020.eu/jenkins/job/bioc_docker_release_metabolomics -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
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