Hi Sean, I think either this email thread or the #containers channel on the community-bioc slack is the best place to discuss implementation of integration tests for these images.
I’m doing some proof-of-concept preliminary work on the integration tests in the next 3 weeks, but I’d say it’s not pre-mature to discuss them. I might have a better sense of what is possible/what is not, in 2-3 weeks time. But I’m open to discussion. Best, Nitesh > On Aug 4, 2020, at 11:03 AM, Sean Davis <seand...@gmail.com> wrote: > > Thanks for operationalizing some of the recent lessons in dockerworld, > Nitesh! Is there a place to start discussing how to implement tests for these > images, or is that premature? > > Sean > > > On Tue, Aug 4, 2020 at 6:33 AM Nitesh Turaga <nturaga.b...@gmail.com > <mailto:nturaga.b...@gmail.com>> wrote: > Hi Levi, > > Within the RStudio terminal console you can check the contents of the file > `/etc/environment`. This should show you a version number > > $ cat /etc/environment > ‘BIOCONDUCTOR_DOCKER_VERSION = 3.11.11' > > (The example above is run on a RELEASE_3_11 image) > > Best, > > Nitesh > > > > On Aug 4, 2020, at 4:31 AM, Levi Waldron <lwaldron.resea...@gmail.com > > <mailto:lwaldron.resea...@gmail.com>> wrote: > > > > Thanks Nitesh! Very much appreciated. I was wondering, is there a way to > > inspect the version from _within_ the image, i.e., that could supplement a > > sessionInfo() command? > > > > On Mon, Aug 3, 2020 at 6:30 PM Turaga, Nitesh > > <nitesh.tur...@roswellpark.org <mailto:nitesh.tur...@roswellpark.org>> > > wrote: > > > >> Hello Bioconductor Community, > >> > >> A quick update about the latest developments on the Bioconductor Docker > >> images. > >> > >> We have updated the ‘devel’ image to inherit from the latest > >> ‘rocker/rstudio:4.0.2’ image. This means that the > >> `bioconductor/Bioconductor_docker:devel` image, which is now available will > >> be running on, > >> > >> > >> 1. Ubuntu 20.04 > >> 2. R version 4.0.2 > >> 3. Bioconductor version 3.12. > >> > >> One major update to the system requirements was the installation of the > >> ‘libglpk-dev’ which seemed to have caused issues installing the ‘igraph’ > >> package. The version number of this image which can be queried through the > >> docker command is going to be 3.12.13. > >> > >> If you pull the updates from dockerhub using, > >> > >> docker pull bioconductor/Bioconductor_docker:devel > >> > >> And check the version number using, (the result is going to be 3.12.13. > >> > >> docker inspect --format '{{ index .Config.Labels.version}}' > >> bioconductor/bioconductor_docker:devel > >> > >> > >> NOTE: The release image stayed exactly the same but with the addition of > >> the `libglpk-dev` package. The RELEASE_3_11 image did not get updated to > >> Ubuntu 20.04. It is still based on Ubuntu 18.04. The devel image now works > >> on a different version of Ubuntu (20.04) as compared to the build system > >> (18.04. The support for the 18.04 image on rocker is no longer available. > >> > >> The inspect label command for RELEASE_3_11 (given below) should produce > >> the new version number 3.11.11. Do not forget to pull. This is a bug fix > >> with regards to the igraph package’s missing dependency. > >> > >> docker inspect --format '{{ index .Config.Labels.version}}' > >> bioconductor/bioconductor_docker:RELEASE_3_11 > >> > >> > >> If you have any further questions, please reply to this thread. > >> > >> Best regards, > >> > >> Nitesh Turaga > >> Bioconductor Core Team > >> > >> > >> This email message may contain legally privileged and/or confidential > >> information. If you are not the intended recipient(s), or the employee or > >> agent responsible for the delivery of this message to the intended > >> recipient(s), you are hereby notified that any disclosure, copying, > >> distribution, or use of this email message is prohibited. If you have > >> received this message in error, please notify the sender immediately by > >> e-mail and delete this email message from your computer. Thank you. > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >> <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > >> > > > > > > -- > > > > Levi Waldron > > > > Associate Professor > > > > Department of Epidemiology and Biostatistics > > > > CUNY Graduate School of Public Health and Health Policy > > > > Institute for Implementation Science in Population Health > > > > 55 W 125th St, New York NY 10035 > > > > https://waldronlab.io <https://waldronlab.io/> > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > > -- > Sean Davis, MD, PhD > Center for Cancer Research > National Cancer Institute > National Institutes of Health > Bethesda, MD 20892 > https://seandavi.github.io/ <https://seandavi.github.io/> > https://twitter.com/seandavis12 <https://twitter.com/seandavis12> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
