[Bioc-devel] bioconductor_docker updates

[Sean Davis]

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.bioc using 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.research using 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.Turaga using 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 using r-project.org mailing list
> >> 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
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> 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://twitter.com/seandavis12

	[[alternative HTML version deleted]]