[Bioc-devel] bioconductor_docker updates

Tue Aug 4 19:28:09 CEST 2020

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 <seandavi using 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.bioc using gmail.com <mailto: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 <mailto: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 <mailto: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
> >> 
> >> 
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> >> _______________________________________________
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> >> 
> > 
> > 
> > -- 
> > 
> > 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/>
> > 
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> 
> -- 
> 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>

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