[Bioc-devel] bioconductor_docker updates

Levi Waldron |w@|dron@re@e@rch @end|ng |rom gm@||@com
Tue Aug 4 10:31:01 CEST 2020

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>

> 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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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


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