[Bioc-devel] bioconductor_docker updates

[Nitesh Turaga]

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
>> 
>> 
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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
> 
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> 
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