Message-ID: <C88F38E1-C9A3-4F1C-8398-C31AFC928D7E@gmail.com>
Date: 2020-08-04T10:33:13Z
From: Nitesh Turaga
Subject: [Bioc-devel] bioconductor_docker updates
In-Reply-To: <CAOUXvx4JNbpJEUH18e44DFhfmwt+j3+b8KMRdj1upCTOmg4tRw@mail.gmail.com>
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 at 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 at 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 at 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 at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
[[alternative HTML version deleted]]