[Bioc-devel] bioconductor_docker updates

[Nitesh Turaga]

Hi Levi,

Just wanted to follow up on this again, I’ve made a few changes to the 3.12.14 image version on the `bioconductor/bioconductor_docker:devel` image, where you should be able to query for the version _within_ the docker image using,

	Sys.getenv(‘BIOCONDUCTOR_DOCKER_VERSION’)

This is a much easier way of interacting with the environment variable. 

And if you want to get a sense of what is the current version number of the “devel” image hosted on Dockerhub, instead of looking up the image version on Github each time, you could use my little package function. This works on your local machine _outside_ the docker container. (I’m planning on extending the functionality of BiocDockerManager::version() to work _within_ the docker image as well)

	> BiocDockerManager::version(repository=‘bioconductor/bioconductor_docker’, tag = ‘devel’)
	[1] “3.12.14"

Best,

Nitesh 


> On 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 <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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>> 
>> 
>> -- 
>> 
>> 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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