[Bioc-devel] New bioconductor_docker image officially released

[Felix Ernst]

Hi Nitesh,

Thanks for the new image.

I have a question regarding the behavior of encountering logicals with a length higher than 1 and its coercion to logical(1) for an if statement.

I encountered a bit of a problem, when a unit test returned an error running R CMD check using the Bioconductor docker image:

'length(x) = 2 > 1' in coercion to 'logical(1)'

However in a normal session this didn't raise an error. After adding 

_R_CHECK_LENGTH_1_CONDITION_=true
_R_CHECK_LENGTH_1_LOGIC2_=true

to /usr/local/lib/R/etc/Renviron.site the behavior matched the output from R CMD check.

Is this behavior intended or would you consider adding this setting to the docker image?

Best regards
Felix

-----Ursprüngliche Nachricht-----
Von: Bioc-devel <bioc-devel-bounces using r-project.org> Im Auftrag von Turaga, Nitesh
Gesendet: Dienstag, 21. Januar 2020 18:41
An: bioc-devel using r-project.org
Betreff: [Bioc-devel] New bioconductor_docker image officially released

Hello developers,

The new "bioconductor/bioconductor_docker" image is officially released.

The link to access it on Dockerhub is:  https://hub.docker.com/repository/docker/bioconductor/bioconductor_docker.

The source code in on GitHub at: https://github.com/bioconductor/bioconductor_docker.

Please note there are currently two versions,

1. bioconductor/bioconductor_docker:devel

2. bioconductor/bioconductor_docker:RELEASE_3_10 or bioconductor/bioconductor_docker:latest

The previous set of images have been deprecated. The previous images have also been updated with a `LABEL` in the Dockerfile which refers to them as "Deprecated". You can see this information on your image if you do a  `docker pull <image_name>; docker inspect <image_name>`. Please note, we will support these images through this release cycle.

We highly recommend that you shift to the new images, and use those containers. They come with all the system dependencies to install almost all of the Bioconductor packages, an RStudio interface, and with customizations which are specific to Bioconductor.

Docker images are now considered similar to Bioconductor packages. There will be official contributions from the community following our list of best practices<https://github.com/Bioconductor/bioconductor_docker/blob/master/best_practices.md>. If you need more information on the docker images please refer to http://bioconductor.org/help/docker/.

As always, if you have any questions, please feel free to reply to this email.

Best regards,

Nitesh





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