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Bioconductor / bioconductor_docker

Docker Containers for Bioconductor
https://bioconductor.org/help/docker/
Artistic License 2.0
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Cannot install packages with BiocManager::install during docker build #92

Closed usu-imeg closed 11 months ago

usu-imeg commented 11 months ago

I wrote a Dockerfile to install some packages using bioconductor/bioconductor_docker as base image and built it, but when I use BiocManager::install() to install When I use BiocManager::install() to install bioconductor packages, I get an error.

BiocManager::install('multtest', update = F) Error: Bioconductor version cannot be validated; no internet connection? See

troubleshooting section in vignette

In addition: Warning messages: 1: In file(con, "r") : URL 'https://bioconductor.org/config.yaml': status was 'Couldn't resolve host name' 2: In file(con, "r") : URL 'http://bioconductor.org/config.yaml': status was 'Couldn't resolve host name' Execution halted

On the other hand, install.packages() installs the packages successfully.

When I did a build a few months ago using the same base image, I did not get this error.

FROM bioconductor/bioconductor_docker:RELEASE_3_16 FROM bioconductor/bioconductor_docker:RELEASE_3_17 FROM bioconductor/bioconductor_docker:RELEASE_3_18

They all have the same error.

I use Docker Engine installed on wsl2 (Ubuntu on Win).

almahmoud commented 11 months ago

Hey @usu-imeg , thanks for the report. It seems bioconductor.org is not properly resolving for you. It seems to be working as expected on my end. Could you try it again to confirm it wasn't a temporary downtime? If not, my best guess are network restrictions of some sort preventing you from hitting the endpoint. If you run the container in the same environment, does a curl on bioconductor.org resolve?

usu-imeg commented 11 months ago

I just did docker build and it completed successfully with no errors. Was this temporary downtime last time? I did not know about the downtime. Thanks for your advice !

almahmoud commented 11 months ago

I don't know of a downtime on our end, and the scripts we have tracking the server did not pick one up. I've seen this happen in VMs before when they lose internet connectivity due to network issues, but connectivity issues can happen at many levels.