Bioconductor/bioconductor_docker

Errors with release 3.16

fortune9 opened this issue · 3 comments

fortune9 commented

The docker image has the following issues when I run the commands within the container:

  • Command: R

    • error message:
      OpenBLAS blas_thread_init: pthread_create failed for thread 1 of 8: Operation not permitted
      OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max

  • Command: apt-get update

    • error message:
      Reading package lists... Done
      E: Problem executing scripts APT::Update::Post-Invoke 'rm -f /var/cache/apt/archives/.deb /var/cache/apt/archives/partial/.deb /var/cache/apt/*.bin || true'
      E: Sub-process returned an error code

Environment:

  • BIOCONDUCTOR_DOCKER_VERSION : 3.16.31
  • My host system: 18.04.1-Ubuntu

Please advise how to address the above issues.

vjcitn commented

Please provide the command you used to invoke docker on the container. You say the command "R" fails in a container started with docker run ... bash? Please give the version of your docker client also. Thanks.

fortune9 commented

Thank you for the quick reply, @vjcitn .

I initiated the docker container using the following command:

docker run -it --rm bioconductor/bioconductor_docker:RELEASE_3_16 bash

And then run the commands in my first post.

Update

Actually, after I posted the issue here, I did some google search and found a fix.

The issue seemed due to my old version of docker, which was 20.10.8. After I updated the docker engine to 20.10.21
instructions here, the issue was fixed.

Thank you for your help all the same!

almahmoud commented

I will close this as it seems to have been resolved. Please let us know if you are experiencing any other issues.