Question

running Bioconductor Docker images only works with versions <= 3.15

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patrick.turko • 0

@103e0196

Last seen 14 months ago

Switzerland

I'm trying to run the bioconductor Docker images. On a terminal, I use this command to run an image on the port 8787:


 sudo docker run -d -p 8787:8787 -e PASSWORD=pass bioconductor/bioconductor_docker:RELEASE_3_15

Then in a browser, I go to http://<my server>:8787, where I'm able to log in to Rstudio-server. This works when using the tags RELEASE_3_15, RELEASE_3_14, and older tags.

However, this does NOT work, when using RELEASE_3_16 or any newer tags. I get the following error message:

Hmmm...this page is not available

<my server> refused a connection.
Try the following:
Search Bing for <my server>
Check the connection
Check proxy and firewall
ERR_CONNECTION_REFUSED

Is there something I need to do extra on the server side?

Bioconductor • 1.0k views

ADD COMMENT • link 16 months ago patrick.turko • 0

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localhost/8787 should be the path to add to your browser if running locally.

ADD REPLY • link 16 months ago ATpoint ★ 4.6k

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Thanks for the reply. I'm not running locally; instead I run the image on a server that can be accessed by browser within my institution. This type of address (http://<my server>:8787) works with bioconductor docker images <= version 3.15, as well as with the shiny apps I deploy from docker images.

ADD REPLY • link 16 months ago patrick.turko • 0

score 1 · Answer 1 · 2023-08-21

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Alexandru ▴ 20

@62443cda

Last seen 9 months ago

United States

Hello this is Alex from Bioconductor core team. We use the new containers in Kubernetes on AMD64 nodes without any issue. I would be happy to help debug the issue if I can to figure out why there might be a difference in your environment. Could you give a little more information about the node (amd/arm and ubuntu/centos etc)? Could you also provide logs from startup? Could you finally try running rocker/rstudio container to figure out if the source of the difference might be in the base container?

ADD COMMENT • link 16 months ago Alexandru ▴ 20

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Hi Alex,

The issue turned out to be an old version of Docker. I don't know what exactly went wrong, but after I updated Docker the Bioconductor images all run perfectly.

I don't know if it's useful to you, but this was happening on a RHEL 7.9 server.

ADD REPLY • link 16 months ago patrick.turko • 0