doHMRF on CODEX dataset in Docker environment

[huBioinfo]

Dear Developers,

I'm running the "doHMRF" function on the Giotto-provided CODEX spleen dataset in the Docker environment (Win10 system). But I got an error "segmentation faults" after running 1 minute. Do you have any clues on this? I searched the previous issues and found a similar one "#133". Is my error also related to "stack limit"? If so, can you help me on the configuration of the stack limit in the Windows Docker environment? Thanks a lot! BTW, I used all defaut parameters when running doHMRF.

[bernard2012]

Yes. It is most likely related to stack limit issue.
The instructions provided in that issue #133 to resolve it is for Native install. I guess since you are using the docker image, you will need to execute the commands in the Docker terminal.
Did you try it, and did it give you any errors?

ulimit -s
ulimit -s 100000

After doing so, you probably want to restart R and RStudio server (if you are using that in the docker).
You can contact me at zqian@jimmy.harvard.edu if you need more info and let me know if it works. I can work with you to develop a solution that we can post on the website or update the Docker image.