-
Notifications
You must be signed in to change notification settings - Fork 97
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
can't build afni with R #584
Comments
It seems that the R install of AFNI is not something we test regularly: https://github.com/ReproNim/neurodocker/actions/runs/6520678281/job/17708466328 We should probably fix that. That being said AFNI is the most "broken" install that neurodocker has at the moment so any help to improve that is most welcome |
Dear @andreifoldes, You can have a look at this neurodocker recipe, which works for installing the R-packages in AFNI: In particular, you could try fedora 35 as a base image, which I have found to work best for AFNI:
The error you get might also be related to singularity - it could be that building this with docker would actually work. It seems that it can't find the executable rPkgsInstall on the PATH, which could be a path error that somehow works in Docker? If you just want an AFNI container with all required dependencies and R-packages installed and tested, you can also use the singularity container from the Neurodesk project (https://www.neurodesk.org/docs/getting-started/neurocontainers/singularity/):
I hope that helps |
Greetings+ Manually editing the recipe from
Amazing! Thx I see that it contains python too! |
I stand corrected... while adding full path in the recipe does get the build issue fixed, once actually trying it out on real life data produces:
This occurs with the neurodesk simg file specifically! In terms of neurodocker - can yum install specific version of R? I have a feeling that if only I could get R 3.6 all 3dLMEr would work. |
Dear @andreifoldes, neurodocker cannot install a specific version of R through yum - the best way I found to get a specific version of R is to choose a baseimage version that brings this R version. Another option could be to install R manually in a specific version. So, 3dLMEr only works with R 3.6? Is that correct? |
I see! Can you recommend which baseimage would be it for R 3.6, how could I check?
I haven't checked this in all Linux distributions, but we have Centos7 on our cluster and there I had trouble getting lme4 working with r-base>=4 and had better success with 3.6. 3dLMEr needs lme4, lmerTest, phia and snow to work. In terms of singularity image I would be happy to have any working solution ^^
Right, but then I would need to install it every time I call the function right? Or would you turn it into a sandbox? |
I think we can close this issue here. As discussed in this issue (NeuroDesk/neurocontainers#505), the problems @andreifoldes experienced come from running the singularity container without --cleanenv and R-packages from the host environment interfered with the container environment. |
Greetings,
I'm trying to run the following code:
but get the following error
The text was updated successfully, but these errors were encountered: