Error when installing from github about immunedeconv HOT 8 CLOSED

I ended up making a Ubuntu docker container to run it which I put here (package is installed in this image):
https://hub.docker.com/r/mahermassoud/immunedeconv/tags

When I follow the conda environment instructions posted on the repo, I get a different error:
#37 (comment)

Thanks for your help. I will be sticking to the docker container for now. Will let you know if I try out the things you mentioned.

from immunedeconv.

Hi @mahermassoud,

thanks for reporting!
The failure to install DescTools seems independent of the upgrade of BiocGenerics.
Can you try to select Upgrade none [n] when updating BiocGenerics? It should still do the upgrade but not attempt to update any other packages.

In any case, the proper version of BiocGenerics should automatically be installed, which will be fixed in #45.

Cheers,
Gregor

from immunedeconv.

Tried and it didn't work. I also tried to pull from #45 and install from source and that didn't work either. All got me the same error. I even deleted the BiocGenerics line from DESCRIPTION and got the same error. I am able to install on a linux machine but I'd like to be able to do it on mac.

from immunedeconv.

Have you considered installing R version 4 and getting the latest version of all Bioconductor packages? Even if you do not have administrator privileges, compiling R from source and installing it to a personal directory is not difficult (relative to most bioinformatics software). You'll have a lot less problems with Bioconductor packages in future if you do that now.

from immunedeconv.

Thanks for investigating! I'll set-up github actions to run the CI also on macos - If this is really a mac-related problem, I'll hopefully find the problem that way.

Regarding R 4.0: I'm not sure if immunedeconv is compatible already...

from immunedeconv.

With the latest update of xCell, immunedeconv should work on R4.0.0.

I cannot reproduce the issue on the macOS CI.

It could be worth trying with a clean R environment. Either

• delete the folder where your packages got installed to (r .libPaths() or
• create a fresh conda environment with just R and remotes installed: conda create -c conda-forge -n R361 r-base=3.6.1 r-remotes

from immunedeconv.

Updating to R v4 fixed this

from immunedeconv.

ok, great!

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