Error creating conda environment package __glibc conflicts for: @/linux-64::__glibc==2.28=0 python=3.7.7 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']

[Marwansha]

Hi,
am trying to use writeH5AD and there is an error for creating conda enviroment due to a confilict, any ideas how to get around that?

> writeH5AD(sce_gene,"test.h5ad")
+ /pasteur/appa/homes/masharaw/.cache/R/basilisk/1.4.0/0/bin/conda 'create' '--yes' '--prefix' '/pasteur/appa/homes/masharaw/.cache/R/basilisk/1.4.0/zellkonverter/1.2.1/zellkonverterAnnDataEnv' 'python=3.7.7' '--quiet' '-c' 'conda-forge'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                                                                                                                                            

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package __glibc conflicts for:
@/linux-64::__glibc==2.28=0
python=3.7.7 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
Note that strict channel priority may have removed packages required for satisfiability.

Error: Error creating conda environment '/pasteur/appa/homes/masharaw/.cache/R/basilisk/1.4.0/zellkonverter/1.2.1/zellkonverterAnnDataEnv' [exit code 1]

[lazappi]

Hi. It looks like the incompatibility is with your system version of glibc (i.e. I think you would have the same problem creating a normal conda environment) so I'm not sure how much I can help.

You are also using a very old version of {zellkonverter} (v1.2.1) which is attempting to use an old conda environment. Upgrading to a newer version of {zellkonverter} (the current release is v1.14.0) would use a much newer environment which might install without issues (plus you get all the other improvements made since then).

[lazappi]

@Marwansha I am closing this issue as I think it is not a {zellkonverter} problem

[DaydreamingElephant]

Hello! I am afraid that is still an issue with zellkonverter_1.16.0 library for linux with reticulate_1.40.0 and basilisk_1.18.0 attached. I have already raised it up with basilisk team, so please give another consideration to the process of environment creation and whether a fallback from basilisk outlined in the mentioned issue should be implemented.

[lazappi]

@DaydreamingElephant Thanks for providing more information, I have created #136 about setting up the fallback mechanism. I'm not sure if it will help in this case though because {zellkonverter} relies on functions in Python anndata and other which it sounds like the fallback does not allow access to.

Another option is to use AnnData2SCE() instead of readH5AD(). This function isn't run using {basilisk} so it allows/requires the user to set up their own environment, which could be the base Python environment or a PyEnv environment which doesn't have the GLIBCXX issues.

There are other changes planned that will avoid needing to using conda but those are still a way off.