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I'm trying to make a very simple conda environment with just r-seurat as a dependency. My environment yaml looks as follow:

channels:
  - bioconda
dependencies:
  - r-seurat

And I'm creating it with conda env create -n myenv -f envs/myenv.yaml

I get the following error:

Collecting package metadata (repodata.json): done
Solving environment: \ 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                          
Solving environment: / 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                          

UnsatisfiableError:

Nothing else. This must be the most unhelpful error message. Anybody that has had a similar issue? I already update conda.

I am running this in macos catalina 10.15.6, with conda version 4.8.4

compuTE
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  • Try it again, but include all the channels that are specified in [the BioConda instructions](https://bioconda.github.io/user/install.html#set-up-channels), i.e., conda-forge, bioconda, and defaults. – merv Sep 19 '20 at 00:05
  • Thank you @merv, but now it has been trying to solve the environment for 6 hours :-( – compuTE Sep 19 '20 at 22:05
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    Here's a fully specified environment for **osx-64** platform: [YAML Gist](https://gist.github.com/mfansler/631c8a1635cd5e2d88354ef034a2a279). This is what results (for me on 10.4) from a YAML with only `r-seurat` and `umap-learn` as dependencies. Can you create and env from that? – merv Sep 20 '20 at 04:59
  • Wow, yes!! This works! Thank you. That yaml is so long that I'm thinking this might have been a super noob question... How did you know what to include?? :-O – compuTE Sep 20 '20 at 16:07
  • Aha! I think you made a new environment, installed it and did conda list. Right? – compuTE Sep 20 '20 at 19:41
  • Yes, that's what I did. I just wanted to make sure that you can potentially create the environment, even if solving is having issues. Could you try creating again from this minimal definition: [YAML Gist](https://gist.github.com/mfansler/631c8a1635cd5e2d88354ef034a2a279#file-so-seurat-min-yaml)? Note that for this one, the only additional specification I provide is to give versions for Python and R (down to minor), which should help constrain the solve. – merv Sep 22 '20 at 20:07

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