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I am trying to install the pairtools (https://github.com/mirnylab/pairtools) package on Mac terminal using the following command:

conda install -c conda-forge -c bioconda pairtools

When I run this I am getting the following error message:

Collecting package metadata (current_repodata.json): done
Solving environment: failed
Collecting package metadata (repodata.json): done
Solving environment: failed

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

  - pip -> python[version='>=3.6,<3.7.0a0']

Is this a version problem? The current version of python I have is 3.7.3. How do I correct this problem? Any help would be greatly appreciated. Thanks!

I updated the packages before running the above command by: conda update anaconda and conda update --all

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  • What happens if you try installing the package into a new environment i.e. conda create -n newenvname ... instead of conda install ...? Commented Jul 8, 2019 at 13:07
  • Thanks for the great suggestion. I did try that way and it worked: conda create -n newenv python=3.7.2; conda activate newenv; conda install -y -c conda-forge -c bioconda pairtools; conda deactivate newenv. Commented Jul 9, 2019 at 18:03
  • Cool, I'll write that as an answer. Commented Jul 10, 2019 at 7:38

1 Answer 1

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To avoid this sort of dependency conflict when using conda, create a new environment with just your chosen packages in it:

conda create -n newenvname -c channelname package1 package2

creates an environment called newenvname containing package1, package2 and their dependencies, and searches channel channelname as well as the default channels (leave out -c channelname to use only the defaults). For more help type conda create --help. If you want to use the Spyder IDE in this env, don't forget to include the spyder-kernels package.

I would actually advise always leaving the base conda environment untouched and creating one or more working environments which you can install into or upgrade to your heart's content, safe in the knowledge that in the worst case you can simply delete that env and recreate it, without messing up your Anaconda installation.

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