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Áine O'Toole edited this page Jul 20, 2020 · 1 revision

ERROR: Command errored out with exit status 128/ CondaEnvException: Pip failed

When solving the pangolin environment, the below error may occur if pip doesn't successfully install the data directories (due to the internet dropping or something along those lines).

conda env create -f environment.yml 
Collecting package metadata (repodata.json): done
Solving environment: done
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Ran pip subprocess with arguments:
['/Users/.../opt/miniconda3/envs/pangolin/bin/python', '-m', 'pip', 'install', '-U', '-r', '/Users/.../pangolin/condaenv.k8h4imy7.requirements.txt']
Pip subprocess output:
Collecting git+https://github.com/cov-ert/datafunk.git (from -r /Users/.../pangolin/condaenv.k8h4imy7.requirements.txt (line 4))
  Cloning https://github.com/cov-ert/datafunk.git to /private/var/folders/7s/hsvkmb7j4m5cc989jrs0l6qw0000gr/T/pip-req-build-c29_54ue
Collecting git+https://github.com/cov-lineages/pangoLEARN.git (from -r /Users/.../pangolin/condaenv.k8h4imy7.requirements.txt (line 5))
  Cloning https://github.com/cov-lineages/pangoLEARN.git to /private/var/folders/7s/hsvkmb7j4m5cc989jrs0l6qw0000gr/T/pip-req-build-13vesmxd

Pip subprocess error:
  Running command git clone -q https://github.com/cov-ert/datafunk.git /private/var/folders/7s/hsvkmb7j4m5cc989jrs0l6qw0000gr/T/pip-req-build-c29_54ue
  Running command git clone -q https://github.com/cov-lineages/pangoLEARN.git /private/var/folders/7s/hsvkmb7j4m5cc989jrs0l6qw0000gr/T/pip-req-build-13vesmxd
  error: RPC failed; curl 18 transfer closed with outstanding read data remaining
  fatal: the remote end hung up unexpectedly
  fatal: early EOF
  fatal: unpack-objects failed
ERROR: Command errored out with exit status 128: git clone -q https://github.com/cov-lineages/pangoLEARN.git /private/var/folders/7s/hsvkmb7j4m5cc989jrs0l6qw0000gr/T/pip-req-build-13vesmxd Check the logs for full command output.


CondaEnvException: Pip failed

The solution: install the data dependencies manually

For example:

# make sure you're in the pangolin environment
conda activate pangolin

# clone the data dependency repository
git clone https://github.com/cov-lineages/pangoLEARN.git
cd pangoLEARN
python setup.py install

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