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malariagen / mgenv

Repository with installation scripts and environment definitions for conda and texlive, for standardising environments across the MalariaGEN resource centre team.
MIT License
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Issue installing #70

Closed SeanTomlinson30 closed 5 years ago

SeanTomlinson30 commented 5 years ago

Having problems installing the environment on the cluster.

sean@india:~/vector-ops$ ./binder/install-conda.sh
[binder] skipping miniconda installation
[binder] installing packages
[binder] install conda
Collecting package metadata (current_repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
  current version: 4.7.11
  latest version: 4.7.12

Please update conda by running

    $ conda update -n base conda

# All requested packages already installed.

conda 4.7.11
[binder] check channel priority - this must be 'true' or 'flexible', ***not*** 'strict'
channel_priority: flexible
[binder] creating environment vector-ops-3d37be2 from /home/sean/vector-ops/binder/environment-pinned-linux.yml
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed
Traceback (most recent call last):
  File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/exceptions.py", line 1062, in __call__
    return func(*args, **kwargs)
  File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda_env/cli/main.py", line 73, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda_env/cli/main_create.py", line 101, in execute
  File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda_env/installers/conda.py", line 27, in install
    unlink_link_transaction = solver.solve_for_transaction(prune=getattr(args, 'prune', False))
  File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/core/solve.py", line 116, in solve_for_transaction
    should_retry_solve)
  File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/core/solve.py", line 157, in solve_for_diff
    force_remove, should_retry_solve)
  File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/core/solve.py", line 274, in solve_final_state
    ssc = self._add_specs(ssc)
  File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/core/solve.py", line 554, in _add_specs
    explicit_pool = ssc.r._get_package_pool(self.specs_to_add)
  File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/resolve.py", line 520, in _get_package_pool
    pool = self.get_reduced_index(specs)
  File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
    return f(*args, **kwds)
  File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/resolve.py", line 541, in get_reduced_index
    explicit_specs, features = self.verify_specs(explicit_specs)
  File "/home/sean/vector-ops/binder/deps/conda/lib/python3.7/site-packages/conda/resolve.py", line 280, in verify_specs
    raise ResolvePackageNotFound(bad_deps)
conda.exceptions.ResolvePackageNotFound: 
  - ipython==7.9.0=py36h5ca1d4c_0

sean@india:~/vector-ops$

Path is 

sean@india:~/vector-ops$ echo @$PATH
@/home/sean/bin:/home/sean/.local/bin:/home/sean/bin:/home/sean/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/opt/puppetlabs/bin
sean@india:~/vector-ops$