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r-future.batchtools

See original GitHub issue

This is a request for r-future.batchtools. I see that conda-forge already has a recipe for r-future, but it appears that conda-forge does not have a recipe for r-future.batchtools, which thus limits the usefulness of r-future. I’ve tried using conda skeleton cran and conda-build to build r-future.batchtools myself. However, I get the following dependency conflict error:

$ conda-build r-future.batchtools/
Adding in variants from internal_defaults
INFO:conda_build.variants:Adding in variants from internal_defaults
Attempting to finalize metadata for r-future.batchtools
INFO:conda_build.metadata:Attempting to finalize metadata for r-future.batchtools
Solving environment: ...working... failed
Adding in variants from config.variant
INFO:conda_build.variants:Adding in variants from config.variant
Missing dependency r-batchtools, but found recipe directory, so building r-batchtools first
Attempting to finalize metadata for r-batchtools
INFO:conda_build.metadata:Attempting to finalize metadata for r-batchtools
Solving environment: ...working... done
Solving environment: ...working... failed
failed to get install actions, retrying.  exception was: The following specifications were found to be in conflict:
  - r-base64url[version='>=1.1']
  - r-checkmate[version='>=1.8.5']
Use "conda info <package>" to see the dependencies for each package.
WARNING:conda_build.environ:failed to get install actions, retrying.  exception was: The following specifications were found to be in conflict:
  - r-base64url[version='>=1.1']
  - r-checkmate[version='>=1.8.5']
Use "conda info <package>" to see the dependencies for each package.
Solving environment: ...working... failed
Solving environment: ...working... failed
Solving environment: ...working... failed
Failed to get install actions, max retries exceeded.
ERROR:conda_build.environ:Failed to get install actions, max retries exceeded.
Traceback (most recent call last):
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/environ.py", line 706, in get_install_actions
    actions = install_actions(prefix, index, specs, force=True)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/common/io.py", line 46, in decorated
    return f(*args, **kwds)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/plan.py", line 541, in install_actions
    txn = solver.solve_for_transaction(prune=prune, ignore_pinned=not pinned)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/core/solve.py", line 505, in solve_for_transaction
    force_remove, force_reinstall)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/core/solve.py", line 438, in solve_for_diff
    final_precs = self.solve_final_state(deps_modifier, prune, ignore_pinned, force_remove)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/core/solve.py", line 331, in solve_final_state
    solution = r.solve(tuple(final_environment_specs))  # return value is List[dist]
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/common/io.py", line 46, in decorated
    return f(*args, **kwds)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/resolve.py", line 857, in solve
    self.find_conflicts(specs)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/resolve.py", line 244, in find_conflicts
    raise UnsatisfiableError(bad_deps)
conda.exceptions.UnsatisfiableError: The following specifications were found to be in conflict:
  - r-base64url[version='>=1.1']
  - r-checkmate[version='>=1.8.5']
Use "conda info <package>" to see the dependencies for each package.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/environ.py", line 706, in get_install_actions
    actions = install_actions(prefix, index, specs, force=True)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/common/io.py", line 46, in decorated
    return f(*args, **kwds)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/plan.py", line 541, in install_actions
    txn = solver.solve_for_transaction(prune=prune, ignore_pinned=not pinned)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/core/solve.py", line 505, in solve_for_transaction
    force_remove, force_reinstall)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/core/solve.py", line 438, in solve_for_diff
    final_precs = self.solve_final_state(deps_modifier, prune, ignore_pinned, force_remove)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/core/solve.py", line 331, in solve_final_state
    solution = r.solve(tuple(final_environment_specs))  # return value is List[dist]
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/common/io.py", line 46, in decorated
    return f(*args, **kwds)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/resolve.py", line 857, in solve
    self.find_conflicts(specs)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/resolve.py", line 244, in find_conflicts
    raise UnsatisfiableError(bad_deps)
conda.exceptions.UnsatisfiableError: The following specifications were found to be in conflict:
  - r-base64url[version='>=1.1']
  - r-checkmate[version='>=1.8.5']
Use "conda info <package>" to see the dependencies for each package.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/environ.py", line 706, in get_install_actions
    actions = install_actions(prefix, index, specs, force=True)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/common/io.py", line 46, in decorated
    return f(*args, **kwds)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/plan.py", line 541, in install_actions
    txn = solver.solve_for_transaction(prune=prune, ignore_pinned=not pinned)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/core/solve.py", line 505, in solve_for_transaction
    force_remove, force_reinstall)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/core/solve.py", line 438, in solve_for_diff
    final_precs = self.solve_final_state(deps_modifier, prune, ignore_pinned, force_remove)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/core/solve.py", line 331, in solve_final_state
    solution = r.solve(tuple(final_environment_specs))  # return value is List[dist]
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/common/io.py", line 46, in decorated
    return f(*args, **kwds)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/resolve.py", line 857, in solve
    self.find_conflicts(specs)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/resolve.py", line 244, in find_conflicts
    raise UnsatisfiableError(bad_deps)
conda.exceptions.UnsatisfiableError: The following specifications were found to be in conflict:
  - r-base64url[version='>=1.1']
  - r-checkmate[version='>=1.8.5']
Use "conda info <package>" to see the dependencies for each package.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/bin/conda-build", line 11, in <module>
    sys.exit(main())
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 420, in main
    execute(sys.argv[1:])
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 411, in execute
    verify=args.verify)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/api.py", line 199, in build
    notest=notest, need_source_download=need_source_download, variants=variants)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/build.py", line 2117, in build_tree
    notest=notest,
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/build.py", line 1169, in build
    output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)])
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/render.py", line 703, in expand_outputs
    for (output_dict, m) in _m.get_output_metadata_set(permit_unsatisfiable_variants=False):
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/metadata.py", line 1873, in get_output_metadata_set
    permit_unsatisfiable_variants=permit_unsatisfiable_variants)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/metadata.py", line 683, in finalize_outputs_pass
    fm = finalize_metadata(om, permit_unsatisfiable_variants=permit_unsatisfiable_variants)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/render.py", line 494, in finalize_metadata
    exclude_pattern)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/render.py", line 352, in add_upstream_pins
    permit_unsatisfiable_variants, exclude_pattern)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/render.py", line 322, in _read_upstream_pin_files
    permit_unsatisfiable_variants=permit_unsatisfiable_variants)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/render.py", line 125, in get_env_dependencies
    channel_urls=tuple(m.config.channel_urls))
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/environ.py", line 742, in get_install_actions
    channel_urls=tuple(channel_urls))
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/environ.py", line 742, in get_install_actions
    channel_urls=tuple(channel_urls))
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/environ.py", line 742, in get_install_actions
    channel_urls=tuple(channel_urls))
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/environ.py", line 706, in get_install_actions
    actions = install_actions(prefix, index, specs, force=True)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/common/io.py", line 46, in decorated
    return f(*args, **kwds)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/plan.py", line 541, in install_actions
    txn = solver.solve_for_transaction(prune=prune, ignore_pinned=not pinned)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/core/solve.py", line 505, in solve_for_transaction
    force_remove, force_reinstall)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/core/solve.py", line 438, in solve_for_diff
    final_precs = self.solve_final_state(deps_modifier, prune, ignore_pinned, force_remove)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/core/solve.py", line 331, in solve_final_state
    solution = r.solve(tuple(final_environment_specs))  # return value is List[dist]
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/common/io.py", line 46, in decorated
    return f(*args, **kwds)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/resolve.py", line 857, in solve
    self.find_conflicts(specs)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda/resolve.py", line 244, in find_conflicts
    raise UnsatisfiableError(bad_deps)
conda.exceptions.UnsatisfiableError: The following specifications were found to be in conflict:
  - r-base64url[version='>=1.1']
  - r-checkmate[version='>=1.8.5']
Use "conda info <package>" to see the dependencies for each package.

I get this error even if I try to remove the specific version requirements from all of the meta.yaml files for r-future.batchtools and its dependency packages. I’ve tried to get help for this issue at the conda-build GitHub repo issues forum, but I haven’t gotten any response (it’s been a couple of weeks).

Maybe this dependency conflict is why r-future.batchtools isn’t already hosted on the conda-forge channel, but I’m hoping that it could be solved so that myself and other researchers can use conda + future + batchtools for running highly paralleled jobs on the compute clusters that we have available.

Issue Analytics

  • State:closed
  • Created 5 years ago
  • Comments:8 (8 by maintainers)

github_iconTop GitHub Comments

1reaction
isurufcommented, Apr 29, 2018

You need to first make sure the dependencies are there.

  1. r-base64url is not packaged yet. Please send a PR to package it.
  2. r-checkmate version in conda-forge is old. Please send a PR to https://github.com/conda-forge/r-checkmate-feedstock to update it.
  3. r-batchtools is not packaged yet. Please send a PR to package it. This needs to happen after the above 2 tasks are done.
  4. After these, send a PR to package r-future.batchtools.
0reactions
jakirkhamcommented, Jul 6, 2018
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