bioconda-recipes: OSX builds fail with ``KeyError: 'https://conda.anaconda.org/conda-forge'``

22:36:43 BIOCONDA ERROR COMMAND FAILED (exited with 1): /opt/mambaforge/envs/bioconda/bin/conda mambabuild --override-channels --no-anaconda-upload -c conda-forge -c bioconda -c defaults -e /opt/mambaforge/envs/bioconda/conda_build_config.yaml -e /opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml recipes/tksm/meta.yaml
22:36:43 BIOCONDA ERROR STDOUT+STDERR:

Traceback (most recent call last):
  File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in <module>
    sys.exit(main())
  File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main
    call_conda_build(action, config)
  File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build
    result = api.build(
  File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build
    return build_tree(
  File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree
    packages_from_this = build(metadata, stats,
  File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build
    output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)])
  File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs
    for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False):
  File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set
    conda_packages = finalize_outputs_pass(
  File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass
    fm = finalize_metadata(
  File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata
    build_unsat, host_unsat = add_upstream_pins(m,
  File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 387, in add_upstream_pins
    build_deps, build_unsat, extra_run_specs_from_build = _read_upstream_pin_files(m, 'build',
  File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files
    deps, actions, unsat = get_env_dependencies(m, env, m.config.variant,
  File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies
    actions = environ.get_install_actions(tmpdir, tuple(dependencies), env,
  File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions
    solution = solver.solve_for_action(_specs, prefix)
    return to_action(
  File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 79, in to_action
    entry = lookup_dict[get_url_from_channel(c)]
KeyError: 'https://conda.anaconda.org/conda-forge'

PR: https://github.com/bioconda/bioconda-recipes/pull/41444 Azure log: https://dev.azure.com/bioconda/bioconda-recipes/_build/results?buildId=34916&view=logs&j=1b052f1d-4456-52f0-9d43-71c4c5bd734d&t=edc48dcd-1fc2-5e3b-7036-7be9cea00123&l=651

About this issue

Original URL
State: closed
Created a year ago
Reactions: 4
Comments: 22 (21 by maintainers)

Commits related to this issue

Update verkko version to 1.4 (#41724) * update version to 1.4 * Reset build number * remove from blacklist * update tests to report failed logs * explicitly add perl * See if a specifi... — committed to bioconda/bioconda-recipes by skoren a year ago
Resume osx build for recipe derna Previously skipped because of issue #41526 which has been resolved — committed to kbseah/bioconda-recipes by kbseah a year ago
Resume osx build for recipe acdc Previously skipped because of issue #41526, now resolved — committed to kbseah/bioconda-recipes by kbseah a year ago
Resume osx build for recipe emvc-2 Previously skipped because of issue #41526, now resolved — committed to kbseah/bioconda-recipes by kbseah a year ago
Update meta.yaml Resume osx build for recipe TKSM Previously skipped because of issue #41526 which has been resolved — committed to f0t1h/bioconda-recipes by f0t1h a year ago
Resume osx build for recipe TKSM Previously skipped because of issue #41526 which has been resolved — committed to f0t1h/bioconda-recipes by f0t1h a year ago
Skip osx build (see #41526). — committed to tmaklin/bioconda-recipes by tmaklin a year ago
Update build targets The OSX build is currently failing with a KeyError like in https://github.com/bioconda/bioconda-recipes/issues/41526. I thought this issue was resolved (maybe a reversion?). For ... — committed to tkaragianes/bioconda-recipes by tkaragianes 10 months ago

Most upvoted comments

This is now fixed with the update to bioconda-utils 2.3.2 which uses boa 0.15.

johanneskoester on Jun 29, 2023

For those of you who have circumvented the issue by deactivating the osx build, it would be great if you could enable them again in follow-up PRs! Thanks a lot! It is always great to see how active the bioconda community is!

johanneskoester on Jun 29, 2023

I appear to have the same issue as well.

PR: https://github.com/bioconda/bioconda-recipes/pull/41525 Log: https://dev.azure.com/bioconda/bioconda-recipes/_build/results?buildId=34918&view=logs&jobId=3e927886-88a5-5ae4-09f7-f53fa1a22322&j=3e927886-88a5-5ae4-09f7-f53fa1a22322&t=577c9198-bb4c-5a92-f06b-21e420caadce

bluenote-1577 on Jun 16, 2023

Xref: https://github.com/mamba-org/boa/issues/350

dpryan79 on Jun 29, 2023

This seems to have re-appeared in the following PRs:

marcelm on Sep 8, 2023

Thanks for the info @dpryan79. Sounds like an updated mamba release should fix that when it is ready.

skoren on Jun 29, 2023

Any updates @bioconda/core?

mbhall88 on Jun 28, 2023

Also in #41724. Any updates or fixes? This has been an issue for weeks now. Between this and the fact that my previously working recipe was broken by maintenance changes and blacklisted last month, it seems bioconda has become a bit unreliable.

skoren on Jun 28, 2023

I tried to understand a bit what’s going on. I didn’t get very far yet but maybe its a hint.

I installed bioconda-utils locally and ran it. I am running on an ARM mac with CONDA_SUBDIR=osx-64 set.

The key that exist in the boa lookup_dict is https://conda.anaconda.org/conda-forge/osx-64. While the requested key is https://conda.anaconda.org/conda-forge.

After adding the debug statements I tried to update to boa 0.15.1, which first didn’t work because it was trying to download the following file: https://conda.anaconda.org/conda-forge/mamba-1.4.2-py38h2cdcfb1_0.conda instead of: https://conda.anaconda.org/conda-forge/osx-64/mamba-1.4.2-py38h2cdcfb1_0.conda

This seems a rather similar symptom.

I deleted the package cache and it could install boa 0.15.1 successfully. However, this version immediately segfaults.

These are my current findings, not sure what to make out of these. Somewhere/something seems to contain the wrong channel url without the OS subdir.

Edit: I reinstalled and now I only get the following error:

Error: bad character '*' in package name dependency '*'

I don’t make it to the key error anymore.

milot-mirdita on Jun 27, 2023