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clairvoyante imporve recipe to install conda native intervaltree and … #10899

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merged 6 commits into from
Sep 14, 2018

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aquaskyline
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@aquaskyline aquaskyline commented Sep 11, 2018

[ * ] I have read the guidelines for bioconda recipes.
[ ] This PR adds a new recipe.
[ * ] AFAIK, this recipe is directly relevant to the biological sciences (otherwise, please submit to the more general purpose conda-forge channel).
[ * ] This PR updates an existing recipe.
[ ] This PR does something else (explain below).

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aquaskyline commented Sep 11, 2018

@bioconda/core Please review, thanks!

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@bioconda/core Please review, thanks!

@aquaskyline
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@corburn You've helped me in the merging my previous pull request on the same recipe. Sorry for pinging you individually to meet my paper's resubmission deadline. Could you please help to review and merge, thank you so very much!

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corburn commented Sep 13, 2018

@aquaskyline sure I'll check it out.

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@corburn done.

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The CircleCI test failure on the new recipe seems to have nothing to do with the changes. conda-build has succeed on my side.

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corburn commented Sep 13, 2018

@aquaskyline I applied the merge instructions from the CircleCI test failure to the pull request. The button to merge the pull request will not appear unless the test passes.

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aquaskyline commented Sep 14, 2018

@corburn I've tried circleCI again and I got the following error msg. It says "conda-bld", does it sound like I have to add something to the build section to get the circleCI working?

Traceback (most recent call last):
  File "/home/circleci/project/miniconda/bin/conda-index", line 11, in <module>
    sys.exit(main())
  File "/home/circleci/project/miniconda/lib/python3.6/site-packages/conda_build/cli/main_index.py", line 71, in main
    return execute(sys.argv[1:])
  File "/home/circleci/project/miniconda/lib/python3.6/site-packages/conda_build/cli/main_index.py", line 67, in execute
    verbose=args.verbose, progress=args.progress)
  File "/home/circleci/project/miniconda/lib/python3.6/site-packages/conda_build/api.py", line 388, in update_index
    patch_generator=patch_generator, threads=threads, verbose=verbose, progress=progress)
  File "/home/circleci/project/miniconda/lib/python3.6/site-packages/conda_build/index.py", line 268, in update_index
    return update_index(base_path, check_md5=check_md5, channel_name=channel_name, threads=threads, verbose=verbose)
  File "/home/circleci/project/miniconda/lib/python3.6/site-packages/conda_build/index.py", line 270, in update_index
    patch_generator=patch_generator, verbose=verbose, progress=progress)
  File "/home/circleci/project/miniconda/lib/python3.6/site-packages/conda_build/index.py", line 744, in index
    detected_subdirs = set(subdir for subdir in os.listdir(self.channel_root)
FileNotFoundError: [Errno 2] No such file or directory: '/home/circleci/project/miniconda/conda-bld'
Exited with code 1

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corburn commented Sep 14, 2018

@aquaskyline conda-bld/ is the directory where the conda-build program writes its output.

Based on the error, it looks like there's been a recent change to conda-build:
conda/conda-build#3114 (comment)

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@corburn Thanks for help from @mbargull All checks have passed.

@corburn corburn merged commit 04872b4 into bioconda:master Sep 14, 2018
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3 participants