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samtools openssl>1.1 #13920

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commented Mar 5, 2019

See #13909

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Bioconda has finished the GCC7 migration. If you are dealing with C/C++ or Python package it can be that you need to rebuild other dependent packages. Bioconda utils - update-pinning will assist you with that. If you have any questions please use issue 13578.


  • 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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commented Mar 6, 2019

So < is ok but > isn't. The fun never ends! :)
I see cases of >= out there so maybe that works.

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commented Mar 6, 2019

Nope.

  File "/home/circleci/project/miniconda/lib/python3.6/site-packages/conda_build/render.py", line 162, in get_pin_from_build
    pin = utils.apply_pin_expressions(version.split()[0], **pin_cfg)
  File "/home/circleci/project/miniconda/lib/python3.6/site-packages/conda_build/utils.py", line 1208, in apply_pin_expressions
    parsed_version = VersionOrder(version).version[1:]
  File "/home/circleci/project/miniconda/lib/python3.6/site-packages/conda/models/version.py", line 163, in __new__
    raise CondaValueError(message + "invalid character(s).")
conda.exceptions.CondaValueError: Malformed version string '>=1.1.1': invalid character(s).
Exited with code 1
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commented Mar 6, 2019

https://github.com/conda/conda/blob/master/conda/models/version.py#L46

I think it needs a space. (I don't know why < works without a space.)

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commented Mar 6, 2019

Error: bad character '>=' in package version dependency 'openssl'
Perhaps you meant 'openssl >=1.1.1'

Ugh! There seems to be inconsistency between conda and conda-build lint.

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commented Mar 6, 2019

@bioconda/core any suggestions how to proceed here?

@dpryan79

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commented Mar 6, 2019

I'm going to start migrating packages to the new OpenSSL pinning this week. Samtools and related packages will be the first to be migrated.

@dpryan79 dpryan79 closed this Mar 6, 2019

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commented Mar 6, 2019

What about the problem with >=? Build wants a space; lint does not. I think there is a bug in the spec parser.

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commented Mar 6, 2019

I wonder if conda-build is throwing an error due to the mismatch in meta.yaml and conda_build_config.yaml. The pinning in the yaml file will get ignored, I think, since there's a conda_build_config.yaml. The >=1.1.1 syntax is actually correct and is used in many recipes (e.g., deepTools).

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commented Mar 6, 2019

% ls recipes/samtools/
0.1.19  1.1  1.6  build.sh  meta.yaml

Hmmm. < worked fine. > and >= both failed.

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