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Bioconda doesn't install latest Pronto #162

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ireneisdoomed opened this issue Mar 28, 2022 · 1 comment
Open

Bioconda doesn't install latest Pronto #162

ireneisdoomed opened this issue Mar 28, 2022 · 1 comment
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question A question about the library.

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@ireneisdoomed
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ireneisdoomed commented Mar 28, 2022

Describe the bug
Pronto installation via Bioconda is out of date.

Observed behaviour
pronto-0.12.2 is downloaded when pulling the package from Bioconda, however the dependency seems up to date on the Bioconda website https://bioconda.github.io/recipes/pronto/README.html#package-pronto

Expected behaviour
For Pronto v2.4.4 to be installed when running conda install --channel bioconda pronto

To Reproduce
Steps to reproduce the behaviour:

  1. Install conda version 4.12
  2. Create test env: conda env create -n test
  3. Add bioconda as a dependency channel: conda config --add channels bioconda
  4. Install pronto: conda install --channel bioconda pronto
  5. See installation message:
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/irene/miniconda3/envs/test

  added / updated specs:
    - pronto


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    pronto-0.12.2              |             py_0          24 KB  bioconda
    ------------------------------------------------------------
                                           Total:          24 KB

The following NEW packages will be INSTALLED:

  pronto             bioconda/noarch::pronto-0.12.2-py_0
@althonos
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Hi @ireneisdoomed !

I think this may be caused by a dependency issue regarding build platforms; pronto is marked noarch but fastobo, the syntax-only library for parsing OBO, is not. Maybe on your platform it cannot install it, and falls back to the newest pronto that didn't require it (0.12.2).

Could you try a conda install fastobo on your machine? In addition, is there anything special about it (e.g. very old specs, or different architecture like a new Apple M1, etc)?

@althonos althonos added the question A question about the library. label Apr 21, 2022
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