bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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Error with click, Python 3 & missing UTF-8 locale #14086

Closed simonvh closed 5 years ago

simonvh commented 5 years ago

I get the following error (for full details see here):

[Mar 19 11:45:24] DEBU Creating container [step-54cc080860]
[Mar 19 11:45:24] DEBU Created container [6ad88087a20b step-54cc080860], starting it
[Mar 19 11:45:24] DEBU Container [6ad88087a20b step-54cc080860] started, waiting for completion
[Mar 19 11:45:24] SERR /usr/local/lib/python3.6/site-packages/norns-0.1.2-py2.7.egg/norns/cfg.py:72: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
[Mar 19 11:45:24] SERR Traceback (most recent call last):
[Mar 19 11:45:24] SERR File "/usr/local/bin/genomepy", line 11, in <module>
[Mar 19 11:45:24] SERR load_entry_point('genomepy==0.5.4', 'console_scripts', 'genomepy')()
[Mar 19 11:45:24] SERR File "/usr/local/lib/python3.6/site-packages/click/core.py", line 764, in __call__
[Mar 19 11:45:24] SERR return self.main(*args, **kwargs)
[Mar 19 11:45:24] SERR File "/usr/local/lib/python3.6/site-packages/click/core.py", line 696, in main
[Mar 19 11:45:24] SERR _verify_python3_env()
[Mar 19 11:45:24] SERR File "/usr/local/lib/python3.6/site-packages/click/_unicodefun.py", line 124, in _verify_python3_env
[Mar 19 11:45:24] SERR ' mitigation steps.' + extra
[Mar 19 11:45:24] SERR RuntimeError: Click will abort further execution because Python 3 was configured to use ASCII as encoding for the environment. Consult https://click.palletsprojects.com/en/7.x/python3/ for mitigation steps.
[Mar 19 11:45:24] SERR 
[Mar 19 11:45:24] SERR Additional information: on this system no suitable UTF-8
[Mar 19 11:45:24] SERR locales were discovered.  This most likely requires resolving
[Mar 19 11:45:24] SERR by reconfiguring the locale system.
[Mar 19 11:45:25] ERRO Task processing failed: Unexpected exit code [1] of container [6ad88087a20b step-54cc080860], container preserved

However, in meta.yaml I have the following lines:

extra:
  container:
    # click requires a unicode locale when used with Python 3
    # extended-base generates en_US.UTF-8 locale and sets LC_ALL, LANG properly
    extended-base: true  # [py3k]

This used to work, what am I doing wrong? @bgruening any idea?

simonvh commented 5 years ago

Looks like this issue bioconda/bioconda-utils#70 @epruesse

simonvh commented 5 years ago

Update: I restarted the the CircleCI check and then it runs fine (at least the Linux build does).