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malariagen / mgenv

Repository with installation scripts and environment definitions for conda and texlive, for standardising environments across the MalariaGEN resource centre team.
MIT License
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numpy error after updating conda #38

Closed amakunin closed 4 years ago

amakunin commented 5 years ago

Steps to reproduce:

Having existing binder installation on Mac OS, do

./binder/install-conda.sh
source binder/env.sh
python
>>> import numpy

Result:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/am60/malaria/vector-ops/binder/deps/conda/envs/vector-ops/lib/python3.6/site-packages/numpy/__init__.py", line 142, in <module>
    from . import core
  File "/Users/am60/malaria/vector-ops/binder/deps/conda/envs/vector-ops/lib/python3.6/site-packages/numpy/core/__init__.py", line 67, in <module>
    raise ImportError(msg.format(path))
ImportError: Something is wrong with the numpy installation. While importing we detected an older version of numpy in ['/Users/am60/malaria/vector-ops/binder/deps/conda/envs/vector-ops/lib/python3.6/site-packages/numpy']. One method of fixing this is to repeatedly uninstall numpy until none is found, then reinstall this version.

Now trying to reinstall binder from scratch by removing binder/deps

UPD binder reinstall from scratch solved this problem

alimanfoo commented 5 years ago

Hi Alex, let me know if this is still a problem, happy to investigate.

On Thu, 21 Feb 2019 at 12:38, Alex Makunin notifications@github.com wrote:

Steps to reproduce:

Having existing binder installation on Mac OS, do

./binder/install-conda.sh source binder/env.sh python

import numpy

Result:

Traceback (most recent call last): File "", line 1, in File "/Users/am60/malaria/vector-ops/binder/deps/conda/envs/vector-ops/lib/python3.6/site-packages/numpy/init.py", line 142, in from . import core File "/Users/am60/malaria/vector-ops/binder/deps/conda/envs/vector-ops/lib/python3.6/site-packages/numpy/core/init.py", line 67, in raise ImportError(msg.format(path)) ImportError: Something is wrong with the numpy installation. While importing we detected an older version of numpy in ['/Users/am60/malaria/vector-ops/binder/deps/conda/envs/vector-ops/lib/python3.6/site-packages/numpy']. One method of fixing this is to repeatedly uninstall numpy until none is found, then reinstall this version.

Now trying to reinstall binder from scratch by removing binder/deps

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--

Alistair Miles Head of Epidemiological Informatics Centre for Genomics and Global Health Big Data Institute Li Ka Shing Centre for Health Information and Discovery University of Oxford Old Road Campus Headington Oxford OX3 7LF United Kingdom Phone: +44 (0)1865 743596 or +44 (0)7866 541624 Email: alimanfoo@googlemail.com Web: http://a http://purl.org/net/alimanlimanfoo.github.io/ Twitter: @alimanfoo https://twitter.com/alimanfoo

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alimanfoo commented 4 years ago

Assuming no longer an issue, shout if otherwise.