Two conda environments conflict

Question

I have installed anaconda for daily use. Recently, I installed an commercial software which support python as well. The software installed miniconda in another folder and created an environment for the itself. But when I activate the environment and use conda or 'pip' to install some packages, error happened. For example, conda install scipy caused:

Traceback (most recent call last):
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\lib\site-packages\conda\common\serialize.py", line 19, in get_yaml
    import ruamel_yaml as yaml
ModuleNotFoundError: No module named 'ruamel_yaml'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\lib\site-packages\conda\common\serialize.py", line 22, in get_yaml
    import ruamel.yaml as yaml
ModuleNotFoundError: No module named 'ruamel'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\lib\site-packages\conda\exceptions.py", line 1074, in __call__
    return func(*args, **kwargs)
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\lib\site-packages\conda\cli\main.py", line 74, in _main
    from ..base.context import context
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\lib\site-packages\conda\base\context.py", line 28, in <module>
    from ..common.configuration import (Configuration, ConfigurationLoadError, MapParameter,
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\lib\site-packages\conda\common\configuration.py", line 40, in <module>
    from .serialize import yaml_load
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\lib\site-packages\conda\common\serialize.py", line 30, in <module>
    yaml = get_yaml()
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\lib\site-packages\conda\_vendor\auxlib\decorators.py", line 59, in _memoized_func
    result = func(*args, **kwargs)
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\lib\site-packages\conda\common\serialize.py", line 24, in get_yaml
    raise ImportError("No yaml library available.\n"
ImportError: No yaml library available.
To proceed, conda install ruamel_yaml

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\lib\site-packages\conda\common\serialize.py", line 19, in get_yaml
    import ruamel_yaml as yaml
ModuleNotFoundError: No module named 'ruamel_yaml'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\lib\site-packages\conda\common\serialize.py", line 22, in get_yaml
    import ruamel.yaml as yaml
ModuleNotFoundError: No module named 'ruamel'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\Scripts\conda-script.py", line 12, in <module>
    sys.exit(main())
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\lib\site-packages\conda\cli\main.py", line 150, in main
    return conda_exception_handler(_main, *args, **kwargs)
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\lib\site-packages\conda\exceptions.py", line 1366, in conda_exception_handler
    return_value = exception_handler(func, *args, **kwargs)
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\lib\site-packages\conda\exceptions.py", line 1077, in __call__
    return self.handle_exception(exc_val, exc_tb)
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\lib\site-packages\conda\exceptions.py", line 1121, in handle_exception
    return self.handle_unexpected_exception(exc_val, exc_tb)
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\lib\site-packages\conda\exceptions.py", line 1132, in handle_unexpected_exception
    self.print_unexpected_error_report(error_report)
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\lib\site-packages\conda\exceptions.py", line 1187, in print_unexpected_error_report
    from .base.context import context
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\lib\site-packages\conda\base\context.py", line 28, in <module>
    from ..common.configuration import (Configuration, ConfigurationLoadError, MapParameter,
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\lib\site-packages\conda\common\configuration.py", line 40, in <module>
    from .serialize import yaml_load
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\lib\site-packages\conda\common\serialize.py", line 30, in <module>
    yaml = get_yaml()
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\lib\site-packages\conda\_vendor\auxlib\decorators.py", line 59, in _memoized_func
    result = func(*args, **kwargs)
  File "C:\ProgramData\Miniconda3\envs\GMS_VENV_PYTHON\lib\site-packages\conda\common\serialize.py", line 24, in get_yaml
    raise ImportError("No yaml library available.\n"
ImportError: No yaml library available.
To proceed, conda install ruamel_yaml

pip install scipy caused:

Collecting scipy
  Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self signed certificate (_ssl.c:1051)'))': /simple/scipy/
  Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self signed certificate (_ssl.c:1051)'))': /simple/scipy/
  Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self signed certificate (_ssl.c:1051)'))': /simple/scipy/
  Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self signed certificate (_ssl.c:1051)'))': /simple/scipy/
  Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self signed certificate (_ssl.c:1051)'))': /simple/scipy/
  Could not fetch URL https://pypi.org/simple/scipy/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='pypi.org', port=443): Max retries exceeded with url: /simple/scipy/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self signed certificate (_ssl.c:1051)'))) - skipping
  Could not find a version that satisfies the requirement scipy (from versions: )
No matching distribution found for scipy

Does anyone know how to fix this problem?

Answer 1

Finally I solve it... It turns out that when the software Gatan GM created an environment, it installed some version of conda. This is the command the software used:

C:\ProgramData\miniconda3\scripts\conda create --prefix C:\ProgramData\miniconda3\envs\GMS_VENV_PYTHON1 --offline --yes python-3.7.1-h8c8aaf0_6.tar.bz2 ca-certificates-2019.10.16-0.tar.bz2 openssl-1.1.1d-he774522_3.tar.bz2 numpy-1.17.1-py37hc71023c_0.tar.bz2 intel-openmp-2019.4-245.tar.bz2 tqdm-4.36.1-py_0.tar.bz2 vs2015_runtime-14.16.27012-hf0eaf9b_0.tar.bz2 libblas-3.8.0-14_mkl.tar.bz2 certifi-2019.9.11-py37_0.tar.bz2 liblapack-3.8.0-14_mkl.tar.bz2 mkl-2019.4-245.tar.bz2 conda-4.7.12-py37_0.tar.bz2 conda-package-handling-1.6.0-py37h62dcd97_0.tar.bz2 libcblas-3.8.0-14_mkl.tar.bz2

After removing the environment and re-creating it without conda related package, the problem was solved.

conda create --prefix C:\ProgramData\miniconda3\envs\GMS_VENV_PYTHON --offline --yes C:\ProgramData\Gatan\Python\python-3.7.1-h8c8aaf0_6.tar.bz2 C:\ProgramData\Gatan\Python\ca-certificates-2019.10.16-0.tar.bz2 C:\ProgramData\Gatan\Python\openssl-1.1.1d-he774522_3.tar.bz2 C:\ProgramData\Gatan\Python\numpy-1.17.1-py37hc71023c_0.tar.bz2 C:\ProgramData\Gatan\Python\intel-openmp-2019.4-245.tar.bz2 C:\ProgramData\Gatan\Python\tqdm-4.36.1-py_0.tar.bz2 C:\ProgramData\Gatan\Python\vs2015_runtime-14.16.27012-hf0eaf9b_0.tar.bz2 C:\ProgramData\Gatan\Python\libblas-3.8.0-14_mkl.tar.bz2 C:\ProgramData\Gatan\Python\certifi-2019.9.11-py37_0.tar.bz2 C:\ProgramData\Gatan\Python\liblapack-3.8.0-14_mkl.tar.bz2 C:\ProgramData\Gatan\Python\mkl-2019.4-245.tar.bz2 C:\ProgramData\Gatan\Python\libcblas-3.8.0-14_mkl.tar.bz2

Answer 2

You should install ruamel.yaml first

pip install ruamel.yaml