AllenInstitute / AllenSDK

code for reading and processing Allen Institute for Brain Science data
https://allensdk.readthedocs.io/en/latest/
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Error: pg_config executable not found. - Installing on Compute Canada #2725

Closed AngCamp closed 2 weeks ago

AngCamp commented 9 months ago

As in title I get this erroe despite having installed psycog2. Not sure why it is telling me to manually install the binaries myself.

    ERROR: Command errored out with exit status 1:
     command: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/python/3.9.6/bin/python3.9 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-1az9ltr4/psycopg2-binary/setup.py'"'"'; __file__='"'"'/tmp/pip-install-1az9ltr4/psycopg2-binary/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-install-1az9ltr4/psycopg2-binary/pip-egg-info
         cwd: /tmp/pip-install-1az9ltr4/psycopg2-binary/
    Complete output (23 lines):
    running egg_info
    creating /tmp/pip-install-1az9ltr4/psycopg2-binary/pip-egg-info/psycopg2_binary.egg-info
    writing /tmp/pip-install-1az9ltr4/psycopg2-binary/pip-egg-info/psycopg2_binary.egg-info/PKG-INFO
    writing dependency_links to /tmp/pip-install-1az9ltr4/psycopg2-binary/pip-egg-info/psycopg2_binary.egg-info/dependency_links.txt
    writing top-level names to /tmp/pip-install-1az9ltr4/psycopg2-binary/pip-egg-info/psycopg2_binary.egg-info/top_level.txt
    writing manifest file '/tmp/pip-install-1az9ltr4/psycopg2-binary/pip-egg-info/psycopg2_binary.egg-info/SOURCES.txt'

    Error: pg_config executable not found.

    pg_config is required to build psycopg2 from source.  Please add the directory
    containing pg_config to the $PATH or specify the full executable path with the
    option:

        python setup.py build_ext --pg-config /path/to/pg_config build ...

    or with the pg_config option in 'setup.cfg'.

    If you prefer to avoid building psycopg2 from source, please install the PyPI
    'psycopg2-binary' package instead.

    For further information please check the 'doc/src/install.rst' file (also at
    <https://www.psycopg.org/docs/install.html>).

    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
morriscb commented 9 months ago

Hi @AngCamp, attempted a pip install of the SDK on a fresh python3.9, conda environment both on Mac and Linux and ran into no issues. Has the problem stopped for you recently? If not I would suggest trying a fresh environment as well.

AngCamp commented 8 months ago

I am trying this on a Compute Canada cluster, and I believe it is missing several bash libraries needed for python development. I don't have sudo privileges on this resource I think I need to set up a docker environment in order to resolve this issue. I will edit this questions title to reflect the bug better.