Conda environment fails to create #28

rickecon · 2021-09-03T16:06:34Z

In the new repo with its dependencies on OG-Core and OpenFisca-UK, I cannot get the conda environment to create. The conda environment.yml file has two pip imports that are likely causing the problem.

- pip:
  ...
  - git+https://github.com/PSLmodels/OG-Core.git
  - git+https://github.com/PSLmodels/openfisca-uk

My conda env create -f environment.yml command ran for 30 minutes in my terminal, then errored out with the following long set of messages, with the concluding message CondaEnvException: Pip failed.

(base) richardevans@Rick-MacBook-Pro-2020 OG-UK % conda env create -f environment.yml
Collecting package metadata (repodata.json): done
Solving environment: done

Downloading and Extracting Packages
pytest-6.2.5         | 432 KB    | ##################################### | 100% 
fsspec-2021.8.1      | 82 KB     | ##################################### | 100% 
astroid-2.7.3        | 334 KB    | ##################################### | 100% 
identify-2.2.13      | 76 KB     | ##################################### | 100% 
regex-2021.8.28      | 344 KB    | ##################################### | 100% 
pre-commit-2.15.0    | 225 KB    | ##################################### | 100% 
python-3.9.7         | 12.5 MB   | ##################################### | 100% 
cfgv-3.3.1           | 11 KB     | ##################################### | 100% 
platformdirs-2.3.0   | 14 KB     | ##################################### | 100% 
tk-8.6.11            | 3.3 MB    | ##################################### | 100% 
openssl-1.1.1l       | 1.9 MB    | ##################################### | 100% 
black-21.8b0         | 116 KB    | ##################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Installing pip dependencies: / Ran pip subprocess with arguments:
['/Users/richardevans/opt/anaconda3/envs/oguk-dev/bin/python', '-m', 'pip', 'install', '-U', '-r', '/Users/richardevans/Documents/Economics/OSE/OG-UK/condaenv.1jg8jqkx.requirements.txt']
Pip subprocess output:
Collecting git+https://github.com/PSLmodels/OG-Core.git (from -r /Users/richardevans/Documents/Economics/OSE/OG-UK/condaenv.1jg8jqkx.requirements.txt (line 2))
  Cloning https://github.com/PSLmodels/OG-Core.git to /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-req-build-wmj5mgj2
  Resolved https://github.com/PSLmodels/OG-Core.git to commit 27729426fcf0268b254951ef7fc279e92396541c
Collecting git+https://github.com/PSLmodels/openfisca-uk (from -r /Users/richardevans/Documents/Economics/OSE/OG-UK/condaenv.1jg8jqkx.requirements.txt (line 3))
  Cloning https://github.com/PSLmodels/openfisca-uk to /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-req-build-qcl_vd4u
  Resolved https://github.com/PSLmodels/openfisca-uk to commit 473fd0b7779dc01f063bb44d4078e0db8b9833de
Collecting jupyter-book>=0.8.0
  Using cached jupyter_book-0.11.3-py3-none-any.whl (42 kB)
Collecting sphinx-book-theme~=0.1.3
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Requirement already satisfied: pyyaml in /Users/richardevans/opt/anaconda3/envs/oguk-dev/lib/python3.9/site-packages (from jupyter-book>=0.8.0->-r /Users/richardevans/Documents/Economics/OSE/OG-UK/condaenv.1jg8jqkx.requirements.txt (line 1)) (5.4.1)
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Requirement already satisfied: click in /Users/richardevans/opt/anaconda3/envs/oguk-dev/lib/python3.9/site-packages (from jupyter-book>=0.8.0->-r /Users/richardevans/Documents/Economics/OSE/OG-UK/condaenv.1jg8jqkx.requirements.txt (line 1)) (7.1.2)
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Collecting openfisca-uk-data@ git+https://github.com/ubicenter/openfisca-uk-data
  Cloning https://github.com/ubicenter/openfisca-uk-data to /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/openfisca-uk-data_f641c6a49da04bbe9b856e2c0eab8c32
  Resolved https://github.com/ubicenter/openfisca-uk-data to commit 43ac91eeab4d0dcbc37e5346d3feb86657ab6b1a
Collecting microdf@ git+https://github.com/PSLmodels/microdf
  Cloning https://github.com/PSLmodels/microdf to /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/microdf_844040ddd99e4e23be17691305c7146a
  Resolved https://github.com/PSLmodels/microdf to commit 85d2739d1c96882424cb51ef1806c9e51f88c085
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Requirement already satisfied: wheel in /Users/richardevans/opt/anaconda3/envs/oguk-dev/lib/python3.9/site-packages (from sphinx-togglebutton->jupyter-book>=0.8.0->-r /Users/richardevans/Documents/Economics/OSE/OG-UK/condaenv.1jg8jqkx.requirements.txt (line 1)) (0.37.0)
Collecting pybtex-docutils>=1.0.0
  Using cached pybtex_docutils-1.0.1-py3-none-any.whl (4.8 kB)
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Collecting greenlet!=0.4.17
  Using cached greenlet-1.1.1-cp39-cp39-macosx_10_14_x86_64.whl (87 kB)
Collecting notebook>=4.4.1
  Using cached notebook-6.4.3-py3-none-any.whl (9.9 MB)
Collecting argon2-cffi
  Downloading argon2_cffi-21.1.0-cp35-abi3-macosx_10_14_x86_64.whl (38 kB)
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  Using cached Send2Trash-1.8.0-py3-none-any.whl (18 kB)
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  Using cached prometheus_client-0.11.0-py2.py3-none-any.whl (56 kB)
Collecting terminado>=0.8.3
  Using cached terminado-0.11.1-py3-none-any.whl (15 kB)
Requirement already satisfied: cffi>=1.0.0 in /Users/richardevans/opt/anaconda3/envs/oguk-dev/lib/python3.9/site-packages (from argon2-cffi->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets<8,>=7.0.0->myst-nb~=0.12.0->jupyter-book>=0.8.0->-r /Users/richardevans/Documents/Economics/OSE/OG-UK/condaenv.1jg8jqkx.requirements.txt (line 1)) (1.14.6)
Requirement already satisfied: pycparser in /Users/richardevans/opt/anaconda3/envs/oguk-dev/lib/python3.9/site-packages (from cffi>=1.0.0->argon2-cffi->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets<8,>=7.0.0->myst-nb~=0.12.0->jupyter-book>=0.8.0->-r /Users/richardevans/Documents/Economics/OSE/OG-UK/condaenv.1jg8jqkx.requirements.txt (line 1)) (2.20)
Collecting webencodings
  Using cached webencodings-0.5.1-py2.py3-none-any.whl (11 kB)
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  Using cached zipp-3.5.0-py3-none-any.whl (5.7 kB)
Collecting matplotlib
  Downloading matplotlib-3.4.3-cp39-cp39-macosx_10_9_x86_64.whl (7.2 MB)
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  Downloading matplotlib_label_lines-0.4.0-py3-none-any.whl (8.2 kB)
Collecting seaborn
  Downloading seaborn-0.11.2-py3-none-any.whl (292 kB)
Collecting kiwisolver>=1.0.1
  Downloading kiwisolver-1.3.2-cp39-cp39-macosx_10_9_x86_64.whl (61 kB)
Collecting cycler>=0.10
  Downloading cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Requirement already satisfied: pillow>=6.2.0 in /Users/richardevans/opt/anaconda3/envs/oguk-dev/lib/python3.9/site-packages (from matplotlib->microdf@ git+https://github.com/PSLmodels/microdf->OpenFisca-UK==0.4.0->-r /Users/richardevans/Documents/Economics/OSE/OG-UK/condaenv.1jg8jqkx.requirements.txt (line 3)) (8.3.1)
Requirement already satisfied: pyparsing>=2.2.1 in /Users/richardevans/opt/anaconda3/envs/oguk-dev/lib/python3.9/site-packages (from matplotlib->microdf@ git+https://github.com/PSLmodels/microdf->OpenFisca-UK==0.4.0->-r /Users/richardevans/Documents/Economics/OSE/OG-UK/condaenv.1jg8jqkx.requirements.txt (line 3)) (2.4.7)
Collecting GitPython!=2.1.4,!=2.1.5,!=2.1.6
  Using cached GitPython-3.1.18-py3-none-any.whl (170 kB)
Collecting jupyter-server-mathjax>=0.2.2
  Using cached jupyter_server_mathjax-0.2.3-py3-none-any.whl (3.1 MB)
Collecting jupyter-server
  Using cached jupyter_server-1.10.2-py3-none-any.whl (392 kB)
Requirement already satisfied: colorama in /Users/richardevans/opt/anaconda3/envs/oguk-dev/lib/python3.9/site-packages (from nbdime->jupyter-cache~=0.4.1->myst-nb~=0.12.0->jupyter-book>=0.8.0->-r /Users/richardevans/Documents/Economics/OSE/OG-UK/condaenv.1jg8jqkx.requirements.txt (line 1)) (0.4.4)
Collecting gitdb<5,>=4.0.1
  Using cached gitdb-4.0.7-py3-none-any.whl (63 kB)
Collecting smmap<5,>=3.0.1
  Using cached smmap-4.0.0-py2.py3-none-any.whl (24 kB)
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  Using cached requests_unixsocket-0.2.0-py2.py3-none-any.whl (11 kB)
Collecting anyio<4,>=3.1.0
  Using cached anyio-3.3.0-py3-none-any.whl (77 kB)
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  Using cached websocket_client-1.2.1-py2.py3-none-any.whl (52 kB)
Collecting sniffio>=1.1
  Using cached sniffio-1.2.0-py3-none-any.whl (10 kB)
Collecting synthimpute@ git+https://github.com/PSLmodels/synthimpute
  Cloning https://github.com/PSLmodels/synthimpute to /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/synthimpute_de9b433a0dee456c93396e0f0d96ca47
  Resolved https://github.com/PSLmodels/synthimpute to commit 0ae4d3aaadd82113093b66a24b049d0aff6ccba9
Collecting pathlib
  Downloading pathlib-1.0.1.tar.gz (49 kB)
Collecting tables
  Downloading tables-3.6.1.tar.gz (4.6 MB)
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  Downloading tables-2.4.0.tar.gz (8.9 MB)
  Downloading tables-2.3.1.tar.gz (8.8 MB)
  Downloading tables-2.3.tar.gz (8.8 MB)
INFO: pip is looking at multiple versions of colorama to determine which version is compatible with other requirements. This could take a while.
Collecting colorama
  Using cached colorama-0.4.4-py2.py3-none-any.whl (16 kB)
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INFO: pip is looking at multiple versions of colorama to determine which version is compatible with other requirements. This could take a while.
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INFO: This is taking longer than usual. You might need to provide the dependency resolver with stricter constraints to reduce runtime. If you want to abort this run, you can press Ctrl + C to do so. To improve how pip performs, tell us what happened here: https://pip.pypa.io/surveys/backtracking
  Downloading colorama-0.3.1.zip (31 kB)
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Pip subprocess error:
  Running command git clone -q https://github.com/PSLmodels/OG-Core.git /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-req-build-wmj5mgj2
  Running command git clone -q https://github.com/PSLmodels/openfisca-uk /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-req-build-qcl_vd4u
  Running command git clone -q https://github.com/ubicenter/openfisca-uk-data /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/openfisca-uk-data_f641c6a49da04bbe9b856e2c0eab8c32
  Running command git clone -q https://github.com/PSLmodels/microdf /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/microdf_844040ddd99e4e23be17691305c7146a
  Running command git clone -q https://github.com/PSLmodels/synthimpute /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/synthimpute_de9b433a0dee456c93396e0f0d96ca47
    ERROR: Command errored out with exit status 1:
     command: /Users/richardevans/opt/anaconda3/envs/oguk-dev/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_aa116f4cef8a41a79db5b141582ace8d/setup.py'"'"'; __file__='"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_aa116f4cef8a41a79db5b141582ace8d/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-pip-egg-info-uax_chlm
         cwd: /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_aa116f4cef8a41a79db5b141582ace8d/
    Complete output (11 lines):
    /var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/H5closeu2yh6f8f.c:2:5: error: implicit declaration of function 'H5close' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
        H5close();
        ^
    1 error generated.
    * Using Python 3.9.7 | packaged by conda-forge | (default, Sep  2 2021, 17:58:46)
    * USE_PKGCONFIG: False
    * Found conda env: ``/Users/richardevans/opt/anaconda3/envs/oguk-dev``
    .. ERROR:: Could not find a local HDF5 installation.
       You may need to explicitly state where your local HDF5 headers and
       library can be found by setting the ``HDF5_DIR`` environment
       variable or by using the ``--hdf5`` command-line option.
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/2b/32/847ee3f521aae6a0be380d923a736162d698586f444df1ac24b98c65025c/tables-3.6.1.tar.gz#sha256=49a972b8a7c27a8a173aeb05f67acb45fe608b64cd8e9fa667c0962a60b71b49 (from https://pypi.org/simple/tables/) (requires-python:>=3.5). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
    ERROR: Command errored out with exit status 1:
     command: /Users/richardevans/opt/anaconda3/envs/oguk-dev/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_a336883cab124cf0bff45877a47edb97/setup.py'"'"'; __file__='"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_a336883cab124cf0bff45877a47edb97/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-pip-egg-info-xu80al60
         cwd: /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_a336883cab124cf0bff45877a47edb97/
    Complete output (11 lines):
    /var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/H5close9uujani7.c:2:5: error: implicit declaration of function 'H5close' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
        H5close();
        ^
    1 error generated.
    * Using Python 3.9.7 | packaged by conda-forge | (default, Sep  2 2021, 17:58:46)
    * USE_PKGCONFIG: False
    * Found conda env: ``/Users/richardevans/opt/anaconda3/envs/oguk-dev``
    .. ERROR:: Could not find a local HDF5 installation.
       You may need to explicitly state where your local HDF5 headers and
       library can be found by setting the ``HDF5_DIR`` environment
       variable or by using the ``--hdf5`` command-line option.
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/73/51/6dabb2b94826e5db3aa2542b80f1382780b96a0cd13e0cfb637b36ede5c5/tables-3.5.2.tar.gz#sha256=b220e32262bab320aa41d33125a7851ff898be97c0de30b456247508e2cc33c2 (from https://pypi.org/simple/tables/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
    ERROR: Command errored out with exit status 1:
     command: /Users/richardevans/opt/anaconda3/envs/oguk-dev/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_ec26222b92024cf2b053961f87dcc688/setup.py'"'"'; __file__='"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_ec26222b92024cf2b053961f87dcc688/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-pip-egg-info-11ds65d9
         cwd: /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_ec26222b92024cf2b053961f87dcc688/
    Complete output (11 lines):
    /var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/H5closeoaw4emvq.c:2:5: error: implicit declaration of function 'H5close' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
        H5close();
        ^
    1 error generated.
    * Using Python 3.9.7 | packaged by conda-forge | (default, Sep  2 2021, 17:58:46)
    * USE_PKGCONFIG: False
    * Found conda env: ``/Users/richardevans/opt/anaconda3/envs/oguk-dev``
    .. ERROR:: Could not find a local HDF5 installation.
       You may need to explicitly state where your local HDF5 headers and
       library can be found by setting the ``HDF5_DIR`` environment
       variable or by using the ``--hdf5`` command-line option.
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/c6/e6/38cdcdc501ff889ea1e60bd5ef61d0573f73606f4dd0169786fd991c6b70/tables-3.5.1.tar.gz#sha256=88e2f3be1f143febc8bf8a7fe49ad51fc12518d6a1ac4eb641778d93e5dc2039 (from https://pypi.org/simple/tables/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
    ERROR: Command errored out with exit status 1:
     command: /Users/richardevans/opt/anaconda3/envs/oguk-dev/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_71e546b31c15426db493ec6f1dd274b5/setup.py'"'"'; __file__='"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_71e546b31c15426db493ec6f1dd274b5/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-pip-egg-info-ococl1uv
         cwd: /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_71e546b31c15426db493ec6f1dd274b5/
    Complete output (11 lines):
    /var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/H5close2aw4_bxv.c:2:5: error: implicit declaration of function 'H5close' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
        H5close();
        ^
    1 error generated.
    * Using Python 3.9.7 | packaged by conda-forge | (default, Sep  2 2021, 17:58:46)
    * USE_PKGCONFIG: False
    * Found conda env: ``/Users/richardevans/opt/anaconda3/envs/oguk-dev``
    .. ERROR:: Could not find a local HDF5 installation.
       You may need to explicitly state where your local HDF5 headers and
       library can be found by setting the ``HDF5_DIR`` environment
       variable or by using the ``--hdf5`` command-line option.
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/4d/53/8f34ce887c2a2ad80518980419a5f6f41defc85a287a355987e559ce9385/tables-3.4.4.tar.gz#sha256=bdc5c073712af2a43babd139c4855fc99496bb2c3f3f5d1b4770a985e6f9ce29 (from https://pypi.org/simple/tables/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
    ERROR: Command errored out with exit status 1:
     command: /Users/richardevans/opt/anaconda3/envs/oguk-dev/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_8f253843ced14cd9b4067cb0070d3150/setup.py'"'"'; __file__='"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_8f253843ced14cd9b4067cb0070d3150/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-pip-egg-info-hqgttcsa
         cwd: /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_8f253843ced14cd9b4067cb0070d3150/
    Complete output (11 lines):
    /var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/H5closez937bstz.c:2:5: error: implicit declaration of function 'H5close' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
        H5close();
        ^
    1 error generated.
    * Using Python 3.9.7 | packaged by conda-forge | (default, Sep  2 2021, 17:58:46)
    * USE_PKGCONFIG: False
    * Found conda env: ``/Users/richardevans/opt/anaconda3/envs/oguk-dev``
    .. ERROR:: Could not find a local HDF5 installation.
       You may need to explicitly state where your local HDF5 headers and
       library can be found by setting the ``HDF5_DIR`` environment
       variable or by using the ``--hdf5`` command-line option.
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/98/bb/0192955689d2e5972e2714300433eff57e5bef4147248cb15c7b6f04ae9e/tables-3.4.3.tar.gz#sha256=b6aafe47154e2140c0a91bb38ebdb6ba67a24dd86263f1c294af8c11cb7deed4 (from https://pypi.org/simple/tables/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
    ERROR: Command errored out with exit status 1:
     command: /Users/richardevans/opt/anaconda3/envs/oguk-dev/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_56b78c18ae5d45c5b1a98c17c2104b6b/setup.py'"'"'; __file__='"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_56b78c18ae5d45c5b1a98c17c2104b6b/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-pip-egg-info-o74y602l
         cwd: /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_56b78c18ae5d45c5b1a98c17c2104b6b/
    Complete output (11 lines):
    /var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/H5closem3n93_5i.c:2:5: error: implicit declaration of function 'H5close' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
        H5close();
        ^
    1 error generated.
    * Using Python 3.9.7 | packaged by conda-forge | (default, Sep  2 2021, 17:58:46)
    * USE_PKGCONFIG: False
    * Found conda env: ``/Users/richardevans/opt/anaconda3/envs/oguk-dev``
    .. ERROR:: Could not find a local HDF5 installation.
       You may need to explicitly state where your local HDF5 headers and
       library can be found by setting the ``HDF5_DIR`` environment
       variable or by using the ``--hdf5`` command-line option.
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/a2/e5/697f7ec96c4808983711635ef2e4c6b217493343938410125bcece1642cf/tables-3.4.2.tar.gz#sha256=fdbbea4edb6bad0ac0e53fc7bc6970e78e12eef4944aa4146bcdcb573201676c (from https://pypi.org/simple/tables/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
    ERROR: Command errored out with exit status 1:
     command: /Users/richardevans/opt/anaconda3/envs/oguk-dev/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_df4dcd9dfee84271b32cb83fa46b6d50/setup.py'"'"'; __file__='"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_df4dcd9dfee84271b32cb83fa46b6d50/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-pip-egg-info-8p5cyc0r
         cwd: /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_df4dcd9dfee84271b32cb83fa46b6d50/
    Complete output (10 lines):
    /var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/H5closeavlmh7c4.c:2:5: error: implicit declaration of function 'H5close' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
        H5close();
        ^
    1 error generated.
    * Using Python 3.9.7 | packaged by conda-forge | (default, Sep  2 2021, 17:58:46)
    * USE_PKGCONFIG: False
    .. ERROR:: Could not find a local HDF5 installation.
       You may need to explicitly state where your local HDF5 headers and
       library can be found by setting the ``HDF5_DIR`` environment
       variable or by using the ``--hdf5`` command-line option.
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/d9/e6/c026063429571f0538bab59166a45bb1b0453217be3f1510aada02741b32/tables-3.4.1.tar.gz#sha256=1587337593133b169d73bc68729b2cb736a3494f93a54188b8cc26f52cd51c67 (from https://pypi.org/simple/tables/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
    ERROR: Command errored out with exit status 1:
     command: /Users/richardevans/opt/anaconda3/envs/oguk-dev/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_737e383cab6c43f69a5c7e5b7f65ab7e/setup.py'"'"'; __file__='"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_737e383cab6c43f69a5c7e5b7f65ab7e/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-pip-egg-info-dyd_e6o4
         cwd: /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_737e383cab6c43f69a5c7e5b7f65ab7e/
    Complete output (10 lines):
    /var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/H5closexn0ad6k2.c:2:5: error: implicit declaration of function 'H5close' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
        H5close();
        ^
    1 error generated.
    * Using Python 3.9.7 | packaged by conda-forge | (default, Sep  2 2021, 17:58:46)
    * USE_PKGCONFIG: False
    .. ERROR:: Could not find a local HDF5 installation.
       You may need to explicitly state where your local HDF5 headers and
       library can be found by setting the ``HDF5_DIR`` environment
       variable or by using the ``--hdf5`` command-line option.
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/59/fb/ac97f34f6cd1863a4a7709fc0dd907efcfe5d10adeba152f20d5e5897d08/tables-3.4.0.tar.gz#sha256=bdd1e3a55b9bfe1c518c874fc730ac34ca42ff7d505e6947229f8a9e5572cac4 (from https://pypi.org/simple/tables/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
    ERROR: Command errored out with exit status 1:
     command: /Users/richardevans/opt/anaconda3/envs/oguk-dev/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_ca699fb8106844548d699b966dbd1207/setup.py'"'"'; __file__='"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_ca699fb8106844548d699b966dbd1207/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-pip-egg-info-ch6j6lax
         cwd: /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_ca699fb8106844548d699b966dbd1207/
    Complete output (10 lines):
    /var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/H5closeu4l28ygb.c:2:5: error: implicit declaration of function 'H5close' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
        H5close();
        ^
    1 error generated.
    * Using Python 3.9.7 | packaged by conda-forge | (default, Sep  2 2021, 17:58:46)
    * USE_PKGCONFIG: False
    .. ERROR:: Could not find a local HDF5 installation.
       You may need to explicitly state where your local HDF5 headers and
       library can be found by setting the ``HDF5_DIR`` environment
       variable or by using the ``--hdf5`` command-line option.
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/97/eb/ea2102f5a210a62f9f7387cf9912cb841f4a9089dbb232e642daa2626769/tables-3.3.0.tar.gz#sha256=8383ccf02e041a5d55494a09fc5514140b4653055a2732c981b5fd0f7408822c (from https://pypi.org/simple/tables/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
    ERROR: Command errored out with exit status 1:
     command: /Users/richardevans/opt/anaconda3/envs/oguk-dev/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_d548aedecef84b63a6615ea9daa74a69/setup.py'"'"'; __file__='"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_d548aedecef84b63a6615ea9daa74a69/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-pip-egg-info-igxddg6e
         cwd: /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_d548aedecef84b63a6615ea9daa74a69/
    Complete output (10 lines):
    /var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/H5close0x1tvqfg.c:2:5: error: implicit declaration of function 'H5close' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
        H5close();
        ^
    1 error generated.
    * Using Python 3.9.7 | packaged by conda-forge | (default, Sep  2 2021, 17:58:46)
    * USE_PKGCONFIG: False
    .. ERROR:: Could not find a local HDF5 installation.
       You may need to explicitly state where your local HDF5 headers and
       library can be found by setting the ``HDF5_DIR`` environment
       variable or by using the ``--hdf5`` command-line option.
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/0c/eb/e2def4cefade4b2427b8737b7c67cd00db8746dbb02dbfcf66a010f13954/tables-3.2.3.1.tar.gz#sha256=20fb453dcfbb28450f4f738ed8ce85943b1cca4bf5e3cd739098cae6dac9dbc8 (from https://pypi.org/simple/tables/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
    ERROR: Command errored out with exit status 1:
     command: /Users/richardevans/opt/anaconda3/envs/oguk-dev/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_50c3850d1f474eeaa5dcf987a993886c/setup.py'"'"'; __file__='"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_50c3850d1f474eeaa5dcf987a993886c/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-pip-egg-info-24eoj_om
         cwd: /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_50c3850d1f474eeaa5dcf987a993886c/
    Complete output (5 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_50c3850d1f474eeaa5dcf987a993886c/setup.py", line 34, in <module>
        import cpuinfo
    ModuleNotFoundError: No module named 'cpuinfo'
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/bd/a5/b6466e504397cbb64bc12075c884b86e2e65c73e007c14048bafb87c6ae2/tables-3.2.3.tar.gz#sha256=c9d4f86f465b18a0fe57d03df17534e26760d9af5d1440bcb86a0189c2cb0639 (from https://pypi.org/simple/tables/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
    ERROR: Command errored out with exit status 1:
     command: /Users/richardevans/opt/anaconda3/envs/oguk-dev/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_e6de11e40ce1412ca4c947c3f282349a/setup.py'"'"'; __file__='"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_e6de11e40ce1412ca4c947c3f282349a/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-pip-egg-info-2q802e6n
         cwd: /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_e6de11e40ce1412ca4c947c3f282349a/
    Complete output (10 lines):
    /var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/H5closeaout2jx9.c:2:5: error: implicit declaration of function 'H5close' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
        H5close();
        ^
    1 error generated.
    * Using Python 3.9.7 | packaged by conda-forge | (default, Sep  2 2021, 17:58:46)
    * USE_PKGCONFIG: False
    .. ERROR:: Could not find a local HDF5 installation.
       You may need to explicitly state where your local HDF5 headers and
       library can be found by setting the ``HDF5_DIR`` environment
       variable or by using the ``--hdf5`` command-line option.
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/af/38/85a4581084ad2aaed4318b7f3a46c5bed3ecb32bae0929add5d7c752d8fc/tables-3.2.2.tar.gz#sha256=3564b351a71ec1737b503b001eb7ceae1f65d5d6e3ffe1ea75aafba10f37fa84 (from https://pypi.org/simple/tables/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
    ERROR: Command errored out with exit status 1:
     command: /Users/richardevans/opt/anaconda3/envs/oguk-dev/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_f7e194de22a44457902edb2329c46583/setup.py'"'"'; __file__='"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_f7e194de22a44457902edb2329c46583/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-pip-egg-info-g0tq7tc4
         cwd: /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_f7e194de22a44457902edb2329c46583/
    Complete output (10 lines):
    /var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/H5closejk0s9zw3.c:2:5: error: implicit declaration of function 'H5close' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
        H5close();
        ^
    1 error generated.
    * Using Python 3.9.7 | packaged by conda-forge | (default, Sep  2 2021, 17:58:46)
    * USE_PKGCONFIG: False
    .. ERROR:: Could not find a local HDF5 installation.
       You may need to explicitly state where your local HDF5 headers and
       library can be found by setting the ``HDF5_DIR`` environment
       variable or by using the ``--hdf5`` command-line option.
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/5e/25/2591b0a60b16c9e65f1a0480dfc756e38c92aa714f9936dd07e965276409/tables-3.2.1.1.tar.gz#sha256=21e9749a60c6acc8a9755a52d95b414bc4f4b2c72a9175af360225883a775358 (from https://pypi.org/simple/tables/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
    ERROR: Command errored out with exit status 1:
     command: /Users/richardevans/opt/anaconda3/envs/oguk-dev/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_4e9daae9a6a642d6a8dbdca37fc59ca0/setup.py'"'"'; __file__='"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_4e9daae9a6a642d6a8dbdca37fc59ca0/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-pip-egg-info-ntaj6iil
         cwd: /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_4e9daae9a6a642d6a8dbdca37fc59ca0/
    Complete output (10 lines):
    /var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/H5closeoi4kesrj.c:2:5: error: implicit declaration of function 'H5close' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
        H5close();
        ^
    1 error generated.
    * Using Python 3.9.7 | packaged by conda-forge | (default, Sep  2 2021, 17:58:46)
    * USE_PKGCONFIG: False
    .. ERROR:: Could not find a local HDF5 installation.
       You may need to explicitly state where your local HDF5 headers and
       library can be found by setting the ``HDF5_DIR`` environment
       variable or by using the ``--hdf5`` command-line option.
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/92/3a/a0fd93a68b98ad2ab788f4f725250515ad2f12c23858f3b8d2b17af454a4/tables-3.2.0.tar.gz#sha256=60980e44676bfe463cdd2582ecdacc0b0763b259477015e866f8af72b4cdba44 (from https://pypi.org/simple/tables/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
    ERROR: Command errored out with exit status 1:
     command: /Users/richardevans/opt/anaconda3/envs/oguk-dev/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_5842b266a2a441c9be76ec53bdbddafe/setup.py'"'"'; __file__='"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_5842b266a2a441c9be76ec53bdbddafe/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-pip-egg-info-m6vrvh6k
         cwd: /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_5842b266a2a441c9be76ec53bdbddafe/
    Complete output (2 lines):
    * Using Python 3.9.7 | packaged by conda-forge | (default, Sep  2 2021, 17:58:46)
    .. ERROR:: You need numpy 1.4.1 or greater to run PyTables!
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/69/db/2c5544686baace15d2e7f3c2363ba865049985cede70d55d7e883240b73d/tables-3.1.1.tar.gz#sha256=39b9036376f1185599771c19276f13b5b9119d98f9108f58595745ded3fe2da3 (from https://pypi.org/simple/tables/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
    ERROR: Command errored out with exit status 1:
     command: /Users/richardevans/opt/anaconda3/envs/oguk-dev/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_1cab06e0cb144c769e9eb2aa4e241c62/setup.py'"'"'; __file__='"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_1cab06e0cb144c769e9eb2aa4e241c62/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-pip-egg-info-9jk_t901
         cwd: /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_1cab06e0cb144c769e9eb2aa4e241c62/
    Complete output (2 lines):
    * Using Python 3.9.7 | packaged by conda-forge | (default, Sep  2 2021, 17:58:46)
    .. ERROR:: You need numpy 1.4.1 or greater to run PyTables!
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/b3/31/d0d47c6187d6dd9594ef165f8dd7252670c9d3c00a546bd5e56f38061a71/tables-3.1.0.tar.gz#sha256=92bd5052c61fef3d55505dcb1162150ea5e274b76c4e41633e8f78a9ad5f4dc1 (from https://pypi.org/simple/tables/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
    ERROR: Command errored out with exit status 1:
     command: /Users/richardevans/opt/anaconda3/envs/oguk-dev/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_1ae21e010af54202b22b384751221fcf/setup.py'"'"'; __file__='"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_1ae21e010af54202b22b384751221fcf/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-pip-egg-info-mrdoo2h4
         cwd: /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_1ae21e010af54202b22b384751221fcf/
    Complete output (2 lines):
    * Using Python 3.9.7 | packaged by conda-forge | (default, Sep  2 2021, 17:58:46)
    .. ERROR:: You need numpy 1.4.1 or greater to run PyTables!
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/eb/e6/49cd67bd44033013e4ca5588c53dcf052e08a25befd3be1e08eba32f1a69/tables-3.0.0.tar.gz#sha256=53532a59c8f03c3c5ef3c73c04f5bfd8384d6a3d508683cb87fc17af4c71dfe1 (from https://pypi.org/simple/tables/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
    ERROR: Command errored out with exit status 1:
     command: /Users/richardevans/opt/anaconda3/envs/oguk-dev/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_613cd9d3a60a427a96c671f138da7360/setup.py'"'"'; __file__='"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_613cd9d3a60a427a96c671f138da7360/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-pip-egg-info-p7li179d
         cwd: /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_613cd9d3a60a427a96c671f138da7360/
    Complete output (6 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_613cd9d3a60a427a96c671f138da7360/setup.py", line 37
        print ".. %s:: %s" % (kind.upper(), head)
              ^
    SyntaxError: invalid syntax
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/2f/04/939d8eab5c005215a6c267639006c68ddf5069d87f8946350aae60a16dab/tables-2.4.0.tar.gz#sha256=2bda3b1ffbe20ee35d5337d97071ff4177a7742b15e7837324ae7c5720e82678 (from https://pypi.org/simple/tables/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
    ERROR: Command errored out with exit status 1:
     command: /Users/richardevans/opt/anaconda3/envs/oguk-dev/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_a31746078aaa48cdb00c75c1c67aa290/setup.py'"'"'; __file__='"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_a31746078aaa48cdb00c75c1c67aa290/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-pip-egg-info-lle3sfdj
         cwd: /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_a31746078aaa48cdb00c75c1c67aa290/
    Complete output (6 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_a31746078aaa48cdb00c75c1c67aa290/setup.py", line 36
        print ".. %s:: %s" % (kind.upper(), head)
              ^
    SyntaxError: invalid syntax
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/58/98/43d8e93ccb6fdae2108f1b42b4f94d396d2f97372b7741237c2fe2e7671a/tables-2.3.1.tar.gz#sha256=6b2992c163219af3b75496271f1645e98705e51df6fb5daeaf83b9eae6b371cc (from https://pypi.org/simple/tables/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
    ERROR: Command errored out with exit status 1:
     command: /Users/richardevans/opt/anaconda3/envs/oguk-dev/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_1ed520d8e88e44d1b214fd36afd86243/setup.py'"'"'; __file__='"'"'/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_1ed520d8e88e44d1b214fd36afd86243/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-pip-egg-info-orw805xp
         cwd: /private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_1ed520d8e88e44d1b214fd36afd86243/
    Complete output (6 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_1ed520d8e88e44d1b214fd36afd86243/setup.py", line 36
        print ".. %s:: %s" % (kind.upper(), head)
              ^
    SyntaxError: invalid syntax
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/6f/65/44351a6a80aeae9548e0d638acdfa393b2d5158c5287620ec2b7704d41be/tables-2.3.tar.gz#sha256=d7350b47a9bbf832693700e6c247967f1e289f1b8be71c593cfe1558f94a9e79 (from https://pypi.org/simple/tables/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
ERROR: File "setup.py" not found for legacy project colorama from https://files.pythonhosted.org/packages/ca/c2/6910ba3f0de55091bf88e96b94475bf72056d08aa0ce2e45f6a7c5d4e725/colorama-0.1.15.zip#sha256=fb55091e0dd982edcfa99f039f8ae85f7acd538626c15de71fed39a6b7faa3fd (from nbdime->jupyter-cache~=0.4.1->myst-nb~=0.12.0->jupyter-book>=0.8.0->-r /Users/richardevans/Documents/Economics/OSE/OG-UK/condaenv.1jg8jqkx.requirements.txt (line 1)).

failed

CondaEnvException: Pip failed

IDENTIFIED PROBLEMS
Reading through all the messages, I have identified 7 possible problems causing this environment to fail. Some of them might be interrelated:

the colorama package takes a long time to analyze compatibility with requirements.

INFO: pip is looking at multiple versions of colorama to determine which version is
compatible with other requirements. This could take a while.
...
INFO: This is taking longer than usual. You might need to provide the dependency
resolver with stricter constraints to reduce runtime. If you want to abort this run, you can
press Ctrl + C to do so. To improve how pip performs, tell us what happened here:
https://pip.pypa.io/surveys/backtracking

Immediately after the colorama package version compatibility search, I get a Pip subprocess error: saying ERROR: Command errored out with exit status 1: after trying to clone OG-Core, openfisca-uk, openfisca-uk-data, microdf, and synthimpute. I suspect that the colorama package is a dependency of at least one of these five packages and is causing a conflict with another of them.
There is an error with hdf5

/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/H5closeu2yh6f8f.c:2:5: error: implicit declaration of function 'H5close' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
        H5close();
        ^
    1 error generated.
    * Using Python 3.9.7 | packaged by conda-forge | (default, Sep  2 2021, 17:58:46)
    * USE_PKGCONFIG: False
    * Found conda env: ``/Users/richardevans/opt/anaconda3/envs/oguk-dev``
    .. ERROR:: Could not find a local HDF5 installation.
       You may need to explicitly state where your local HDF5 headers and
       library can be found by setting the ``HDF5_DIR`` environment
       variable or by using the ``--hdf5`` command-line option.

ERROR: Command errored out with exit status 1: occurs with install of from https://pypi.org/simple/tables/) (requires-python:>=3.5)
An error about cpuinfo package

    import cpuinfo
    ModuleNotFoundError: No module named 'cpuinfo'
    ----------------------------------------

An error suggesting that numpy>=1.4.1 might need to be a dependency because of PyTables: ERROR:: You need numpy 1.4.1 or greater to run PyTables!
There seems to be an old Python 2.7 print error in one or more of the setup.py files

File "/private/var/folders/_2/fkr0rfrx2fz2r4_zpbgtdvzw0000gn/T/pip-install-f361zhjc/tables_613cd9d3a60a427a96c671f138da7360/setup.py", line 37
        print ".. %s:: %s" % (kind.upper(), head)
              ^
    SyntaxError: invalid syntax

@jdebacker @nikhilwoodruff @MaxGhenis @jpycroft

The text was updated successfully, but these errors were encountered:

rickecon · 2021-09-03T16:55:44Z

I commented out the - git+https://github.com/PSLmodels/openfisca-uk line in environment.py, cleared any old oguk-dev conda environment material, and created the new oguk-dev environment. Everything went well and smoothly, although it took 26 minutes (2 minutes for the initial environment dependencies and 24 minutes for the pip install of OG-Core). But it worked. So the conflict is definitely being generated by the pip install of openfisca-uk.

@jdebacker @nikhilwoodruff @MaxGhenis @jpycroft

jdebacker · 2021-09-03T17:09:26Z

@rickecon Thanks for this detailed report and for drilling down on the source of the errors.

I'm getting the same errors your report when I try to create the environment on my machine (running Mac OS 11.5.2). Note that in PR #22, the GH Actions were able to build the environment without problem on Linux and Windows.

rickecon · 2021-09-03T17:14:58Z

We need to find out why this is not working on Mac OSX.
We need to confirm that the environment can build on a Windows and/or Linux machine (e.g., like @jpycroft's or @nikhilwoodruff's)
Should we add OSX to the matrix.os in the OG-UK GH Action?

@jdebacker

nikhilwoodruff · 2021-09-03T17:21:20Z

@rickecon I should be able to test this later, but at first glance it looks like the (or at least one) issue is that the Python version is 3.9 - currently we're only building OpenFisca-UK on 3.7.7, so might need to add a <= condition in the version requirement?

jdebacker · 2021-09-03T17:22:24Z

@rickecon asks:

Should we add OSX to the matrix.os in the OG-UK GH Action?

Unfortunately, adding OS X to the testing matrix isn't straight-forward (see this Tax-Calculator PR for discussion and links to more info).

jdebacker · 2021-09-03T20:29:02Z

Per @nikhilwoodruff's suggestion, I set python<=3.7.11 and my environment built and I can create the oguk package and run the model.

jdebacker · 2021-09-04T18:22:25Z

@rickecon Can you try again using the main branch now that I've merged PR #29?

jpycroft · 2021-09-08T16:42:09Z

@jdebacker @rickecon @nikhilwoodruff

Hi Jason,

I’ve been trying out the new oguk-dev environment and (drum roll please … ) it installs! The conda activate oguk-dev worked fine. And no errors with the “pip install -e .” I've attached the conda output below.

Then I thought I’d try to run the example “python run_oguk.py” in the “examples/” folder. This generated over 5000 lines of errors. Many errors reference matplotlib (I checked that my matplotlib is up-to-date, of course). I've also attached that output below.

Best, Jon

Conda_output-oguk-dev_08sep2021.txt

Conda_output-run_oguk_08sep2021.txt

jdebacker · 2021-09-08T16:49:33Z

@jpycroft Thank you for the report!

I'll close this issue (since you were able install the environment). And I'll take a look at the tracebacks from your trying to run the example. I'll also open up an issue to discuss that.

rickecon added the bug Something isn't working label Sep 3, 2021

jdebacker mentioned this issue Sep 3, 2021

Limit to Python 3.7 #29

Merged

jdebacker closed this as completed Sep 8, 2021

jdebacker mentioned this issue Sep 8, 2021

Error running the example script #31

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Conda environment fails to create #28

Conda environment fails to create #28

rickecon commented Sep 3, 2021

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jdebacker commented Sep 3, 2021

jdebacker commented Sep 4, 2021

jpycroft commented Sep 8, 2021

jdebacker commented Sep 8, 2021

Conda environment fails to create #28

Conda environment fails to create #28

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rickecon commented Sep 3, 2021

rickecon commented Sep 3, 2021

jdebacker commented Sep 3, 2021

rickecon commented Sep 3, 2021

nikhilwoodruff commented Sep 3, 2021

jdebacker commented Sep 3, 2021

jdebacker commented Sep 3, 2021

jdebacker commented Sep 4, 2021

jpycroft commented Sep 8, 2021

jdebacker commented Sep 8, 2021