[sfepy] Re: Installation error - RuntimeError: tables is missing

Hi Josh,

This might be related [1]. The pip support is new, and we still use the now-being-deprecated numpy.distutils, so there are "mysteries" and maintenance tasks to do. I have currently no idea why this happens (on platforms that I do not have an easy access to). I assume 'import tables' works in the python that pip uses, right?

Provided you have the dependencies installed, can you try installing the sfepy package from sources and/or the in-place build/use [2]? I can try assisting with that.

Thanks for the report, r.

[1] https://github.com/sfepy/sfepy/issues/889 [2] https://sfepy.org/doc/installation.html#installing-sfepy-from-sources

On 11/21/22 18:09, Joshua Meggitt via SfePy wrote:

Hello sfepy!

I am having trouble installing sfepy on my M1 mac using pip – I am getting an error which I am struggling to decode – it seems to be suggesting I don’t have pytables installed, but I do…

joshuameggitt@joshuas-mbp-2 bin % pip3 install sfepy -v

Using pip 22.3.1 from /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip (python 3.9)

Collecting sfepy

Using cached sfepy-2022.3.tar.gz (16.1 MB)

Running command pip subprocess to install build dependencies

Collecting setuptools<60.0

 Using cached setuptools-59.8.0-py3-none-any.whl (952 kB)

Collecting wheel

 Using cached wheel-0.38.4-py3-none-any.whl (36 kB)

Collecting Cython<3.0,>=0.29.30

 Using cached Cython-0.29.32-py2.py3-none-any.whl (986 kB)

Collecting matplotlib

 Using cached matplotlib-3.6.2-cp39-cp39-macosx_11_0_arm64.whl (7.2 MB)

Collecting meshio

 Using cached meshio-5.3.4-py3-none-any.whl (167 kB)

Collecting oldest-supported-numpy

 Using cached oldest_supported_numpy-2022.11.19-py3-none-any.whl (4.9 kB)

Collecting pyparsing

 Using cached pyparsing-3.0.9-py3-none-any.whl (98 kB)

Collecting scipy

 Using cached scipy-1.9.3-cp39-cp39-macosx_12_0_arm64.whl (28.6 MB)

Collecting tables

 Using cached tables-3.7.0-cp39-cp39-macosx_10_9_universal2.whl

Collecting contourpy>=1.0.1

 Using cached contourpy-1.0.6-cp39-cp39-macosx_11_0_arm64.whl (226 kB)

Collecting cycler>=0.10

 Using cached cycler-0.11.0-py3-none-any.whl (6.4 kB)

Collecting fonttools>=4.22.0

 Using cached fonttools-4.38.0-py3-none-any.whl (965 kB)

Collecting numpy>=1.19

 Using cached numpy-1.23.5-cp39-cp39-macosx_11_0_arm64.whl (13.4 MB)

Collecting python-dateutil>=2.7

 Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)

Collecting kiwisolver>=1.0.1

 Using cached kiwisolver-1.4.4-cp39-cp39-macosx_11_0_arm64.whl (63 kB)

Collecting pillow>=6.2.0

 Using cached Pillow-9.3.0-cp39-cp39-macosx_11_0_arm64.whl (2.9 MB)

Collecting packaging>=20.0

 Using cached packaging-21.3-py3-none-any.whl (40 kB)

Collecting rich

 Using cached rich-12.6.0-py3-none-any.whl (237 kB)

Collecting numpy>=1.19

 Using cached numpy-1.21.0-cp39-cp39-macosx_11_0_arm64.whl (12.1 MB)

Collecting numexpr>=2.6.2

 Using cached numexpr-2.8.4-cp39-cp39-macosx_11_0_arm64.whl (89 kB)

Collecting six>=1.5

 Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)

Collecting pygments<3.0.0,>=2.6.0

 Using cached Pygments-2.13.0-py3-none-any.whl (1.1 MB)

Collecting commonmark<0.10.0,>=0.9.0

 Using cached commonmark-0.9.1-py2.py3-none-any.whl (51 kB)

Installing collected packages: commonmark, wheel, six, setuptools, pyparsing, pygments, pillow, numpy, kiwisolver, fonttools, Cython, cycler, scipy, rich, python-dateutil, packaging, oldest-supported-numpy, numexpr, contourpy, tables, meshio, matplotlib

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.

nbconvert 7.1.0 requires jupyter-core>=4.7, which is not installed.

Successfully installed Cython-0.29.32 commonmark-0.9.1 contourpy-1.0.6 cycler-0.11.0 fonttools-4.38.0 kiwisolver-1.4.4 matplotlib-3.6.2 meshio-5.3.4 numexpr-2.8.4 numpy-1.21.0 oldest-supported-numpy-2022.11.19 packaging-21.3 pillow-9.3.0 pygments-2.13.0 pyparsing-3.0.9 python-dateutil-2.8.2 rich-12.6.0 scipy-1.9.3 setuptools-59.8.0 six-1.16.0 tables-3.7.0 wheel-0.38.4

Installing build dependencies ... done

Running command Getting requirements to build wheel

Traceback (most recent call last):

 File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module>

   main()

 File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main

   json_out['return_val'] = hook(**hook_input['kwargs'])

 File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel

   return hook(config_settings)

 File "/private/var/folders/2_/j_j8jwdd0kv41r_ny80h_lfw0000gn/T/pip-build-env-_zl19961/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 162, in get_requires_for_build_wheel

   return self._get_build_requires(

 File "/private/var/folders/2_/j_j8jwdd0kv41r_ny80h_lfw0000gn/T/pip-build-env-_zl19961/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 143, in _get_build_requires

   self.run_setup()

 File "/private/var/folders/2_/j_j8jwdd0kv41r_ny80h_lfw0000gn/T/pip-build-env-_zl19961/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 267, in run_setup

   super(_BuildMetaLegacyBackend,

 File "/private/var/folders/2_/j_j8jwdd0kv41r_ny80h_lfw0000gn/T/pip-build-env-_zl19961/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 158, in run_setup

   exec(compile(code, __file__, 'exec'), locals())

 File "setup.py", line 214, in <module>

   check_versions()

 File "setup.py", line 106, in check_versions

   package_check('tables', INFO.PYTABLES_MIN_VERSION,

 File "/private/var/folders/2_/j_j8jwdd0kv41r_ny80h_lfw0000gn/T/pip-install-6wjrcx5t/sfepy_ed194f740f8244c08f12a5b98619886b/./tools/build_helpers.py", line 314, in package_check

   raise RuntimeError(msgs['missing'] % pkg_name)

RuntimeError: tables is missing

error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.

│ exit code: 1

╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

full command: /Library/Frameworks/Python.framework/Versions/3.9/bin/python3 /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py get_requires_for_build_wheel /var/folders/2_/j_j8jwdd0kv41r_ny80h_lfw0000gn/T/tmpbv5i16rb

cwd: /private/var/folders/2_/j_j8jwdd0kv41r_ny80h_lfw0000gn/T/pip-install-6wjrcx5t/sfepy_ed194f740f8244c08f12a5b98619886b

Getting requirements to build wheel ... error

error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.

│ exit code: 1

╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

Any advice on what I could try to do to fix this issue would be greatly appreciated!

BR Josh

[University of Salford] Dr Joshua WR Meggitt Lecturer in Acoustical Engineering 1st Floor Newton Building, Room 105 University of Salford, Greater Manchester M5 4WT s://mail.python.org/mailman3/lists/sfepy.python.org/ Member address: cimrman3@ntc.zcu.cz