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4DNucleome / PartSeg

Tool for segmentation in bioimaging
https://partseg.github.io/
BSD 3-Clause "New" or "Revised" License
30 stars 10 forks source link

Installation on Windows fails #400

Closed haesleinhuepf closed 3 years ago

haesleinhuepf commented 3 years ago

Hi @Czaki ,

I just tried to install PartSeg in my Napari in a pretty fresh conda environment on Windows. There is an error with PyOpenGL-accelerate because MS buildtools is not installed. You may want to put another hint/note on the readme helping users with this issue. You can for example link to our blog: https://biapol.github.io/blog/robert_haase/ms_build_tools/

Best, Robert

Here comes the full error log:

Collecting partseg

  Downloading PartSeg-0.13.11-py3-none-any.whl (311 kB)

Collecting czifile>=2019.5.22

  Using cached czifile-2019.7.2-py2.py3-none-any.whl (18 kB)

Collecting xlrd>=1.1.0

  Using cached xlrd-2.0.1-py2.py3-none-any.whl (96 kB)

Requirement already satisfied: napari>=0.4.8 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from partseg) (0.4.11)

Requirement already satisfied: requests>=2.18.0 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from partseg) (2.26.0)

Collecting sympy>=1.1.1

  Downloading sympy-1.9-py3-none-any.whl (6.2 MB)

Collecting oiffile>=2019.1.1

  Using cached oiffile-2021.6.6-py3-none-any.whl (12 kB)

Collecting h5py>=2.8.0

  Downloading h5py-3.4.0-cp39-cp39-win_amd64.whl (2.8 MB)

Requirement already satisfied: vispy>=0.6.4 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from partseg) (0.9.0)

Collecting openpyxl>=2.4.9

  Using cached openpyxl-3.0.9-py2.py3-none-any.whl (242 kB)

Collecting PartSegData==0.10.0

  Using cached PartSegData-0.10.0-py3-none-any.whl (7.5 MB)

Requirement already satisfied: tifffile>=2020.9.30 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from partseg) (2021.10.12)

Requirement already satisfied: scipy>=1.2.0 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from partseg) (1.7.1)

Requirement already satisfied: QtPy>=1.7.0 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from partseg) (1.11.2)

Requirement already satisfied: numpy>=1.18.0 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from partseg) (1.21.2)

Collecting PyOpenGL-accelerate>=3.1.5

  Downloading PyOpenGL-accelerate-3.1.5.tar.gz (538 kB)

  Preparing metadata (setup.py): started

  Preparing metadata (setup.py): finished with status 'done'

Collecting pandas>=0.24.0

  Downloading pandas-1.3.3-cp39-cp39-win_amd64.whl (10.2 MB)

Collecting imagecodecs>=2020.5.30

  Downloading imagecodecs-2021.8.26-cp39-cp39-win_amd64.whl (13.4 MB)

Collecting mahotas>=1.4.9

  Downloading mahotas-1.4.11.tar.gz (1.5 MB)

  Preparing metadata (setup.py): started

  Preparing metadata (setup.py): finished with status 'done'

Collecting sentry-sdk>=0.14.3

  Using cached sentry_sdk-1.4.3-py2.py3-none-any.whl (139 kB)

Requirement already satisfied: superqt>=0.2.4 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from partseg) (0.2.4)

Requirement already satisfied: appdirs>=1.4.4 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from partseg) (1.4.4)

Requirement already satisfied: six>=1.11.0 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from partseg) (1.16.0)

Collecting PartSegCore-compiled-backend>=0.13.11

  Downloading PartSegCore_compiled_backend-0.13.11-cp39-cp39-win_amd64.whl (687 kB)

Requirement already satisfied: packaging>=20.0 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from partseg) (21.0)

Collecting defusedxml>=0.6.0

  Using cached defusedxml-0.7.1-py2.py3-none-any.whl (25 kB)

Collecting SimpleITK>=1.1.0

  Downloading SimpleITK-2.1.1-cp39-cp39-win_amd64.whl (26.2 MB)

Collecting xlsxwriter

  Using cached XlsxWriter-3.0.1-py3-none-any.whl (148 kB)

Requirement already satisfied: imageio>=2.5.0 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from partseg) (2.9.0)

Requirement already satisfied: pillow in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from imageio>=2.5.0->partseg) (8.3.2)

Requirement already satisfied: toolz>=0.10.0 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from napari>=0.4.8->partseg) (0.11.1)

Requirement already satisfied: napari-console>=0.0.4 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from napari>=0.4.8->partseg) (0.0.4)

Requirement already satisfied: PyOpenGL>=3.1.0 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from napari>=0.4.8->partseg) (3.1.5)

Requirement already satisfied: PyYAML>=5.1 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from napari>=0.4.8->partseg) (6.0)

Requirement already satisfied: typing-extensions in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from napari>=0.4.8->partseg) (3.10.0.2)

Requirement already satisfied: pydantic>=1.8.1 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from napari>=0.4.8->partseg) (1.8.2)

Requirement already satisfied: tqdm>=4.56.0 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from napari>=0.4.8->partseg) (4.62.3)

Requirement already satisfied: pint>=0.17 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from napari>=0.4.8->partseg) (0.17)

Requirement already satisfied: napari-svg>=0.1.4 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from napari>=0.4.8->partseg) (0.1.5)

Requirement already satisfied: jsonschema>=3.2.0 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from napari>=0.4.8->partseg) (4.1.0)

Requirement already satisfied: wrapt>=1.11.1 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from napari>=0.4.8->partseg) (1.13.2)

Requirement already satisfied: psutil>=5.0 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from napari>=0.4.8->partseg) (5.8.0)

Requirement already satisfied: magicgui>=0.2.6 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from napari>=0.4.8->partseg) (0.3.0)
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Requirement already satisfied: napari-plugin-engine>=0.1.9 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from napari>=0.4.8->partseg) (0.2.0)

Requirement already satisfied: dask[array]!=2.28.0,>=2.1.0 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from napari>=0.4.8->partseg) (2021.9.1)

Requirement already satisfied: cachey>=0.2.1 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from napari>=0.4.8->partseg) (0.2.1)

Collecting et-xmlfile

  Using cached et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB)

Requirement already satisfied: pyparsing>=2.0.2 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from packaging>=20.0->partseg) (2.4.7)

Requirement already satisfied: python-dateutil>=2.7.3 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from pandas>=0.24.0->partseg) (2.8.2)

Requirement already satisfied: pytz>=2017.3 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from pandas>=0.24.0->partseg) (2021.3)

Requirement already satisfied: certifi>=2017.4.17 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from requests>=2.18.0->partseg) (2021.10.8)

Requirement already satisfied: idna<4,>=2.5 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from requests>=2.18.0->partseg) (3.3)

Requirement already satisfied: urllib3<1.27,>=1.21.1 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from requests>=2.18.0->partseg) (1.26.7)

Requirement already satisfied: charset-normalizer~=2.0.0 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from requests>=2.18.0->partseg) (2.0.7)

Collecting mpmath>=0.19

  Using cached mpmath-1.2.1-py3-none-any.whl (532 kB)

Requirement already satisfied: hsluv in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from vispy>=0.6.4->partseg) (5.0.2)

Requirement already satisfied: kiwisolver in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from vispy>=0.6.4->partseg) (1.3.2)

Requirement already satisfied: freetype-py in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from vispy>=0.6.4->partseg) (2.2.0)

Requirement already satisfied: heapdict in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from cachey>=0.2.1->napari>=0.4.8->partseg) (1.0.1)

Requirement already satisfied: fsspec>=0.6.0 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from dask[array]!=2.28.0,>=2.1.0->napari>=0.4.8->partseg) (2021.10.0)

Requirement already satisfied: cloudpickle>=1.1.1 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from dask[array]!=2.28.0,>=2.1.0->napari>=0.4.8->partseg) (2.0.0)

Requirement already satisfied: partd>=0.3.10 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from dask[array]!=2.28.0,>=2.1.0->napari>=0.4.8->partseg) (1.2.0)

Requirement already satisfied: pyrsistent!=0.17.0,!=0.17.1,!=0.17.2,>=0.14.0 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from jsonschema>=3.2.0->napari>=0.4.8->partseg) (0.18.0)

Requirement already satisfied: attrs>=17.4.0 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from jsonschema>=3.2.0->napari>=0.4.8->partseg) (21.2.0)

Requirement already satisfied: docstring-parser in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from magicgui>=0.2.6->napari>=0.4.8->partseg) (0.11)

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Requirement already satisfied: IPython>=7.7.0 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from napari-console>=0.0.4->napari>=0.4.8->partseg) (7.28.0)

Requirement already satisfied: ipykernel>=5.2.0 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from napari-console>=0.0.4->napari>=0.4.8->partseg) (6.4.1)

Requirement already satisfied: qtconsole!=4.7.6,>=4.5.1 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from napari-console>=0.0.4->napari>=0.4.8->partseg) (5.1.1)

Requirement already satisfied: Jinja2>=2.3 in c:\users\rober\miniconda3\envs\bio3\lib\site-packages (from numpydoc>=0.9.2->napari>=0.4.8->partseg) (3.0.2)

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Building wheels for collected packages: mahotas, PyOpenGL-accelerate

  Building wheel for mahotas (setup.py): started

  Building wheel for mahotas (setup.py): finished with status 'error'

  ERROR: Command errored out with exit status 1:
   command: 'C:\Users\rober\miniconda3\envs\bio3\python.exe' -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Windows\\Temp\\pip-install-gfid79yk\\mahotas_ca5b0dbe7b7d4d11a280c7a4790d83d8\\setup.py'"'"'; __file__='"'"'C:\\Windows\\Temp\\pip-install-gfid79yk\\mahotas_ca5b0dbe7b7d4d11a280c7a4790d83d8\\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'"'"'))' bdist_wheel -d 'C:\Windows\Temp\pip-wheel-cmyi84zi'
       cwd: C:\Windows\Temp\pip-install-gfid79yk\mahotas_ca5b0dbe7b7d4d11a280c7a4790d83d8\
  Complete output (123 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build\lib.win-amd64-3.9
  creating build\lib.win-amd64-3.9\mahotas
  copying mahotas\bbox.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\bwperim.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\center_of_mass.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\colors.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\convolve.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\distance.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\edge.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\euler.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\features_cli.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\freeimage.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\histogram.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\internal.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\interpolate.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\labeled.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\lbp.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\mahotas_version.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\moments.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\morph.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\polygon.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\resize.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\segmentation.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\stretch.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\surf.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\tas.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\texture.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\thin.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\thresholding.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\zernike.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\_filters.py -> build\lib.win-amd64-3.9\mahotas
  copying mahotas\__init__.py -> build\lib.win-amd64-3.9\mahotas
  creating build\lib.win-amd64-3.9\mahotas\demos
  copying mahotas\demos\distance.py -> build\lib.win-amd64-3.9\mahotas\demos
  copying mahotas\demos\edge_demo.py -> build\lib.win-amd64-3.9\mahotas\demos
  copying mahotas\demos\morphology.py -> build\lib.win-amd64-3.9\mahotas\demos
  copying mahotas\demos\nuclear.py -> build\lib.win-amd64-3.9\mahotas\demos
  copying mahotas\demos\nuclear_distance_watershed.py -> build\lib.win-amd64-3.9\mahotas\demos
  copying mahotas\demos\superpixels.py -> build\lib.win-amd64-3.9\mahotas\demos
  copying mahotas\demos\surf_gaussians.py -> build\lib.win-amd64-3.9\mahotas\demos
  copying mahotas\demos\surf_luispedro.py -> build\lib.win-amd64-3.9\mahotas\demos
  copying mahotas\demos\thresholding.py -> build\lib.win-amd64-3.9\mahotas\demos
  copying mahotas\demos\wally.py -> build\lib.win-amd64-3.9\mahotas\demos
  copying mahotas\demos\wavelet_compress.py -> build\lib.win-amd64-3.9\mahotas\demos
  copying mahotas\demos\__init__.py -> build\lib.win-amd64-3.9\mahotas\demos
  creating build\lib.win-amd64-3.9\mahotas\features
  copying mahotas\features\lbp.py -> build\lib.win-amd64-3.9\mahotas\features
  copying mahotas\features\moments.py -> build\lib.win-amd64-3.9\mahotas\features
  copying mahotas\features\shape.py -> build\lib.win-amd64-3.9\mahotas\features
  copying mahotas\features\surf.py -> build\lib.win-amd64-3.9\mahotas\features
  copying mahotas\features\tas.py -> build\lib.win-amd64-3.9\mahotas\features
  copying mahotas\features\texture.py -> build\lib.win-amd64-3.9\mahotas\features
  copying mahotas\features\zernike.py -> build\lib.win-amd64-3.9\mahotas\features
  copying mahotas\features\__init__.py -> build\lib.win-amd64-3.9\mahotas\features
  creating build\lib.win-amd64-3.9\mahotas\io
  copying mahotas\io\freeimage.py -> build\lib.win-amd64-3.9\mahotas\io
  copying mahotas\io\pil.py -> build\lib.win-amd64-3.9\mahotas\io
  copying mahotas\io\__init__.py -> build\lib.win-amd64-3.9\mahotas\io
  creating build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\pymorph_copy.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_bbox.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_bwperim.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_center_of_mass.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_citation.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_close_holes.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_colors.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_convolve.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_demos.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_dilate_erode.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_distance.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_edge.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_euler.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_features_shape.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_filters.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_find.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_freeimage.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_gvoronoi.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_histogram.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_hitmiss.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_imresize.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_internal.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_interpolate.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_io.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_label.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_labeled.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_lbp.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_mahotas.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_majority.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_mean_filter.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_median_filter.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_moments.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_morph.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_polygon.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_segmentation.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_stretch.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_surf.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_surf_regression.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_tas.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_template_match.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_texture.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_thin.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_thresholding.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_watershed.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\test_zernike.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\utils.py -> build\lib.win-amd64-3.9\mahotas\tests
  copying mahotas\tests\__init__.py -> build\lib.win-amd64-3.9\mahotas\tests
  creating build\lib.win-amd64-3.9\mahotas\demos\data
  copying mahotas\demos\data\DepartmentStore.jpg -> build\lib.win-amd64-3.9\mahotas\demos\data
  copying mahotas\demos\data\lena.jpg -> build\lib.win-amd64-3.9\mahotas\demos\data
  copying mahotas\demos\data\luispedro.jpg -> build\lib.win-amd64-3.9\mahotas\demos\data
  copying mahotas\demos\data\nuclear.png -> build\lib.win-amd64-3.9\mahotas\demos\data
  creating build\lib.win-amd64-3.9\mahotas\tests\data
  copying mahotas\tests\data\1bpp.bmp -> build\lib.win-amd64-3.9\mahotas\tests\data
  copying mahotas\tests\data\determinant_zero.png -> build\lib.win-amd64-3.9\mahotas\tests\data
  copying mahotas\tests\data\luispedro.npy -> build\lib.win-amd64-3.9\mahotas\tests\data
  copying mahotas\tests\data\rgba.png -> build\lib.win-amd64-3.9\mahotas\tests\data
  running build_ext
  building 'mahotas._bbox' extension
  error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/
  ----------------------------------------

  ERROR: Failed building wheel for mahotas
  Running setup.py clean for mahotas

  Building wheel for PyOpenGL-accelerate (setup.py): started

  Building wheel for PyOpenGL-accelerate (setup.py): finished with status 'error'

  ERROR: Command errored out with exit status 1:
   command: 'C:\Users\rober\miniconda3\envs\bio3\python.exe' -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Windows\\Temp\\pip-install-gfid79yk\\pyopengl-accelerate_e2018e6749c8409aae25df080ec990d9\\setup.py'"'"'; __file__='"'"'C:\\Windows\\Temp\\pip-install-gfid79yk\\pyopengl-accelerate_e2018e6749c8409aae25df080ec990d9\\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'"'"'))' bdist_wheel -d 'C:\Windows\Temp\pip-wheel-_63t8x6w'
       cwd: C:\Windows\Temp\pip-install-gfid79yk\pyopengl-accelerate_e2018e6749c8409aae25df080ec990d9\
  Complete output (10 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build\lib.win-amd64-3.9
  creating build\lib.win-amd64-3.9\OpenGL_accelerate
  copying OpenGL_accelerate\__init__.py -> build\lib.win-amd64-3.9\OpenGL_accelerate
  running build_ext
  building 'OpenGL_accelerate.wrapper' extension
  error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/
  ----------------------------------------

  ERROR: Failed building wheel for PyOpenGL-accelerate

  Running setup.py clean for PyOpenGL-accelerate

Failed to build mahotas PyOpenGL-accelerate

Installing collected packages: mpmath, imagecodecs, et-xmlfile, xlsxwriter, xlrd, sympy, SimpleITK, sentry-sdk, PyOpenGL-accelerate, PartSegData, PartSegCore-compiled-backend, pandas, openpyxl, oiffile, mahotas, h5py, defusedxml, czifile, partseg

    Running setup.py install for PyOpenGL-accelerate: started

    Running setup.py install for PyOpenGL-accelerate: finished with status 'error'

    ERROR: Command errored out with exit status 1:
     command: 'C:\Users\rober\miniconda3\envs\bio3\python.exe' -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Windows\\Temp\\pip-install-gfid79yk\\pyopengl-accelerate_e2018e6749c8409aae25df080ec990d9\\setup.py'"'"'; __file__='"'"'C:\\Windows\\Temp\\pip-install-gfid79yk\\pyopengl-accelerate_e2018e6749c8409aae25df080ec990d9\\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'"'"'))' install --record 'C:\Windows\Temp\pip-record-m9o9xkfj\install-record.txt' --single-version-externally-managed --compile --install-headers 'C:\Users\rober\miniconda3\envs\bio3\Include\PyOpenGL-accelerate'
         cwd: C:\Windows\Temp\pip-install-gfid79yk\pyopengl-accelerate_e2018e6749c8409aae25df080ec990d9\
    Complete output (10 lines):
    running install
    running build
    running build_py
    creating build
    creating build\lib.win-amd64-3.9
    creating build\lib.win-amd64-3.9\OpenGL_accelerate
    copying OpenGL_accelerate\__init__.py -> build\lib.win-amd64-3.9\OpenGL_accelerate
    running build_ext
    building 'OpenGL_accelerate.wrapper' extension
    error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/
    ----------------------------------------

ERROR: Command errored out with exit status 1: 'C:\Users\rober\miniconda3\envs\bio3\python.exe' -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Windows\\Temp\\pip-install-gfid79yk\\pyopengl-accelerate_e2018e6749c8409aae25df080ec990d9\\setup.py'"'"'; __file__='"'"'C:\\Windows\\Temp\\pip-install-gfid79yk\\pyopengl-accelerate_e2018e6749c8409aae25df080ec990d9\\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'"'"'))' install --record 'C:\Windows\Temp\pip-record-m9o9xkfj\install-record.txt' --single-version-externally-managed --compile --install-headers 'C:\Users\rober\miniconda3\envs\bio3\Include\PyOpenGL-accelerate' Check the logs for full command output.
haesleinhuepf commented 3 years ago

I just updated buildtools (I had installed them before actually) and the issue persists.

Czaki commented 3 years ago

I see that mahotas and PyOpenGL-accelerate do not publish wheels for python 3.9.

What did you mean that issue persist. You have a newer version than 14.0 and still, fail with the message that it requires such a version. Or does it fail because of different reasons?

haesleinhuepf commented 3 years ago

After updating the build tools, the issue persisted. Unfortunately, I don't know where I can see the version of installed buildtools.

haesleinhuepf commented 3 years ago

In python 3.8 it works!

haesleinhuepf commented 3 years ago

Alternatively, installation also works after installing the PyOpenCL-accelerate wheel you suggested in zulip:

https://www.lfd.uci.edu/~gohlke/pythonlibs/#pyopengl (PyOpenGL_accelerate‑3.1.5‑cp39‑cp39‑win_amd64.whl)

Btw. my napari info:

napari: 0.4.11
Platform: Windows-10-10.0.19042-SP0
Python: 3.9.7 | packaged by conda-forge | (default, Sep 29 2021, 19:20:16) [MSC v.1916 64 bit (AMD64)]
Qt: 5.15.2
PyQt5: 5.15.4
NumPy: 1.21.2
SciPy: 1.7.1
Dask: 2021.09.1
VisPy: 0.9.0

OpenGL:
- GL version: 4.6.14761 Compatibility Profile Context 21.30.02.01 30.0.13002.1001
- MAX_TEXTURE_SIZE: 16384

Screens:
- screen 1: resolution 1920x1200, scale 1.0

Plugins:
- PartSeg Analysis project reader: 0.13.11
- PartSeg Image reader: 0.13.11
- PartSeg Image tiff writer: 0.13.11
- PartSeg Mask project reader: 0.13.11
- PartSeg Mask project writer: 0.13.11
- PartSeg Masked Tiff reader: 0.13.11
- PartSeg widgets: 0.13.11
- Segmentation (Accelerated Pixel and Object Classification): 0.5.2
- console: 0.0.4
- scikit-image: 0.4.11
- svg: 0.1.5
Czaki commented 3 years ago

@haesleinhuepf could you check this text: https://github.com/4DNucleome/PartSeg/wiki/Instalation-troubleshoot

haesleinhuepf commented 3 years ago

Sounds good @Czaki , I would maybe extend "to download wheels build" and specify which wheel, namely "PyOpenGL_accelerate-...‑cp39‑cp39‑win_amd64.whl" just to be sure