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Installing on mac M1 - fastremap #607

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neurologic opened this issue Feb 14, 2024 · 2 comments
Open

Installing on mac M1 - fastremap #607

neurologic opened this issue Feb 14, 2024 · 2 comments
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installation Issue affecting installation.

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@neurologic
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OS: 14.1.2
Mac mini M1 chip

command tried: pip install cloud-volume

error:

Full Traceback
Collecting cloud-volume Using cached cloud_volume-8.29.1-py3-none-any.whl (238 kB) Collecting compressed-segmentation>=2.1.1 Using cached compressed_segmentation-2.2.2-cp38-cp38-macosx_10_9_x86_64.whl (178 kB) Requirement already satisfied: protobuf>=3.3.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (3.20.3) Requirement already satisfied: google-cloud-storage>=1.24.1 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (2.7.0) Requirement already satisfied: pyspng-seunglab>=1.0.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (1.1.1) Collecting python-jsonschema-objects>=0.3.3 Using cached python_jsonschema_objects-0.5.2-py2.py3-none-any.whl (29 kB) Requirement already satisfied: urllib3[brotli]>=1.25.7 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (1.26.14) Requirement already satisfied: python-dateutil in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (2.8.2) Collecting compresso>=3.0.0 Using cached compresso-3.2.2-cp38-cp38-macosx_10_9_x86_64.whl (330 kB) Requirement already satisfied: zfpc in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (0.1.2) Requirement already satisfied: simplejpeg in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (1.7.2) Requirement already satisfied: boto3>=1.4.7 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (1.24.28) Requirement already satisfied: DracoPy<2.0.0,>=1.0.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (1.4.0) Requirement already satisfied: posix-ipc>=1.0.4 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (1.1.1) Collecting cloud-files>=4.18.1 Using cached cloud_files-4.21.1-py3-none-any.whl (60 kB) Collecting gevent Using cached gevent-24.2.1-cp38-cp38-macosx_10_9_x86_64.whl Requirement already satisfied: jsonschema!=4.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (4.17.3) Collecting fastremap>=1.14.0 Using cached fastremap-1.14.1.tar.gz (44 kB) Preparing metadata (setup.py) ... done Requirement already satisfied: pysimdjson>=3.1.1 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (6.0.2) Requirement already satisfied: google-auth>=1.10.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (2.16.1) Requirement already satisfied: tenacity>=4.10.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (8.0.1) Collecting pathos Using cached pathos-0.3.2-py3-none-any.whl (82 kB) Requirement already satisfied: psutil in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (5.9.0) Requirement already satisfied: chardet>=3.0.4 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (4.0.0) Requirement already satisfied: json5 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (0.9.6) Requirement already satisfied: networkx in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (2.8.4) Requirement already satisfied: google-cloud-core>=1.1.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (2.3.2) Requirement already satisfied: numpy>=1.13.3 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (1.21.5) Requirement already satisfied: tqdm in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (4.64.1) Requirement already satisfied: Pillow>=4.2.1 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (9.3.0) Requirement already satisfied: six>=1.10.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (1.16.0) Requirement already satisfied: fpzip<2.0.0,>=1.2.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (1.2.3) Requirement already satisfied: requests>=2.22.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-volume) (2.28.1) Collecting crackle-codec Using cached crackle_codec-0.7.1-cp38-cp38-macosx_10_9_x86_64.whl (381 kB) Requirement already satisfied: botocore<1.28.0,>=1.27.28 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from boto3>=1.4.7->cloud-volume) (1.27.59) Requirement already satisfied: jmespath<2.0.0,>=0.7.1 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from boto3>=1.4.7->cloud-volume) (0.10.0) Requirement already satisfied: s3transfer<0.7.0,>=0.6.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from boto3>=1.4.7->cloud-volume) (0.6.0) Requirement already satisfied: rsa>=4.7.2 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-files>=4.18.1->cloud-volume) (4.9) Requirement already satisfied: google-crc32c>=1.0.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-files>=4.18.1->cloud-volume) (1.1.2) Requirement already satisfied: zstandard in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-files>=4.18.1->cloud-volume) (0.18.0) Collecting deflate>=0.2.0 Using cached deflate-0.5.0-cp38-cp38-macosx_10_9_x86_64.whl (60 kB) Requirement already satisfied: click in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-files>=4.18.1->cloud-volume) (8.0.4) Requirement already satisfied: brotli in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-files>=4.18.1->cloud-volume) (1.1.0) Requirement already satisfied: orjson in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-files>=4.18.1->cloud-volume) (3.9.14) Requirement already satisfied: fasteners in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-files>=4.18.1->cloud-volume) (0.18) Requirement already satisfied: crc32c in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cloud-files>=4.18.1->cloud-volume) (2.3.post0) Requirement already satisfied: pytest in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from compressed-segmentation>=2.1.1->cloud-volume) (7.1.2) Requirement already satisfied: cachetools<6.0,>=2.0.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from google-auth>=1.10.0->cloud-volume) (5.3.0) Requirement already satisfied: pyasn1-modules>=0.2.1 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from google-auth>=1.10.0->cloud-volume) (0.2.8) Requirement already satisfied: google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.6 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from google-cloud-core>=1.1.0->cloud-volume) (2.8.1) Requirement already satisfied: google-resumable-media>=2.3.2 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from google-cloud-storage>=1.24.1->cloud-volume) (2.4.1) Requirement already satisfied: pkgutil-resolve-name>=1.3.10 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from jsonschema!=4.0->cloud-volume) (1.3.10) Requirement already satisfied: pyrsistent!=0.17.0,!=0.17.1,!=0.17.2,>=0.14.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from jsonschema!=4.0->cloud-volume) (0.18.0) Requirement already satisfied: importlib-resources>=1.4.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from jsonschema!=4.0->cloud-volume) (5.2.0) Requirement already satisfied: attrs>=17.4.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from jsonschema!=4.0->cloud-volume) (22.1.0) Requirement already satisfied: Markdown>=2.4 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from python-jsonschema-objects>=0.3.3->cloud-volume) (3.4.1) Requirement already satisfied: inflection>=0.2 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from python-jsonschema-objects>=0.3.3->cloud-volume) (0.5.1) Collecting jsonschema!=4.0 Using cached jsonschema-4.21.1-py3-none-any.whl (85 kB) Collecting attrs>=17.4.0 Using cached attrs-23.2.0-py3-none-any.whl (60 kB) Collecting jsonschema-specifications>=2023.03.6 Using cached jsonschema_specifications-2023.12.1-py3-none-any.whl (18 kB) Requirement already satisfied: rpds-py>=0.7.1 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from jsonschema!=4.0->cloud-volume) (0.18.0) Collecting referencing>=0.28.4 Using cached referencing-0.33.0-py3-none-any.whl (26 kB) Requirement already satisfied: charset-normalizer<3,>=2 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from requests>=2.22.0->cloud-volume) (2.0.4) Requirement already satisfied: certifi>=2017.4.17 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from requests>=2.22.0->cloud-volume) (2022.12.7) Requirement already satisfied: idna<4,>=2.5 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from requests>=2.22.0->cloud-volume) (3.4) Requirement already satisfied: pybind11 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from crackle-codec->cloud-volume) (2.11.1) Requirement already satisfied: zope.event in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from gevent->cloud-volume) (5.0) Requirement already satisfied: greenlet>=2.0.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from gevent->cloud-volume) (2.0.1) Requirement already satisfied: zope.interface in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from gevent->cloud-volume) (5.4.0) Requirement already satisfied: ppft>=1.7.6.8 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from pathos->cloud-volume) (1.7.6.8) Requirement already satisfied: pox>=0.3.4 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from pathos->cloud-volume) (0.3.4) Collecting dill>=0.3.8 Using cached dill-0.3.8-py3-none-any.whl (116 kB) Collecting multiprocess>=0.70.16 Using cached multiprocess-0.70.16-py38-none-any.whl (132 kB) Requirement already satisfied: zfpy in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from zfpc->cloud-volume) (1.0.0) Requirement already satisfied: googleapis-common-protos<2.0dev,>=1.56.2 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0dev,>=1.31.6->google-cloud-core>=1.1.0->cloud-volume) (1.57.0) Requirement already satisfied: cffi>=1.0.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from google-crc32c>=1.0.0->cloud-files>=4.18.1->cloud-volume) (1.15.1) Requirement already satisfied: zipp>=3.1.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from importlib-resources>=1.4.0->jsonschema!=4.0->cloud-volume) (3.11.0) Requirement already satisfied: importlib-metadata>=4.4 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from Markdown>=2.4->python-jsonschema-objects>=0.3.3->cloud-volume) (4.11.3) Requirement already satisfied: pyasn1<0.5.0,>=0.4.6 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from pyasn1-modules>=0.2.1->google-auth>=1.10.0->cloud-volume) (0.4.8) Requirement already satisfied: iniconfig in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from pytest->compressed-segmentation>=2.1.1->cloud-volume) (1.1.1) Requirement already satisfied: packaging in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from pytest->compressed-segmentation>=2.1.1->cloud-volume) (22.0) Requirement already satisfied: pluggy<2.0,>=0.12 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from pytest->compressed-segmentation>=2.1.1->cloud-volume) (1.0.0) Requirement already satisfied: py>=1.8.2 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from pytest->compressed-segmentation>=2.1.1->cloud-volume) (1.11.0) Requirement already satisfied: tomli>=1.0.0 in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from pytest->compressed-segmentation>=2.1.1->cloud-volume) (2.0.1) Requirement already satisfied: setuptools in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from zope.event->gevent->cloud-volume) (65.6.3) Requirement already satisfied: pycparser in /Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages (from cffi>=1.0.0->google-crc32c>=1.0.0->cloud-files>=4.18.1->cloud-volume) (2.21) Building wheels for collected packages: fastremap Building wheel for fastremap (setup.py) ... error error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [35 lines of output]
/Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages/setuptools/_distutils/extension.py:134: UserWarning: Unknown Extension options: 'language_level'
warnings.warn(msg)
/Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages/setuptools/installer.py:27: SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer.
warnings.warn(
/Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages/setuptools/command/easy_install.py:144: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
/Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running bdist_wheel
running build
running build_ext
cythoning fastremap.pyx to fastremap.cpp

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
    elif (cx == sx and cy == sy and cz == sz):
      return [ image.tobytes(order) ]
  
    cdef cnp.ndarray[NUMBER] arr
  
    cdef list[cnp.ndarray[NUMBER]] array_grid = [
                               ^
  ------------------------------------------------------------
  
  fastremap.pyx:1369:30: Invalid type.
  building 'fastremap' extension
  creating build
  creating build/temp.macosx-10.9-x86_64-cpython-38
  gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/kperks/opt/anaconda3/envs/ell/include -arch x86_64 -I/Users/kperks/opt/anaconda3/envs/ell/include -arch x86_64 -I/Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages/numpy/core/include -I/Users/kperks/opt/anaconda3/envs/ell/include/python3.8 -c fastremap.cpp -o build/temp.macosx-10.9-x86_64-cpython-38/fastremap.o -std=c++11 -O3 -stdlib=libc++ -mmacosx-version-min=10.9
  fastremap.cpp:1:2: error: Do not use this file, it is the result of a failed Cython compilation.
  #error Do not use this file, it is the result of a failed Cython compilation.
   ^
  1 error generated.
  error: command '/usr/bin/gcc' failed with exit code 1
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for fastremap
Running setup.py clean for fastremap
Failed to build fastremap
Installing collected packages: fastremap, dill, deflate, compresso, attrs, referencing, multiprocess, gevent, crackle-codec, pathos, jsonschema-specifications, compressed-segmentation, jsonschema, python-jsonschema-objects, cloud-files, cloud-volume
Running setup.py install for fastremap ... error
error: subprocess-exited-with-error

× Running setup.py install for fastremap did not run successfully.
│ exit code: 1
╰─> [37 lines of output]
/Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages/setuptools/_distutils/extension.py:134: UserWarning: Unknown Extension options: 'language_level'
warnings.warn(msg)
/Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages/setuptools/installer.py:27: SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer.
warnings.warn(
/Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages/setuptools/command/easy_install.py:144: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
/Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running install
[pbr] Generating AUTHORS
[pbr] AUTHORS complete (0.0s)
running build
running build_ext
cythoning fastremap.pyx to fastremap.cpp

  Error compiling Cython file:
  ------------------------------------------------------------
  ...
    elif (cx == sx and cy == sy and cz == sz):
      return [ image.tobytes(order) ]
  
    cdef cnp.ndarray[NUMBER] arr
  
    cdef list[cnp.ndarray[NUMBER]] array_grid = [
                               ^
  ------------------------------------------------------------
  
  fastremap.pyx:1369:30: Invalid type.
  building 'fastremap' extension
  creating build
  creating build/temp.macosx-10.9-x86_64-cpython-38
  gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/kperks/opt/anaconda3/envs/ell/include -arch x86_64 -I/Users/kperks/opt/anaconda3/envs/ell/include -arch x86_64 -I/Users/kperks/opt/anaconda3/envs/ell/lib/python3.8/site-packages/numpy/core/include -I/Users/kperks/opt/anaconda3/envs/ell/include/python3.8 -c fastremap.cpp -o build/temp.macosx-10.9-x86_64-cpython-38/fastremap.o -std=c++11 -O3 -stdlib=libc++ -mmacosx-version-min=10.9
  fastremap.cpp:1:2: error: Do not use this file, it is the result of a failed Cython compilation.
  #error Do not use this file, it is the result of a failed Cython compilation.
   ^
  1 error generated.
  error: command '/usr/bin/gcc' failed with exit code 1
  [end of output]

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

× Encountered error while trying to install package.
╰─> fastremap

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.

Other version info:
python 3.8.13
numpy 1.21.5

Steps tried:

  • I tried to install fastremap directly: 1) directly with pip (failed with similar error) and 2) with pip install numpy pip install fastremap --no-binary :all:
  • I tried to install g++ with brew install gcc and it seemed to work
  • I checked that I have command line tools, and I do (CLT: 15.1.0.0.1.1700200546)

I am trying to install on an environment that already has numpy (I need to use cloudvolume simultaneously with other packages for handling the .jsons for my neurons -- in CREST format (from Alex Shapsoncoe). Not sure if that has to do with any issues.

I am new to working with this sort of data (though have been interacting with neuroglancer for a while now via python scripts, and I have used some example colab notebooks to interact with our cloudvolume mesh and skeleton data... I am trying to get it to work now on my local computer so that I can integrate it into the rest of the workflow I have... some of which I cannot reproduce on colab).

Let me know if you see any solutions I am not seeing. Thank you so much!

-Krista

@neurologic
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I think I might have gotten it to work by starting with a new conda environment and doing pip install could-volume before pip install neuroglancer.

@william-silversmith
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william-silversmith commented Feb 20, 2024 via email

@william-silversmith william-silversmith added installation Issue affecting installation. labels Jul 3, 2024
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