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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)
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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
The text was updated successfully, but these errors were encountered:
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
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
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:
pip install numpy pip install fastremap --no-binary :all:
brew install gcc
and it seemed to workI 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
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