306 lines
20 KiB
Plaintext
306 lines
20 KiB
Plaintext
#########################################################
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#########################################################
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INSTALLATION PROCESS
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#########################################################
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#########################################################
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#########################################################
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Installation of MorphoCut development version:
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#########################################################
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$ pip install -U git+https://github.com/morphocut/morphocut.git
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Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
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Collecting git+https://github.com/morphocut/morphocut.git
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Cloning https://github.com/morphocut/morphocut.git to /tmp/pip-req-build-NnGYk4
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Installing build dependencies ... error
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Complete output from command /usr/bin/python -m pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-e4DHrk --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple --extra-index-url https://www.piwheels.org/simple -- setuptools wheel:
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Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple, https://www.piwheels.org/simple
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Collecting setuptools
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Downloading https://www.piwheels.org/simple/setuptools/setuptools-45.0.0-py2.py3-none-any.whl (583kB)
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setuptools requires Python '>=3.5' but the running Python is 2.7.16
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----------------------------------------
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Command "/usr/bin/python -m pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-e4DHrk --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple --extra-index-url https://www.piwheels.org/simple -- setuptools wheel" failed with error code 1 in None
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#########################################################
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Installation of MorphoCut packaged on PyPI via pip
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#########################################################
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$ pip install morphocut
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Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
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Collecting morphocut
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Could not find a version that satisfies the requirement morphocut (from versions: )
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No matching distribution found for morphocut
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#########################################################
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Installation of MorphoCut packaged on PyPI via pip3
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#########################################################
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$ pip3 install morphocut
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Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
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Collecting morphocut
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Downloading https://files.pythonhosted.org/packages/7e/c7/1addaf867234dd30db6d1f4bf8d3b685d93b743023a863814451abd5cef8/morphocut-0.1.1-py3-none-any.whl
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Collecting scikit-image>=0.16.0 (from morphocut)
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Downloading https://www.piwheels.org/simple/scikit-image/scikit_image-0.16.2-cp37-cp37m-linux_armv7l.whl (39.7MB)
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100% |████████████████████████████████| 39.7MB 10kB/s
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Collecting tqdm (from morphocut)
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Downloading https://files.pythonhosted.org/packages/72/c9/7fc20feac72e79032a7c8138fd0d395dc6d8812b5b9edf53c3afd0b31017/tqdm-4.41.1-py2.py3-none-any.whl (56kB)
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100% |████████████████████████████████| 61kB 1.6MB/s
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Collecting scipy (from morphocut)
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Downloading https://files.pythonhosted.org/packages/04/ab/e2eb3e3f90b9363040a3d885ccc5c79fe20c5b8a3caa8fe3bf47ff653260/scipy-1.4.1.tar.gz (24.6MB)
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100% |████████████████████████████████| 24.6MB 17kB/s
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Installing build dependencies ... done
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Requirement already satisfied: numpy in /usr/lib/python3/dist-packages (from morphocut) (1.16.2)
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Collecting pandas (from morphocut)
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Downloading https://www.piwheels.org/simple/pandas/pandas-0.25.3-cp37-cp37m-linux_armv7l.whl (33.1MB)
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100% |████████████████████████████████| 33.1MB 12kB/s
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Collecting PyWavelets>=0.4.0 (from scikit-image>=0.16.0->morphocut)
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Downloading https://www.piwheels.org/simple/pywavelets/PyWavelets-1.1.1-cp37-cp37m-linux_armv7l.whl (6.1MB)
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100% |████████████████████████████████| 6.1MB 67kB/s
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Collecting networkx>=2.0 (from scikit-image>=0.16.0->morphocut)
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Downloading https://files.pythonhosted.org/packages/41/8f/dd6a8e85946def36e4f2c69c84219af0fa5e832b018c970e92f2ad337e45/networkx-2.4-py3-none-any.whl (1.6MB)
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100% |████████████████████████████████| 1.6MB 255kB/s
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Requirement already satisfied: pillow>=4.3.0 in /usr/lib/python3/dist-packages (from scikit-image>=0.16.0->morphocut) (5.4.1)
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Collecting imageio>=2.3.0 (from scikit-image>=0.16.0->morphocut)
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Downloading https://files.pythonhosted.org/packages/1a/de/f7f985018f462ceeffada7f6e609919fbcc934acd9301929cba14bc2c24a/imageio-2.6.1-py3-none-any.whl (3.3MB)
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100% |████████████████████████████████| 3.3MB 123kB/s
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Collecting python-dateutil>=2.6.1 (from pandas->morphocut)
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Downloading https://files.pythonhosted.org/packages/d4/70/d60450c3dd48ef87586924207ae8907090de0b306af2bce5d134d78615cb/python_dateutil-2.8.1-py2.py3-none-any.whl (227kB)
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100% |████████████████████████████████| 235kB 822kB/s
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Collecting pytz>=2017.2 (from pandas->morphocut)
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Downloading https://files.pythonhosted.org/packages/e7/f9/f0b53f88060247251bf481fa6ea62cd0d25bf1b11a87888e53ce5b7c8ad2/pytz-2019.3-py2.py3-none-any.whl (509kB)
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100% |████████████████████████████████| 512kB 660kB/s
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Collecting decorator>=4.3.0 (from networkx>=2.0->scikit-image>=0.16.0->morphocut)
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Downloading https://files.pythonhosted.org/packages/8f/b7/f329cfdc75f3d28d12c65980e4469e2fa373f1953f5df6e370e84ea2e875/decorator-4.4.1-py2.py3-none-any.whl
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Requirement already satisfied: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil>=2.6.1->pandas->morphocut) (1.12.0)
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Building wheels for collected packages: scipy
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Running setup.py bdist_wheel for scipy ... error
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Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-vrivsnzz/scipy/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/pip-wheel-2w9xwni0 --python-tag cp37:
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Traceback (most recent call last):
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File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/core/__init__.py", line 16, in <module>
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from . import multiarray
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ImportError: libf77blas.so.3: cannot open shared object file: No such file or directory
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During handling of the above exception, another exception occurred:
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Traceback (most recent call last):
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File "<string>", line 1, in <module>
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File "/tmp/pip-install-vrivsnzz/scipy/setup.py", line 540, in <module>
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setup_package()
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File "/tmp/pip-install-vrivsnzz/scipy/setup.py", line 516, in setup_package
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from numpy.distutils.core import setup
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File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/__init__.py", line 142, in <module>
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from . import add_newdocs
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File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/add_newdocs.py", line 13, in <module>
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from numpy.lib import add_newdoc
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File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/lib/__init__.py", line 8, in <module>
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from .type_check import *
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File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/lib/type_check.py", line 11, in <module>
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import numpy.core.numeric as _nx
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File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/core/__init__.py", line 26, in <module>
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raise ImportError(msg)
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ImportError:
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Importing the multiarray numpy extension module failed. Most
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likely you are trying to import a failed build of numpy.
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If you're working with a numpy git repo, try `git clean -xdf` (removes all
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files not under version control). Otherwise reinstall numpy.
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Original error was: libf77blas.so.3: cannot open shared object file: No such file or directory
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----------------------------------------
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Failed building wheel for scipy
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Running setup.py clean for scipy
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Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-vrivsnzz/scipy/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" clean --all:
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`setup.py clean` is not supported, use one of the following instead:
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- `git clean -xdf` (cleans all files)
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- `git clean -Xdf` (cleans all versioned files, doesn't touch
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files that aren't checked into the git repo)
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Add `--force` to your command to use it anyway if you must (unsupported).
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----------------------------------------
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Failed cleaning build dir for scipy
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Failed to build scipy
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Installing collected packages: PyWavelets, decorator, networkx, imageio, scikit-image, tqdm, scipy, python-dateutil, pytz, pandas, morphocut
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Running setup.py install for scipy ... error
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Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-vrivsnzz/scipy/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-s4uxcq_l/install-record.txt --single-version-externally-managed --compile --user --prefix=:
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Note: if you need reliable uninstall behavior, then install
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with pip instead of using `setup.py install`:
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- `pip install .` (from a git repo or downloaded source
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release)
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- `pip install scipy` (last SciPy release on PyPI)
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Traceback (most recent call last):
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File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/core/__init__.py", line 16, in <module>
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from . import multiarray
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ImportError: libf77blas.so.3: cannot open shared object file: No such file or directory
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During handling of the above exception, another exception occurred:
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Traceback (most recent call last):
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File "<string>", line 1, in <module>
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File "/tmp/pip-install-vrivsnzz/scipy/setup.py", line 540, in <module>
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setup_package()
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File "/tmp/pip-install-vrivsnzz/scipy/setup.py", line 516, in setup_package
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from numpy.distutils.core import setup
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File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/__init__.py", line 142, in <module>
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from . import add_newdocs
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File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/add_newdocs.py", line 13, in <module>
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from numpy.lib import add_newdoc
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File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/lib/__init__.py", line 8, in <module>
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from .type_check import *
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File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/lib/type_check.py", line 11, in <module>
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import numpy.core.numeric as _nx
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File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/core/__init__.py", line 26, in <module>
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raise ImportError(msg)
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ImportError:
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Importing the multiarray numpy extension module failed. Most
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likely you are trying to import a failed build of numpy.
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If you're working with a numpy git repo, try `git clean -xdf` (removes all
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files not under version control). Otherwise reinstall numpy.
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Original error was: libf77blas.so.3: cannot open shared object file: No such file or directory
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----------------------------------------
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Command "/usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-vrivsnzz/scipy/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-s4uxcq_l/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /tmp/pip-install-vrivsnzz/scipy/
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#########################################################
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Installation of Scipy using sudo apt-get
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#########################################################
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$ sudo apt-get install python3-scipy
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Lecture des listes de paquets... Fait
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Construction de l'arbre des dépendances
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Lecture des informations d'état... Fait
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Les paquets supplémentaires suivants seront installés :
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python3-decorator
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Paquets suggérés :
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python-scipy-doc
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Les NOUVEAUX paquets suivants seront installés :
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python3-decorator python3-scipy
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0 mis à jour, 2 nouvellement installés, 0 à enlever et 41 non mis à jour.
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Il est nécessaire de prendre 8 925 ko dans les archives.
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Après cette opération, 38,0 Mo d'espace disque supplémentaires seront utilisés.
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Souhaitez-vous continuer ? [O/n] o
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Réception de :1 http://ftp.igh.cnrs.fr/pub/os/linux/raspbian/raspbian buster/main armhf python3-decorator all 4.3.0-1.1 [14,5 kB]
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Réception de :2 http://ftp.igh.cnrs.fr/pub/os/linux/raspbian/raspbian buster/main armhf python3-scipy armhf 1.1.0-7 [8 910 kB]
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8 925 ko réceptionnés en 3s (2 561 ko/s)
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Sélection du paquet python3-decorator précédemment désélectionné.
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(Lecture de la base de données... 99960 fichiers et répertoires déjà installés.)
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Préparation du dépaquetage de .../python3-decorator_4.3.0-1.1_all.deb ...
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Dépaquetage de python3-decorator (4.3.0-1.1) ...
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Sélection du paquet python3-scipy précédemment désélectionné.
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Préparation du dépaquetage de .../python3-scipy_1.1.0-7_armhf.deb ...
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Dépaquetage de python3-scipy (1.1.0-7) ...
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Paramétrage de python3-decorator (4.3.0-1.1) ...
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Paramétrage de python3-scipy (1.1.0-7) ...
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#########################################################
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Installation of MorphoCut packaged on PyPI via pip3 using sudo
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#########################################################
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$ sudo pip3 install morphocut
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Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
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Collecting morphocut
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Using cached https://files.pythonhosted.org/packages/7e/c7/1addaf867234dd30db6d1f4bf8d3b685d93b743023a863814451abd5cef8/morphocut-0.1.1-py3-none-any.whl
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Requirement already satisfied: scikit-image>=0.16.0 in /usr/local/lib/python3.7/dist-packages (from morphocut) (0.16.2)
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Requirement already satisfied: numpy in /usr/lib/python3/dist-packages (from morphocut) (1.16.2)
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Requirement already satisfied: tqdm in /usr/local/lib/python3.7/dist-packages (from morphocut) (4.41.1)
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Requirement already satisfied: pandas in /usr/local/lib/python3.7/dist-packages (from morphocut) (0.25.3)
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Requirement already satisfied: scipy in /usr/lib/python3/dist-packages (from morphocut) (1.1.0)
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Requirement already satisfied: imageio>=2.3.0 in /usr/local/lib/python3.7/dist-packages (from scikit-image>=0.16.0->morphocut) (2.6.1)
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Requirement already satisfied: PyWavelets>=0.4.0 in /usr/local/lib/python3.7/dist-packages (from scikit-image>=0.16.0->morphocut) (1.1.1)
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Requirement already satisfied: networkx>=2.0 in /usr/local/lib/python3.7/dist-packages (from scikit-image>=0.16.0->morphocut) (2.4)
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Requirement already satisfied: pillow>=4.3.0 in /usr/lib/python3/dist-packages (from scikit-image>=0.16.0->morphocut) (5.4.1)
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Requirement already satisfied: python-dateutil>=2.6.1 in /usr/local/lib/python3.7/dist-packages (from pandas->morphocut) (2.8.1)
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Requirement already satisfied: pytz>=2017.2 in /usr/local/lib/python3.7/dist-packages (from pandas->morphocut) (2019.3)
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Requirement already satisfied: decorator>=4.3.0 in /usr/local/lib/python3.7/dist-packages (from networkx>=2.0->scikit-image>=0.16.0->morphocut) (4.4.1)
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Requirement already satisfied: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil>=2.6.1->pandas->morphocut) (1.12.0)
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Installing collected packages: morphocut
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Successfully installed morphocut-0.1.1
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#########################################################
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#########################################################
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USAGE ERROR
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#########################################################
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#########################################################
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Processing images under /home/pi/Desktop/PlanktonScope_acquisition/01_16_2020/15...
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0it [00:00, ?it/s]
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0it [00:00, ?it/s]Found 94 files in /home/pi/Desktop/PlanktonScope_acquisition/01_16_2020/15.
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Object 35_41_180124_84: : 85it [00:17, 5.95it/s]
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Frame 35_41_180124: : 1it [00:17, 17.03s/it]
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Object 35_41_763395_168: : 169it [00:24, 47.97it/s]
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Frame 35_41_763395: : 2it [00:24, 14.11s/it]
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Object 35_42_339153_245: : 245it [00:31, 44.73it/s]
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Frame 35_42_339153: : 3it [00:31, 11.93s/it]
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Object 35_42_899894_320: : 319it [00:38, 42.28it/s]
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Frame 35_42_899894: : 4it [00:38, 10.44s/it]
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Object 35_43_467613_394: : 394it [00:45, 44.59it/s]
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Frame 35_43_467613: : 5it [00:44, 9.36s/it]
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Object 35_44_040639_465: : 466it [00:56, 32.28it/s]
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Frame 35_44_040639: : 6it [00:59, 9.95s/it]
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Object 35_44_040639_465: : 466it [00:59, 7.78it/s]
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Traceback (most recent call last):
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File "/home/pi/Downloads/Morphocut.py", line 115, in <module>
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p.run()
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 748, in run
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for _ in self.transform_stream():
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/stream.py", line 68, in transform_stream
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for obj in progress:
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File "/home/pi/.local/lib/python3.7/site-packages/tqdm/std.py", line 1104, in __iter__
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for obj in iterable:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/contrib/ecotaxa.py", line 111, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/stream.py", line 184, in transform_stream
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for i, obj in enumerate(stream, start=self.start):
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
|
||
for obj in stream:
|
||
File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
|
||
for obj in stream:
|
||
File "/home/pi/.local/lib/python3.7/site-packages/morphocut/image.py", line 142, in transform_stream
|
||
for obj in stream:
|
||
File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
|
||
for obj in stream:
|
||
File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
|
||
for obj in stream:
|
||
File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
|
||
for obj in stream:
|
||
File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
|
||
for obj in stream:
|
||
File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
|
||
for obj in stream:
|
||
File "/home/pi/.local/lib/python3.7/site-packages/morphocut/stream.py", line 68, in transform_stream
|
||
for obj in progress:
|
||
File "/home/pi/.local/lib/python3.7/site-packages/tqdm/std.py", line 1104, in __iter__
|
||
for obj in iterable:
|
||
File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
|
||
for obj in stream:
|
||
File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 492, in transform_stream
|
||
result = self.transform(*parameters) # pylint: disable=no-member
|
||
File "/home/pi/.local/lib/python3.7/site-packages/morphocut/image.py", line 78, in transform
|
||
image, in_range=in_range, out_range=self.out_range
|
||
File "/home/pi/.local/lib/python3.7/site-packages/skimage/exposure/exposure.py", line 352, in rescale_intensity
|
||
image = (image - imin) / float(imax - imin)
|
||
MemoryError
|