planktoscope/morphocut/README.md at 78d82871768ded5bd977b424048b273b714c342b

2020-07-22 10:03:46 +02:00

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######################################################### Installation of MorphoCut development version: #########################################################

$ pip install -U git+https://github.com/morphocut/morphocut.git Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple Collecting git+https://github.com/morphocut/morphocut.git Cloning https://github.com/morphocut/morphocut.git to /tmp/pip-req-build-NnGYk4 Installing build dependencies ... error 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: Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple, https://www.piwheels.org/simple Collecting setuptools Downloading https://www.piwheels.org/simple/setuptools/setuptools-45.0.0-py2.py3-none-any.whl (583kB) setuptools requires Python '>=3.5' but the running Python is 2.7.16

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

######################################################### Installation of MorphoCut packaged on PyPI via pip #########################################################

$ pip install morphocut Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple Collecting morphocut Could not find a version that satisfies the requirement morphocut (from versions: ) No matching distribution found for morphocut

######################################################### Installation of MorphoCut packaged on PyPI via pip3 #########################################################

$ pip3 install morphocut Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple Collecting morphocut Downloading 1addaf8672/morphocut-0.1.1-py3-none-any.whl Collecting scikit-image>=0.16.0 (from morphocut) Downloading https://www.piwheels.org/simple/scikit-image/scikit_image-0.16.2-cp37-cp37m-linux_armv7l.whl (39.7MB) 100% |████████████████████████████████| 39.7MB 10kB/s Collecting tqdm (from morphocut) Downloading 7fc20feac7/tqdm-4.41.1-py2.py3-none-any.whl (56kB) 100% |████████████████████████████████| 61kB 1.6MB/s Collecting scipy (from morphocut) Downloading e2eb3e3f90/scipy-1.4.1.tar.gz (24.6MB) 100% |████████████████████████████████| 24.6MB 17kB/s Installing build dependencies ... done Requirement already satisfied: numpy in /usr/lib/python3/dist-packages (from morphocut) (1.16.2) Collecting pandas (from morphocut) Downloading https://www.piwheels.org/simple/pandas/pandas-0.25.3-cp37-cp37m-linux_armv7l.whl (33.1MB) 100% |████████████████████████████████| 33.1MB 12kB/s Collecting PyWavelets>=0.4.0 (from scikit-image>=0.16.0->morphocut) Downloading https://www.piwheels.org/simple/pywavelets/PyWavelets-1.1.1-cp37-cp37m-linux_armv7l.whl (6.1MB) 100% |████████████████████████████████| 6.1MB 67kB/s Collecting networkx>=2.0 (from scikit-image>=0.16.0->morphocut) Downloading dd6a8e8594/networkx-2.4-py3-none-any.whl (1.6MB) 100% |████████████████████████████████| 1.6MB 255kB/s Requirement already satisfied: pillow>=4.3.0 in /usr/lib/python3/dist-packages (from scikit-image>=0.16.0->morphocut) (5.4.1) Collecting imageio>=2.3.0 (from scikit-image>=0.16.0->morphocut) Downloading f7f985018f/imageio-2.6.1-py3-none-any.whl (3.3MB) 100% |████████████████████████████████| 3.3MB 123kB/s Collecting python-dateutil>=2.6.1 (from pandas->morphocut) Downloading d60450c3dd/python_dateutil-2.8.1-py2.py3-none-any.whl (227kB) 100% |████████████████████████████████| 235kB 822kB/s Collecting pytz>=2017.2 (from pandas->morphocut) Downloading f0b53f8806/pytz-2019.3-py2.py3-none-any.whl (509kB) 100% |████████████████████████████████| 512kB 660kB/s Collecting decorator>=4.3.0 (from networkx>=2.0->scikit-image>=0.16.0->morphocut) Downloading f329cfdc75/decorator-4.4.1-py2.py3-none-any.whl Requirement already satisfied: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil>=2.6.1->pandas->morphocut) (1.12.0) Building wheels for collected packages: scipy Running setup.py bdist_wheel for scipy ... error 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: Traceback (most recent call last): File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/core/init.py", line 16, in from . import multiarray ImportError: libf77blas.so.3: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "", line 1, in File "/tmp/pip-install-vrivsnzz/scipy/setup.py", line 540, in setup_package() File "/tmp/pip-install-vrivsnzz/scipy/setup.py", line 516, in setup_package from numpy.distutils.core import setup File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/init.py", line 142, in from . import add_newdocs File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/add_newdocs.py", line 13, in from numpy.lib import add_newdoc File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/lib/init.py", line 8, in from .type_check import * File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/lib/type_check.py", line 11, in import numpy.core.numeric as _nx File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/core/init.py", line 26, in raise ImportError(msg) ImportError: Importing the multiarray numpy extension module failed. Most likely you are trying to import a failed build of numpy. If you're working with a numpy git repo, try git clean -xdf (removes all files not under version control). Otherwise reinstall numpy.

Original error was: libf77blas.so.3: cannot open shared object file: No such file or directory

Failed building wheel for scipy Running setup.py clean for scipy 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:

setup.py clean is not supported, use one of the following instead:

- `git clean -xdf` (cleans all files)
- `git clean -Xdf` (cleans all versioned files, doesn't touch
                    files that aren't checked into the git repo)

Add --force to your command to use it anyway if you must (unsupported).

Failed cleaning build dir for scipy Failed to build scipy Installing collected packages: PyWavelets, decorator, networkx, imageio, scikit-image, tqdm, scipy, python-dateutil, pytz, pandas, morphocut Running setup.py install for scipy ... error 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=:

Note: if you need reliable uninstall behavior, then install
with pip instead of using `setup.py install`:

  - `pip install .`       (from a git repo or downloaded source
                           release)
  - `pip install scipy`   (last SciPy release on PyPI)


Traceback (most recent call last):
  File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/core/__init__.py", line 16, in <module>
    from . import multiarray
ImportError: libf77blas.so.3: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/tmp/pip-install-vrivsnzz/scipy/setup.py", line 540, in <module>
    setup_package()
  File "/tmp/pip-install-vrivsnzz/scipy/setup.py", line 516, in setup_package
    from numpy.distutils.core import setup
  File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/__init__.py", line 142, in <module>
    from . import add_newdocs
  File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/add_newdocs.py", line 13, in <module>
    from numpy.lib import add_newdoc
  File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/lib/__init__.py", line 8, in <module>
    from .type_check import *
  File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/lib/type_check.py", line 11, in <module>
    import numpy.core.numeric as _nx
  File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/core/__init__.py", line 26, in <module>
    raise ImportError(msg)
ImportError:
Importing the multiarray numpy extension module failed.  Most
likely you are trying to import a failed build of numpy.
If you're working with a numpy git repo, try `git clean -xdf` (removes all
files not under version control).  Otherwise reinstall numpy.

Original error was: libf77blas.so.3: cannot open shared object file: No such file or directory


----------------------------------------

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/ ######################################################### Installation of Scipy using sudo apt-get #########################################################

$ sudo apt-get install python3-scipy Lecture des listes de paquets... Fait Construction de l'arbre des dépendances
Lecture des informations d'état... Fait Les paquets supplémentaires suivants seront installés : python3-decorator Paquets suggérés : python-scipy-doc Les NOUVEAUX paquets suivants seront installés : python3-decorator python3-scipy 0 mis à jour, 2 nouvellement installés, 0 à enlever et 41 non mis à jour. Il est nécessaire de prendre 8 925 ko dans les archives. Après cette opération, 38,0 Mo d'espace disque supplémentaires seront utilisés. Souhaitez-vous continuer ? [O/n] o 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] 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] 8 925 ko réceptionnés en 3s (2 561 ko/s)
Sélection du paquet python3-decorator précédemment désélectionné. (Lecture de la base de données... 99960 fichiers et répertoires déjà installés.) Préparation du dépaquetage de .../python3-decorator_4.3.0-1.1_all.deb ... Dépaquetage de python3-decorator (4.3.0-1.1) ... Sélection du paquet python3-scipy précédemment désélectionné. Préparation du dépaquetage de .../python3-scipy_1.1.0-7_armhf.deb ... Dépaquetage de python3-scipy (1.1.0-7) ... Paramétrage de python3-decorator (4.3.0-1.1) ... Paramétrage de python3-scipy (1.1.0-7) ...

######################################################### Installation of MorphoCut packaged on PyPI via pip3 using sudo #########################################################

$ sudo pip3 install morphocut Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple Collecting morphocut Using cached 1addaf8672/morphocut-0.1.1-py3-none-any.whl Requirement already satisfied: scikit-image>=0.16.0 in /usr/local/lib/python3.7/dist-packages (from morphocut) (0.16.2) Requirement already satisfied: numpy in /usr/lib/python3/dist-packages (from morphocut) (1.16.2) Requirement already satisfied: tqdm in /usr/local/lib/python3.7/dist-packages (from morphocut) (4.41.1) Requirement already satisfied: pandas in /usr/local/lib/python3.7/dist-packages (from morphocut) (0.25.3) Requirement already satisfied: scipy in /usr/lib/python3/dist-packages (from morphocut) (1.1.0) 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) 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) Requirement already satisfied: networkx>=2.0 in /usr/local/lib/python3.7/dist-packages (from scikit-image>=0.16.0->morphocut) (2.4) Requirement already satisfied: pillow>=4.3.0 in /usr/lib/python3/dist-packages (from scikit-image>=0.16.0->morphocut) (5.4.1) Requirement already satisfied: python-dateutil>=2.6.1 in /usr/local/lib/python3.7/dist-packages (from pandas->morphocut) (2.8.1) Requirement already satisfied: pytz>=2017.2 in /usr/local/lib/python3.7/dist-packages (from pandas->morphocut) (2019.3) 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) Requirement already satisfied: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil>=2.6.1->pandas->morphocut) (1.12.0) Installing collected packages: morphocut Successfully installed morphocut-0.1.1

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