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pip3 install labours fails on Linux
I'm on KDE Neon (Ubuntu 20.04LTS based).
pip3 install labours fails with the message below (sorry, it's long):
`Building wheels for collected packages: scipy Building wheel for scipy (setup.py) ... error ERROR: Command errored out with exit status 1: command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ow2zb3l9/scipy/setup.py'"'"'; file='"'"'/tmp/pip-install-ow2zb3l9/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-d3ia2upg
cwd: /tmp/pip-install-ow2zb3l9/scipy/
Complete output (98 lines):
/tmp/pip-install-ow2zb3l9/scipy/setup.py:114: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
import imp
Running from scipy source directory.
lapack_opt_info:
lapack_mkl_info:
customize UnixCCompiler
libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLEopenblas_lapack_info:
libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLEopenblas_clapack_info:
libraries openblas,lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLEflame_info:
libraries flame not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLEatlas_3_10_threads_info:
Setting PTATLAS=ATLAS
libraries lapack_atlas not found in /usr/local/lib
libraries tatlas,tatlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib
libraries tatlas,tatlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
libraries tatlas,tatlas not found in /usr/lib/x86_64-linux-gnu
<class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
NOT AVAILABLEatlas_3_10_info:
libraries lapack_atlas not found in /usr/local/lib
libraries satlas,satlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib
libraries satlas,satlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
libraries satlas,satlas not found in /usr/lib/x86_64-linux-gnu
<class 'numpy.distutils.system_info.atlas_3_10_info'>
NOT AVAILABLEatlas_threads_info:
Setting PTATLAS=ATLAS
libraries lapack_atlas not found in /usr/local/lib
libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib
libraries ptf77blas,ptcblas,atlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
libraries ptf77blas,ptcblas,atlas not found in /usr/lib/x86_64-linux-gnu
<class 'numpy.distutils.system_info.atlas_threads_info'>
NOT AVAILABLEatlas_info:
libraries lapack_atlas not found in /usr/local/lib
libraries f77blas,cblas,atlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib
libraries f77blas,cblas,atlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
libraries f77blas,cblas,atlas not found in /usr/lib/x86_64-linux-gnu
<class 'numpy.distutils.system_info.atlas_info'>
NOT AVAILABLEaccelerate_info:
NOT AVAILABLElapack_info:
libraries lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE/usr/local/lib/python3.8/dist-packages/numpy/distutils/system_info.py:1748: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
return getattr(self, 'calc_info{}'.format(name))()
lapack_src_info:
NOT AVAILABLE/usr/local/lib/python3.8/dist-packages/numpy/distutils/system_info.py:1748: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
return getattr(self, 'calc_info{}'.format(name))()
NOT AVAILABLETraceback (most recent call last):
File "", line 1, in
File "/tmp/pip-install-ow2zb3l9/scipy/setup.py", line 492, in
setup_package()
File "/tmp/pip-install-ow2zb3l9/scipy/setup.py", line 488, in setup_package
setup(**metadata)
File "/usr/local/lib/python3.8/dist-packages/numpy/distutils/core.py", line 135, in setup
config = configuration()
File "/tmp/pip-install-ow2zb3l9/scipy/setup.py", line 395, in configuration
raise NotFoundError(msg)
numpy.distutils.system_info.NotFoundError: No lapack/blas resources found.ERROR: Failed building wheel for scipy Running setup.py clean for scipy ERROR: Command errored out with exit status 1: command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ow2zb3l9/scipy/setup.py'"'"'; file='"'"'/tmp/pip-install-ow2zb3l9/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
cwd: /tmp/pip-install-ow2zb3l9/scipy
Complete output (11 lines):
/tmp/pip-install-ow2zb3l9/scipy/setup.py:114: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
import imp
setup.py cleanis 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
--forceto your command to use it anyway if you must (unsupported).
ERROR: Failed cleaning build dir for scipy Failed to build scipy Installing collected packages: joblib, cython, scipy, scikit-learn, hdbscan, patsy, future, autograd, autograd-gamma, lifelines, labours Attempting uninstall: scipy Found existing installation: scipy 1.5.2 Uninstalling scipy-1.5.2: Successfully uninstalled scipy-1.5.2 Running setup.py install for scipy ... error ERROR: Command errored out with exit status 1: command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ow2zb3l9/scipy/setup.py'"'"'; file='"'"'/tmp/pip-install-ow2zb3l9/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-7zy4tbys/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/nando/.local/include/python3.8/scipy
cwd: /tmp/pip-install-ow2zb3l9/scipy/
Complete output (107 lines):
/tmp/pip-install-ow2zb3l9/scipy/setup.py:114: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
import impNote: 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) Running from scipy source directory. lapack_opt_info: lapack_mkl_info: customize UnixCCompiler libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu'] NOT AVAILABLE openblas_lapack_info: libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu'] NOT AVAILABLE openblas_clapack_info: libraries openblas,lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu'] NOT AVAILABLE flame_info: libraries flame not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu'] NOT AVAILABLE atlas_3_10_threads_info: Setting PTATLAS=ATLAS libraries lapack_atlas not found in /usr/local/lib libraries tatlas,tatlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/lib libraries tatlas,tatlas not found in /usr/lib libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu libraries tatlas,tatlas not found in /usr/lib/x86_64-linux-gnu <class 'numpy.distutils.system_info.atlas_3_10_threads_info'> NOT AVAILABLE atlas_3_10_info: libraries lapack_atlas not found in /usr/local/lib libraries satlas,satlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/lib libraries satlas,satlas not found in /usr/lib libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu libraries satlas,satlas not found in /usr/lib/x86_64-linux-gnu <class 'numpy.distutils.system_info.atlas_3_10_info'> NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS libraries lapack_atlas not found in /usr/local/lib libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/lib libraries ptf77blas,ptcblas,atlas not found in /usr/lib libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu libraries ptf77blas,ptcblas,atlas not found in /usr/lib/x86_64-linux-gnu <class 'numpy.distutils.system_info.atlas_threads_info'> NOT AVAILABLE atlas_info: libraries lapack_atlas not found in /usr/local/lib libraries f77blas,cblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/lib libraries f77blas,cblas,atlas not found in /usr/lib libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu libraries f77blas,cblas,atlas not found in /usr/lib/x86_64-linux-gnu <class 'numpy.distutils.system_info.atlas_info'> NOT AVAILABLE accelerate_info: NOT AVAILABLE lapack_info: libraries lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu'] NOT AVAILABLE /usr/local/lib/python3.8/dist-packages/numpy/distutils/system_info.py:1748: UserWarning: Lapack (http://www.netlib.org/lapack/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [lapack]) or by setting the LAPACK environment variable. return getattr(self, '_calc_info_{}'.format(name))() lapack_src_info: NOT AVAILABLE /usr/local/lib/python3.8/dist-packages/numpy/distutils/system_info.py:1748: UserWarning: Lapack (http://www.netlib.org/lapack/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [lapack_src]) or by setting the LAPACK_SRC environment variable. return getattr(self, '_calc_info_{}'.format(name))() NOT AVAILABLE Traceback (most recent call last): File "<string>", line 1, in <module> File "/tmp/pip-install-ow2zb3l9/scipy/setup.py", line 492, in <module> setup_package() File "/tmp/pip-install-ow2zb3l9/scipy/setup.py", line 488, in setup_package setup(**metadata) File "/usr/local/lib/python3.8/dist-packages/numpy/distutils/core.py", line 135, in setup config = configuration() File "/tmp/pip-install-ow2zb3l9/scipy/setup.py", line 395, in configuration raise NotFoundError(msg) numpy.distutils.system_info.NotFoundError: No lapack/blas resources found. ----------------------------------------Rolling back uninstall of scipy Moving to /home/nando/.local/lib/python3.8/site-packages/scipy-1.5.2.dist-info/ from /home/nando/.local/lib/python3.8/site-packages/~cipy-1.5.2.dist-info Moving to /home/nando/.local/lib/python3.8/site-packages/scipy.libs/ from /home/nando/.local/lib/python3.8/site-packages/~cipy.libs Moving to /home/nando/.local/lib/python3.8/site-packages/scipy/ from /home/nando/.local/lib/python3.8/site-packages/~cipy ERROR: Command errored out with exit status 1: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ow2zb3l9/scipy/setup.py'"'"'; file='"'"'/tmp/pip-install-ow2zb3l9/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-7zy4tbys/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/nando/.local/include/python3.8/scipy Check the logs for full command output.
Even pip3 install scipy fails.
I solved installing these dependencies:
sudo apt-get install libatlas-base-dev gfortran
here is osx catalina output
% pip3 install labours
Collecting labours
Using cached labours-10.7.2-py3-none-any.whl (69 kB)
Collecting fastdtw<2.0,>=0.3.2
Using cached fastdtw-0.3.4.tar.gz (133 kB)
Requirement already satisfied: protobuf<4.0,>=3.5.0 in /usr/local/lib/python3.9/site-packages (from labours) (3.14.0)
Collecting munch<3.0,>=2.0
Using cached munch-2.5.0-py2.py3-none-any.whl (10 kB)
Collecting matplotlib<4.0,>=2.0
Using cached matplotlib-3.3.3-cp39-cp39-macosx_10_9_x86_64.whl (8.5 MB)
Collecting lifelines<2.0,>=0.20.0
Using cached lifelines-0.25.6-py3-none-any.whl (347 kB)
Collecting PyYAML<6.0,>=3.0
Using cached PyYAML-5.3.1.tar.gz (269 kB)
Collecting numpy<2.0,>=1.12.0
Using cached numpy-1.19.4-cp39-cp39-macosx_10_9_x86_64.whl (15.4 MB)
Collecting hdbscan<2.0,>=0.8.0
Using cached hdbscan-0.8.26.tar.gz (4.7 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing wheel metadata ... done
Collecting scipy<1.2.2,>=0.19.0
Using cached scipy-1.2.1.tar.gz (23.1 MB)
Collecting seriate<2.0,>=1.1.2
Using cached seriate-1.1.2-py3-none-any.whl (8.5 kB)
Collecting pandas<1.0,>=0.20.0
Using cached pandas-0.25.3.tar.gz (12.6 MB)
Collecting tqdm<5.0,>=4.3
Using cached tqdm-4.53.0-py2.py3-none-any.whl (70 kB)
Collecting python-dateutil<3.0,>=2.6.0
Using cached python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
Requirement already satisfied: six>=1.9 in /usr/local/lib/python3.9/site-packages (from protobuf<4.0,>=3.5.0->labours) (1.15.0)
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3
Using cached pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
Collecting cycler>=0.10
Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting kiwisolver>=1.0.1
Using cached kiwisolver-1.3.1-cp39-cp39-macosx_10_9_x86_64.whl (61 kB)
Collecting pillow>=6.2.0
Using cached Pillow-8.0.1-cp39-cp39-macosx_10_10_x86_64.whl (2.2 MB)
Collecting autograd>=1.3
Using cached autograd-1.3.tar.gz (38 kB)
Collecting autograd-gamma>=0.3
Using cached autograd-gamma-0.5.0.tar.gz (4.0 kB)
Collecting patsy>=0.5.0
Using cached patsy-0.5.1-py2.py3-none-any.whl (231 kB)
Collecting scikit-learn>=0.17
Using cached scikit-learn-0.23.2.tar.gz (7.2 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing wheel metadata ... done
Collecting joblib
Using cached joblib-0.17.0-py3-none-any.whl (301 kB)
Collecting cython>=0.27
Using cached Cython-0.29.21-py2.py3-none-any.whl (974 kB)
ERROR: Could not find a version that satisfies the requirement ortools<8,>=6.7.4973 (from seriate<2.0,>=1.1.2->labours) (from versions: 8.0.8283)
ERROR: No matching distribution found for ortools<8,>=6.7.4973 (from seriate<2.0,>=1.1.2->labours)
Same problem, sudo apt-get install libatlas-base-dev gfortran did not solve it.
On Ubuntu 20.04 installing the dependencies below works:
sudo apt-get install gfortran libopenblas-dev liblapack-dev
From https://github.com/scipy/scipy/issues/9005#issuecomment-623528512
Since Pip version of numpy depends on OpenBLAS, we must install OpenBLAS to build NumPy from scratch. This can be skipped using a wheel of numpy package. Details here: https://numpy.org/install/
The NumPy wheels on PyPI, which is what pip installs, are built with OpenBLAS. The OpenBLAS libraries are included in the wheel.
So first run pip3 install wheel and then install labours. I can install labours by this method using Python 3.7.
Hi, Just tried to install labours on linux and also fails, using python 3.10
