Jetson tx2 running Jetpack 4.2 pip install scikit_learn install fails

Manodieatra · July 16, 2019, 2:59pm

I am running into an issue installing when using the following:
sudo pip install scikit_learn

I have researched this issue and it has come up before. I have tried the fixes for those including those in this post:

gfortran --version
returns:
GNU Fortran (Ubuntu/Linaro 7.4.0-1ubuntu1~18.04.1) 7.4.0

Any help would be greatly appreciated.

sudo pip install scikit-learn
Traceback:

ERROR: Complete output from command /usr/bin/python3 -u -c ‘import setuptools, tokenize;file=’“'”‘/tmp/pip-install-v81_wsnx/scikit-learn/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-u5y654b0 --python-tag cp36:
ERROR: Partial import of sklearn during the build process.
blas_opt_info:
blas_mkl_info:
customize UnixCCompiler
libraries mkl_rt not found in [‘/usr/local/lib’, ‘/usr/lib’, ‘/usr/lib/aarch64-linux-gnu’]
NOT AVAILABLE

blis_info:
customize UnixCCompiler
libraries blis not found in [‘/usr/local/lib’, ‘/usr/lib’, ‘/usr/lib/aarch64-linux-gnu’]
NOT AVAILABLE

openblas_info:
customize UnixCCompiler
customize UnixCCompiler
libraries openblas not found in [‘/usr/local/lib’, ‘/usr/lib’, ‘/usr/lib/aarch64-linux-gnu’]
NOT AVAILABLE

atlas_3_10_blas_threads_info:
Setting PTATLAS=ATLAS
customize UnixCCompiler
libraries tatlas not found in [‘/usr/local/lib’, ‘/usr/lib’, ‘/usr/lib/aarch64-linux-gnu/atlas’, ‘/usr/lib/aarch64-linux-gnu’]
NOT AVAILABLE

atlas_3_10_blas_info:
customize UnixCCompiler
libraries satlas not found in [‘/usr/local/lib’, ‘/usr/lib’, ‘/usr/lib/aarch64-linux-gnu/atlas’, ‘/usr/lib/aarch64-linux-gnu’]
NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
customize UnixCCompiler
libraries ptf77blas,ptcblas,atlas not found in [‘/usr/local/lib’, ‘/usr/lib’, ‘/usr/lib/aarch64-linux-gnu/atlas’, ‘/usr/lib/aarch64-linux-gnu’]
NOT AVAILABLE

atlas_blas_info:
customize UnixCCompiler
get_default_fcompiler: matching types: ‘[‘gnu95’, ‘intel’, ‘lahey’, ‘pg’, ‘absoft’, ‘nag’, ‘vast’, ‘compaq’, ‘intele’, ‘intelem’, ‘gnu’, ‘g95’, ‘pathf95’, ‘nagfor’]’
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using config
compiling ‘_configtest.c’:

/* This file is generated from numpy/distutils/system_info.py */
void ATL_buildinfo(void);
int main(void) {
ATL_buildinfo();
return 0;
}

C compiler: aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

compile options: ‘-c’
aarch64-linux-gnu-gcc: _configtest.c
aarch64-linux-gnu-gcc -pthread _configtest.o -lf77blas -lcblas -latlas -o _configtest
customize UnixCCompiler
customize UnixCCompiler
FOUND:
language = c
define_macros = [(‘HAVE_CBLAS’, None), (‘NO_ATLAS_INFO’, -1)]
libraries = [‘f77blas’, ‘cblas’, ‘atlas’, ‘f77blas’, ‘cblas’]
library_dirs = [‘/usr/lib/aarch64-linux-gnu’]

accelerate_info:
NOT AVAILABLE

FOUND:
  language = c
  define_macros = [('HAVE_CBLAS', None), ('NO_ATLAS_INFO', -1)]
  libraries = ['f77blas', 'cblas', 'atlas', 'f77blas', 'cblas']
  library_dirs = ['/usr/lib/aarch64-linux-gnu']

Traceback (most recent call last):
File “”, line 1, in
File “/tmp/pip-install-v81_wsnx/scikit-learn/setup.py”, line 290, in
setup_package()
File “/tmp/pip-install-v81_wsnx/scikit-learn/setup.py”, line 286, in setup_package
setup(**metadata)
File “/usr/local/lib/python3.6/dist-packages/numpy/distutils/core.py”, line 137, in setup
config = configuration()
File “/tmp/pip-install-v81_wsnx/scikit-learn/setup.py”, line 174, in configuration
config.add_subpackage(‘sklearn’)
File “/usr/local/lib/python3.6/dist-packages/numpy/distutils/misc_util.py”, line 1036, in add_subpackage
caller_level = 2)
File “/usr/local/lib/python3.6/dist-packages/numpy/distutils/misc_util.py”, line 1005, in get_subpackage
caller_level = caller_level + 1)
File “/usr/local/lib/python3.6/dist-packages/numpy/distutils/misc_util.py”, line 942, in _get_configuration_from_setup_py
config = setup_module.configuration(args)
File “sklearn/setup.py”, line 66, in configuration
config.add_subpackage(‘utils’)
File “/usr/local/lib/python3.6/dist-packages/numpy/distutils/misc_util.py”, line 1036, in add_subpackage
caller_level = 2)
File “/usr/local/lib/python3.6/dist-packages/numpy/distutils/misc_util.py”, line 1005, in get_subpackage
caller_level = caller_level + 1)
File “/usr/local/lib/python3.6/dist-packages/numpy/distutils/misc_util.py”, line 942, in _get_configuration_from_setup_py
config = setup_module.configuration(args)
File “sklearn/utils/setup.py”, line 8, in configuration
from Cython import Tempita
ModuleNotFoundError: No module named ‘Cython’

ERROR: Failed building wheel for scikit-learn
Running setup.py clean for scikit-learn
Failed to build scikit-learn
Installing collected packages: scikit-learn
Running setup.py install for scikit-learn … error
ERROR: Complete output from command /usr/bin/python3 -u -c ‘import setuptools, tokenize;file=’“'”‘/tmp/pip-install-v81_wsnx/scikit-learn/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-cz3_v8cu/install-record.txt --single-version-externally-managed --compile:
ERROR: Partial import of sklearn during the build process.
blas_opt_info:
blas_mkl_info:
customize UnixCCompiler
libraries mkl_rt not found in [‘/usr/local/lib’, ‘/usr/lib’, ‘/usr/lib/aarch64-linux-gnu’]
NOT AVAILABLE

blis_info:
customize UnixCCompiler
  libraries blis not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/aarch64-linux-gnu']
  NOT AVAILABLE

openblas_info:
customize UnixCCompiler
customize UnixCCompiler
  libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/aarch64-linux-gnu']
  NOT AVAILABLE

atlas_3_10_blas_threads_info:
Setting PTATLAS=ATLAS
customize UnixCCompiler
  libraries tatlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/aarch64-linux-gnu/atlas', '/usr/lib/aarch64-linux-gnu']
  NOT AVAILABLE

atlas_3_10_blas_info:
customize UnixCCompiler
  libraries satlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/aarch64-linux-gnu/atlas', '/usr/lib/aarch64-linux-gnu']
  NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
customize UnixCCompiler
  libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/aarch64-linux-gnu/atlas', '/usr/lib/aarch64-linux-gnu']
  NOT AVAILABLE

atlas_blas_info:
customize UnixCCompiler
get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using config
compiling '_configtest.c':

/* This file is generated from numpy/distutils/system_info.py */
void ATL_buildinfo(void);
int main(void) {
  ATL_buildinfo();
  return 0;
}

C compiler: aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

compile options: '-c'
aarch64-linux-gnu-gcc: _configtest.c
aarch64-linux-gnu-gcc -pthread _configtest.o -lf77blas -lcblas -latlas -o _configtest
customize UnixCCompiler
customize UnixCCompiler
  FOUND:
    language = c
    define_macros = [('HAVE_CBLAS', None), ('NO_ATLAS_INFO', -1)]
    libraries = ['f77blas', 'cblas', 'atlas', 'f77blas', 'cblas']
    library_dirs = ['/usr/lib/aarch64-linux-gnu']

accelerate_info:
  NOT AVAILABLE

  FOUND:
    language = c
    define_macros = [('HAVE_CBLAS', None), ('NO_ATLAS_INFO', -1)]
    libraries = ['f77blas', 'cblas', 'atlas', 'f77blas', 'cblas']
    library_dirs = ['/usr/lib/aarch64-linux-gnu']

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/tmp/pip-install-v81_wsnx/scikit-learn/setup.py", line 290, in <module>
    setup_package()
  File "/tmp/pip-install-v81_wsnx/scikit-learn/setup.py", line 286, in setup_package
    setup(**metadata)
  File "/usr/local/lib/python3.6/dist-packages/numpy/distutils/core.py", line 137, in setup
    config = configuration()
  File "/tmp/pip-install-v81_wsnx/scikit-learn/setup.py", line 174, in configuration
    config.add_subpackage('sklearn')
  File "/usr/local/lib/python3.6/dist-packages/numpy/distutils/misc_util.py", line 1036, in add_subpackage
    caller_level = 2)
  File "/usr/local/lib/python3.6/dist-packages/numpy/distutils/misc_util.py", line 1005, in get_subpackage
    caller_level = caller_level + 1)
  File "/usr/local/lib/python3.6/dist-packages/numpy/distutils/misc_util.py", line 942, in _get_configuration_from_setup_py
    config = setup_module.configuration(*args)
  File "sklearn/setup.py", line 66, in configuration
    config.add_subpackage('utils')
  File "/usr/local/lib/python3.6/dist-packages/numpy/distutils/misc_util.py", line 1036, in add_subpackage
    caller_level = 2)
  File "/usr/local/lib/python3.6/dist-packages/numpy/distutils/misc_util.py", line 1005, in get_subpackage
    caller_level = caller_level + 1)
  File "/usr/local/lib/python3.6/dist-packages/numpy/distutils/misc_util.py", line 942, in _get_configuration_from_setup_py
    config = setup_module.configuration(*args)
  File "sklearn/utils/setup.py", line 8, in configuration
    from Cython import Tempita
ModuleNotFoundError: No module named 'Cython'
----------------------------------------

ERROR: Command “/usr/bin/python3 -u -c ‘import setuptools, tokenize;file=’”‘"’/tmp/pip-install-v81_wsnx/scikit-learn/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-cz3_v8cu/install-record.txt --single-version-externally-managed --compile” failed with error code 1 in /tmp/pip-install-v81_wsnx/scikit-learn/

ShaneCCC · July 19, 2019, 7:07am

Try “pip install Cython” first

Manodieatra · July 19, 2019, 5:44pm

That worked. Thabk you! Sorry for not catching such a simple mistake.

Topic		Replies	Views
pip install something but error with could not find a satisfies version Jetson TX2	8	30092	October 18, 2021
Cannot install scikit-learn on Jetson Nano Jetson Nano	2	1831	October 14, 2021
Errors during install sklearn. Jetson Nano	19	15109	October 14, 2021
How to install numpy 、scikit-image、scikit-learn on Jetson TX2? Jetson TX2	6	8820	October 18, 2021
cannot import scipy on jetson nano Jetson Nano	2	5514	October 18, 2021
Cannot install scipy Jetson Nano	18	7822	October 14, 2021
Scikit-image Jetson AGX Xavier pytorch	2	834	November 4, 2022
Install scikit-image Jetson TX2 jetson-inference	18	12068	October 18, 2021
Issue with installing SciPy on Jetson AGX Xavier Jetson AGX Xavier	9	3688	January 27, 2020
Keras and scipy throwing weird errors....while installing on jetson nano.. no links could help me. Jetson Nano	13	6426	October 14, 2021

Jetson tx2 running Jetpack 4.2 pip install scikit_learn install fails

Related Topics