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Hi, I has had this problem when run the test (python setup.py test) #1

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sebacornnejo opened this issue Jan 6, 2023 · 1 comment

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@sebacornnejo
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running test
running egg_info
writing src/lagrangian.egg-info/PKG-INFO
writing dependency_links to src/lagrangian.egg-info/dependency_links.txt
writing entry points to src/lagrangian.egg-info/entry_points.txt
writing top-level names to src/lagrangian.egg-info/top_level.txt
reading manifest file 'src/lagrangian.egg-info/SOURCES.txt'
adding license file 'COPYING'
writing manifest file 'src/lagrangian.egg-info/SOURCES.txt'
running build_ext
cmake /home/sebacornnejo/Software/aviso-lagrangian-main -DCMAKE_BUILD_TYPE=Release -DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/home/sebacornnejo/Software/aviso-lagrangian-main/build/lib.linux-x86_64-3.7/lagrangian -DPYTHON_EXECUTABLE=/home/sebacornnejo/anaconda3/envs/env_FSLE/bin/python -DBoost_NO_SYSTEM_PATHS=TRUE -DBoost_NO_BOOST_CMAKE=TRUE -DBOOST_ROOT=/home/sebacornnejo/anaconda3/envs/env_FSLE -DUDUNITS2_ROOT=/home/sebacornnejo/anaconda3/envs/env_FSLE -DNETCDF_DIR=/home/sebacornnejo/anaconda3/envs/env_FSLE -DCMAKE_PREFIX_PATH=/home/sebacornnejo/anaconda3/envs/env_FSLE -DCMAKE_BUILD_TYPE=Release
Re-run cmake no build system arguments
-- pybind11 v2.11.0 dev1
-- Configuring done
-- Generating done
-- Build files have been written to: /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37
cmake --build . --target core --config Release -- -j12
/home/sebacornnejo/anaconda3/envs/env_FSLE/bin/cmake -S/home/sebacornnejo/Software/aviso-lagrangian-main -B/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37 --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/gmake -f CMakeFiles/Makefile2 core
gmake[1]: se entra en el directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37'
/home/sebacornnejo/anaconda3/envs/env_FSLE/bin/cmake -S/home/sebacornnejo/Software/aviso-lagrangian-main -B/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37 --check-build-system CMakeFiles/Makefile.cmake 0
/home/sebacornnejo/anaconda3/envs/env_FSLE/bin/cmake -E cmake_progress_start /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles 54
/usr/bin/gmake -f CMakeFiles/Makefile2 CMakeFiles/core.dir/all
gmake[2]: se entra en el directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37'
/usr/bin/gmake -f CMakeFiles/lagrangian.dir/build.make CMakeFiles/lagrangian.dir/depend
/usr/bin/gmake -f CMakeFiles/ncxx4.dir/build.make CMakeFiles/ncxx4.dir/depend
gmake[3]: se entra en el directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37'
cd /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37 && /home/sebacornnejo/anaconda3/envs/env_FSLE/bin/cmake -E cmake_depends "Unix Makefiles" /home/sebacornnejo/Software/aviso-lagrangian-main /home/sebacornnejo/Software/aviso-lagrangian-main /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37 /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37 /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles/lagrangian.dir/DependInfo.cmake --color=
gmake[3]: se entra en el directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37'
cd /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37 && /home/sebacornnejo/anaconda3/envs/env_FSLE/bin/cmake -E cmake_depends "Unix Makefiles" /home/sebacornnejo/Software/aviso-lagrangian-main /home/sebacornnejo/Software/aviso-lagrangian-main /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37 /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37 /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles/ncxx4.dir/DependInfo.cmake --color=
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Dependencies file "CMakeFiles/ncxx4.dir/third_party/netcdf-cxx4/cxx4/ncAtt.cpp.o.d" is newer than depends file "/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles/ncxx4.dir/compiler_depend.internal".
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Dependencies file "CMakeFiles/lagrangian.dir/src/lib/netcdf/scale_missing.cpp.o.d" is newer than depends file "/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles/lagrangian.dir/compiler_depend.internal".
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Dependencies file "CMakeFiles/lagrangian.dir/src/lib/parameter.cpp.o.d" is newer than depends file "/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles/lagrangian.dir/compiler_depend.internal".
Dependencies file "CMakeFiles/lagrangian.dir/src/lib/reader/netcdf.cpp.o.d" is newer than depends file "/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles/lagrangian.dir/compiler_depend.internal".
Dependencies file "CMakeFiles/lagrangian.dir/src/lib/time_serie.cpp.o.d" is newer than depends file "/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles/lagrangian.dir/compiler_depend.internal".
Dependencies file "CMakeFiles/lagrangian.dir/src/lib/trace.cpp.o.d" is newer than depends file "/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles/lagrangian.dir/compiler_depend.internal".
Dependencies file "CMakeFiles/lagrangian.dir/src/lib/units.cpp.o.d" is newer than depends file "/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles/lagrangian.dir/compiler_depend.internal".
Consolidate compiler generated dependencies of target ncxx4
gmake[3]: se sale del directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37'
/usr/bin/gmake -f CMakeFiles/ncxx4.dir/build.make CMakeFiles/ncxx4.dir/build
gmake[3]: se entra en el directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37'
gmake[3]: No se hace nada para 'CMakeFiles/ncxx4.dir/build'.
gmake[3]: se sale del directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37'
[ 50%] Built target ncxx4
Consolidate compiler generated dependencies of target lagrangian
gmake[3]: se sale del directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37'
/usr/bin/gmake -f CMakeFiles/lagrangian.dir/build.make CMakeFiles/lagrangian.dir/build
gmake[3]: se entra en el directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37'
gmake[3]: No se hace nada para 'CMakeFiles/lagrangian.dir/build'.
gmake[3]: se sale del directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37'
[ 83%] Built target lagrangian
/usr/bin/gmake -f CMakeFiles/core.dir/build.make CMakeFiles/core.dir/depend
gmake[3]: se entra en el directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37'
cd /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37 && /home/sebacornnejo/anaconda3/envs/env_FSLE/bin/cmake -E cmake_depends "Unix Makefiles" /home/sebacornnejo/Software/aviso-lagrangian-main /home/sebacornnejo/Software/aviso-lagrangian-main /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37 /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37 /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles/core.dir/DependInfo.cmake --color=
Dependencies file "CMakeFiles/core.dir/src/core/axis.cpp.o.d" is newer than depends file "/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles/core.dir/compiler_depend.internal".
Dependencies file "CMakeFiles/core.dir/src/core/datetime.cpp.o.d" is newer than depends file "/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles/core.dir/compiler_depend.internal".
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Consolidate compiler generated dependencies of target core
gmake[3]: se sale del directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37'
/usr/bin/gmake -f CMakeFiles/core.dir/build.make CMakeFiles/core.dir/build
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gmake[3]: No se hace nada para 'CMakeFiles/core.dir/build'.
gmake[3]: se sale del directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37'
[100%] Built target core
gmake[2]: se sale del directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37'
/home/sebacornnejo/anaconda3/envs/env_FSLE/bin/cmake -E cmake_progress_start /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles 0
gmake[1]: se sale del directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37'
============================= test session starts ==============================
platform linux -- Python 3.7.12, pytest-6.2.3, py-1.10.0, pluggy-0.13.1
rootdir: /home/sebacornnejo/Software/aviso-lagrangian-main
collected 2 items / 5 errors

==================================== ERRORS ====================================
___________________ ERROR collecting tests/test_datetime.py ____________________
ImportError while importing test module '/home/sebacornnejo/Software/aviso-lagrangian-main/tests/test_datetime.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../anaconda3/envs/env_FSLE/lib/python3.7/importlib/init.py:127: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests/test_datetime.py:17: in
import lagrangian
src/lagrangian/init.py:15: in
from .core import (
E ImportError: dynamic module does not define module export function (PyInit_core)
_____________________ ERROR collecting tests/test_field.py _____________________
ImportError while importing test module '/home/sebacornnejo/Software/aviso-lagrangian-main/tests/test_field.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../anaconda3/envs/env_FSLE/lib/python3.7/importlib/init.py:127: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests/test_field.py:18: in
import lagrangian
src/lagrangian/init.py:15: in
from .core import (
E ImportError: dynamic module does not define module export function (PyInit_core)
__________________ ERROR collecting tests/test_integration.py __________________
ImportError while importing test module '/home/sebacornnejo/Software/aviso-lagrangian-main/tests/test_integration.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../anaconda3/envs/env_FSLE/lib/python3.7/importlib/init.py:127: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests/test_integration.py:17: in
import lagrangian
src/lagrangian/init.py:15: in
from .core import (
E ImportError: dynamic module does not define module export function (PyInit_core)
______________________ ERROR collecting tests/test_map.py ______________________
ImportError while importing test module '/home/sebacornnejo/Software/aviso-lagrangian-main/tests/test_map.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../anaconda3/envs/env_FSLE/lib/python3.7/importlib/init.py:127: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests/test_map.py:18: in
import lagrangian
src/lagrangian/init.py:15: in
from .core import (
E ImportError: dynamic module does not define module export function (PyInit_core)
____________________ ERROR collecting tests/test_reader.py _____________________
ImportError while importing test module '/home/sebacornnejo/Software/aviso-lagrangian-main/tests/test_reader.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../anaconda3/envs/env_FSLE/lib/python3.7/importlib/init.py:127: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests/test_reader.py:19: in
import lagrangian
src/lagrangian/init.py:15: in
from .core import (
E ImportError: dynamic module does not define module export function (PyInit_core)
=========================== short test summary info ============================
ERROR tests/test_datetime.py
ERROR tests/test_field.py
ERROR tests/test_integration.py
ERROR tests/test_map.py
ERROR tests/test_reader.py
!!!!!!!!!!!!!!!!!!! Interrupted: 5 errors during collection !!!!!!!!!!!!!!!!!!!!
============================== 5 errors in 0.46s ===============================

Regards!!!

@albertotb
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I've also had this problem when building from source. Installing from conda is an alternative that seems to work:

conda install -c fbriol lagrangian

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