Fail to build environment_cp both Day 4 and Day 5
Closed this issue · 1 comments
pwalczysko commented
On the Linux VM Day 4 cellprofiler env build fails with
/tmp/pip-build-env-2pbks69z/normal/lib/python3.8/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /tmp/pip-install-pmbnfk13/centrosome_2b604ded1ce8454f91ccb472bbdfc7a2/centrosome/_propagate.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
Error compiling Cython file:
------------------------------------------------------------
...
heap.ptrs[child][k] = new_elem[k]
heap.items += 1
# restore heap invariant, all parents <= children
while child>0:
parent = (child + 1) / 2 - 1 # __parent(i)
^
------------------------------------------------------------
centrosome/heap.pxd:148:31: Cannot assign type 'double' to 'unsigned int'
Compiling centrosome/_propagate.pyx because it changed.
Compiling centrosome/_cpmorphology2.pyx because it changed.
Compiling centrosome/_convex_hull.pyx because it changed.
Compiling centrosome/_fastemd.pyx because it changed.
Compiling centrosome/_filter.pyx because it changed.
Compiling centrosome/_lapjv.pyx because it changed.
[1/6] Cythonizing centrosome/_convex_hull.pyx
[2/6] Cythonizing centrosome/_cpmorphology2.pyx
[3/6] Cythonizing centrosome/_fastemd.pyx
[4/6] Cythonizing centrosome/_filter.pyx
[5/6] Cythonizing centrosome/_lapjv.pyx
[6/6] Cythonizing centrosome/_propagate.pyx
Traceback (most recent call last):
File "/home/training/miniconda3/envs/imaging_course_cp_day4_2024/lib/python3.8/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/home/training/miniconda3/envs/imaging_course_cp_day4_2024/lib/python3.8/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/home/training/miniconda3/envs/imaging_course_cp_day4_2024/lib/python3.8/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 149, in prepare_metadata_for_build_wheel
return hook(metadata_directory, config_settings)
File "/tmp/pip-build-env-2pbks69z/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 366, in prepare_metadata_for_build_wheel
self.run_setup()
File "/tmp/pip-build-env-2pbks69z/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 487, in run_setup
super().run_setup(setup_script=setup_script)
File "/tmp/pip-build-env-2pbks69z/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 311, in run_setup
exec(code, locals())
File "<string>", line 89, in <module>
File "/tmp/pip-build-env-2pbks69z/normal/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 1154, in cythonize
cythonize_one(*args)
File "/tmp/pip-build-env-2pbks69z/normal/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 1321, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: centrosome/_propagate.pyx
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
failed
CondaEnvException: Pip failed
On the Linux VM Day 5 Cellprofiler build fails with
stall-bxlzz3lv/centrosome_0d701048d79245f88a0b4e72628ad0a5/centrosome/_cpmorphology2.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/tmp/pip-build-env-b66uhii6/normal/lib/python3.8/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /tmp/pip-install-bxlzz3lv/centrosome_0d701048d79245f88a0b4e72628ad0a5/centrosome/_fastemd.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/tmp/pip-build-env-b66uhii6/normal/lib/python3.8/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /tmp/pip-install-bxlzz3lv/centrosome_0d701048d79245f88a0b4e72628ad0a5/centrosome/_filter.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/tmp/pip-build-env-b66uhii6/normal/lib/python3.8/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /tmp/pip-install-bxlzz3lv/centrosome_0d701048d79245f88a0b4e72628ad0a5/centrosome/_lapjv.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
warning: centrosome/_lapjv.pyx:281:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: centrosome/_lapjv.pyx:281:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
/tmp/pip-build-env-b66uhii6/normal/lib/python3.8/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /tmp/pip-install-bxlzz3lv/centrosome_0d701048d79245f88a0b4e72628ad0a5/centrosome/_propagate.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
Error compiling Cython file:
------------------------------------------------------------
...
heap.ptrs[child][k] = new_elem[k]
heap.items += 1
# restore heap invariant, all parents <= children
while child>0:
parent = (child + 1) / 2 - 1 # __parent(i)
^
------------------------------------------------------------
centrosome/heap.pxd:148:31: Cannot assign type 'double' to 'unsigned int'
Compiling centrosome/_propagate.pyx because it changed.
Compiling centrosome/_cpmorphology2.pyx because it changed.
Compiling centrosome/_convex_hull.pyx because it changed.
Compiling centrosome/_fastemd.pyx because it changed.
Compiling centrosome/_filter.pyx because it changed.
Compiling centrosome/_lapjv.pyx because it changed.
[1/6] Cythonizing centrosome/_convex_hull.pyx
[2/6] Cythonizing centrosome/_cpmorphology2.pyx
[3/6] Cythonizing centrosome/_fastemd.pyx
[4/6] Cythonizing centrosome/_filter.pyx
[5/6] Cythonizing centrosome/_lapjv.pyx
[6/6] Cythonizing centrosome/_propagate.pyx
Traceback (most recent call last):
File "/home/training/miniconda3/envs/imaging_course_cp_day5_2024/lib/python3.8/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/home/training/miniconda3/envs/imaging_course_cp_day5_2024/lib/python3.8/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/home/training/miniconda3/envs/imaging_course_cp_day5_2024/lib/python3.8/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 149, in prepare_metadata_for_build_wheel
return hook(metadata_directory, config_settings)
File "/tmp/pip-build-env-b66uhii6/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 366, in prepare_metadata_for_build_wheel
self.run_setup()
File "/tmp/pip-build-env-b66uhii6/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 487, in run_setup
super().run_setup(setup_script=setup_script)
File "/tmp/pip-build-env-b66uhii6/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 311, in run_setup
exec(code, locals())
File "<string>", line 89, in <module>
File "/tmp/pip-build-env-b66uhii6/normal/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 1154, in cythonize
cythonize_one(*args)
File "/tmp/pip-build-env-b66uhii6/normal/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 1321, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: centrosome/_propagate.pyx
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
failed
CondaEnvException: Pip failed