Closed predicative closed 5 years ago
I can also reproduce the problem at 76e78ef10f209956c6ddd96471b872db6be797c4, prior to using scikit-build. However, if I run pip install -e .
, I can then run pip install .
without problems, unlike what we find with the newest commits.
Processing /home/neal/work/problem_htk/HistomicsTK
Complete output from command python setup.py egg_info:
Error compiling Cython file:
------------------------------------------------------------
...
import numpy as np
^
------------------------------------------------------------
histomicstk/segmentation/label/_trace_object_boundaries_cython.pyx:1:0: 'pip-Ew3mV8-build.histomicstk.segmentation.label._trace_object_boundaries_cython' is not a valid module name
Warning: Extension name 'histomicstk.segmentation.label._trace_object_boundaries_cython' does not match fully qualified name 'pip-Ew3mV8-build.histomicstk.segmentation.label._trace_object_boundaries_cython' of 'histomicstk/segmentation/label/_trace_object_boundaries_cython.pyx'
Warning: Extension name 'histomicstk.segmentation.nuclear._max_clustering_cython' does not match fully qualified name 'pip-Ew3mV8-build.histomicstk.segmentation.nuclear._max_clustering_cython' of 'histomicstk/segmentation/nuclear/_max_clustering_cython.pyx'
Compiling histomicstk/segmentation/label/_trace_object_boundaries_cython.pyx because it changed.
Compiling histomicstk/segmentation/nuclear/_max_clustering_cython.pyx because it changed.
[1/2] Cythonizing histomicstk/segmentation/label/_trace_object_boundaries_cython.pyx
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-Ew3mV8-build/setup.py", line 88, in <module>
ext_modules = cythonize(ext_list)
File "/home/neal/work/problem_htk/venv/lib/python2.7/site-packages/Cython/Build/Dependencies.py", line 1016, in cythonize
cythonize_one(*args)
File "/home/neal/work/problem_htk/venv/lib/python2.7/site-packages/Cython/Build/Dependencies.py", line 1138, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: histomicstk/segmentation/label/_trace_object_boundaries_cython.pyx
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-Ew3mV8-build/
please see https://github.com/DigitalSlideArchive/HistomicsTK/issues/346
https://stackoverflow.com/questions/42102656/cython-compile-error-is-not-a-valid-module-name according to this, I delete init.py then it's installed successfully.
The following script to set up HistomicsTK fails on current master (07ec26a60bd64666eb4c989b39c60a0a031276f4):
The output from the last install command is at the end of this message. Cython encounters some build error apparently related to NumPy. However, if I add
-e
to the last install command, it works. I observe the same pattern if I follow the install instructions more closely, like so:Attempting to run
pip install ./HistomicsTK
again after it initially failed, while it still errors, gives a different, CMake-related error. It also seems to fail similarly on the first commit introducing scikit-build, c34b5e9d9c0e78b3cd1f1b78fe379ce53eaa846a (with the caveat that it uses the most up-to-date packages).The output and error: