I’m trying to install openslide-python via pip_install to support reading NRRD files with
@MONAI
. I am getting the following error with Slicer 5.0.2 on Linux:
>>> pip_install('openslide-python')
Collecting openslide-python
Using cached openslide-python-1.2.0.tar.gz (338 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: Pillow in ./lib/Python/lib/python3.9/site-packages (from openslide-python) (9.0.1)
Building wheels for collected packages: openslide-python
Building wheel for openslide-python (setup.py): started
Building wheel for openslide-python (setup.py): finished with status 'error'
error: subprocess-exited-with-error
� python setup.py bdist_wheel did not run successfully.
? exit code: 1
??> [16 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.9
creating build/lib.linux-x86_64-3.9/openslide
copying openslide/__init__.py -> build/lib.linux-x86_64-3.9/openslide
copying openslide/_version.py -> build/lib.linux-x86_64-3.9/openslide
copying openslide/lowlevel.py -> build/lib.linux-x86_64-3.9/openslide
copying openslide/deepzoom.py -> build/lib.linux-x86_64-3.9/openslide
running build_ext
building 'openslide._convert' extension
creating build/temp.linux-x86_64-3.9
creating build/temp.linux-x86_64-3.9/openslide
/opt/rh/devtoolset-7/root/usr/bin/gcc -pthread -std=c99 -Wall -Wstrict-prototypes -fno-strict-aliasing -fwrapv -g -fPIC -I/home/sara/Slicer_stable/Slicer-5.0.2-linux-amd64/lib/Python/include/python3.9 -c openslide/_convert.c -o build/temp.linux-x86_64-3.9/openslide/_convert.o
error: command '/opt/rh/devtoolset-7/root/usr/bin/gcc' failed: No such file or directory
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for openslide-python
Running setup.py clean for openslide-python
Failed to build openslide-python
Installing collected packages: openslide-python
Running setup.py install for openslide-python: started
Running setup.py install for openslide-python: finished with status 'error'
error: subprocess-exited-with-error
� Running setup.py install for openslide-python did not run successfully.
? exit code: 1
??> [18 lines of output]
running install
/home/sara/Slicer_stable/Slicer-5.0.2-linux-amd64/lib/Python/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.9
creating build/lib.linux-x86_64-3.9/openslide
copying openslide/__init__.py -> build/lib.linux-x86_64-3.9/openslide
copying openslide/_version.py -> build/lib.linux-x86_64-3.9/openslide
copying openslide/lowlevel.py -> build/lib.linux-x86_64-3.9/openslide
copying openslide/deepzoom.py -> build/lib.linux-x86_64-3.9/openslide
running build_ext
building 'openslide._convert' extension
creating build/temp.linux-x86_64-3.9
creating build/temp.linux-x86_64-3.9/openslide
/opt/rh/devtoolset-7/root/usr/bin/gcc -pthread -std=c99 -Wall -Wstrict-prototypes -fno-strict-aliasing -fwrapv -g -fPIC -I/home/sara/Slicer_stable/Slicer-5.0.2-linux-amd64/lib/Python/include/python3.9 -c openslide/_convert.c -o build/temp.linux-x86_64-3.9/openslide/_convert.o
error: command '/opt/rh/devtoolset-7/root/usr/bin/gcc' failed: No such file or directory
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure
� Encountered error while trying to install package.
??> openslide-python
note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.
WARNING: You are using pip version 22.0.3; however, version 22.1.2 is available.
You should consider upgrading via the '/home/sara/Slicer_stable/Slicer-5.0.2-linux-amd64/bin/./python-real -m pip install --upgrade pip' command.
Traceback (most recent call last):
File "<console>", line 1, in <module>
File "/home/sara/Slicer_stable/Slicer-5.0.2-linux-amd64/bin/Python/slicer/util.py", line 3431, in pip_install
_executePythonModule('pip', args)
File "/home/sara/Slicer_stable/Slicer-5.0.2-linux-amd64/bin/Python/slicer/util.py", line 3394, in _executePythonModule
logProcessOutput(proc)
File "/home/sara/Slicer_stable/Slicer-5.0.2-linux-amd64/bin/Python/slicer/util.py", line 3363, in logProcessOutput
raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command '['/home/sara/Slicer_stable/Slicer-5.0.2-linux-amd64/bin/../bin/PythonSlicer', '-m', 'pip', 'install', 'openslide-python']' returned non-zero exit status 1.
It seems there is a gcc binary it cannot find. This is working on Windows OS with no issues. I would appreciate any advice.
It builds the whl from source successfully? Or just not an issue on Windows because it uses the pre-built whl from PyPI?
