Related to what @VikingofRock posted, has anyone using this package been able to install the Cython debugging extensions in a project that is using a conda environment as the Python interpreter? The extensions compile fine when using the system-wide python, but fail when using conda's python. I receive the following error when trying to compile the extensions manually:
$ sudo /path/to/miniconda/python /opt/pycharm-professional/helpers/pydev/setup_cython.py build_ext --inplace
running build_ext
building '_pydevd_bundle.pydevd_cython' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/_pydevd_bundle
gcc -pthread -B /home/xxx/.conda/envs/xxx/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xxx/.conda/envs/xxx/include/python3.6m -c _pydevd_bundle/pydevd_cython.c -o build/temp.linux-x86_64-3.6/_pydevd_bundle/pydevd_cython.o
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/_pydevd_bundle
gcc -pthread -shared -B /home/xxx/.conda/envs/xxx/compiler_compat -L/home/xxx/.conda/envs/xxx/lib -Wl,-rpath=/home/xxx/.conda/envs/xxx/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/_pydevd_bundle/pydevd_cython.o -o build/lib.linux-x86_64-3.6/_pydevd_bundle/pydevd_cython.cpython-36m-x86_64-linux-gnu.so
/home/xxx/.conda/envs/xxx/compiler_compat/ld: build/temp.linux-x86_64-3.6/_pydevd_bundle/pydevd_cython.o: unable to initialize decompress status for section .debug_info
/home/xxx/.conda/envs/xxx/compiler_compat/ld: build/temp.linux-x86_64-3.6/_pydevd_bundle/pydevd_cython.o: unable to initialize decompress status for section .debug_info
/home/xxx/.conda/envs/xxx/compiler_compat/ld: build/temp.linux-x86_64-3.6/_pydevd_bundle/pydevd_cython.o: unable to initialize decompress status for section .debug_info
/home/xxx/.conda/envs/xxx/compiler_compat/ld: build/temp.linux-x86_64-3.6/_pydevd_bundle/pydevd_cython.o: unable to initialize decompress status for section .debug_info
build/temp.linux-x86_64-3.6/_pydevd_bundle/pydevd_cython.o: file not recognized: file format not recognized
collect2: error: ld returned 1 exit status
error: command 'gcc' failed with exit status 1
(x-posting this comment to the miniconda3 AUR page)
Pinned Comments
Meaulnes commented on 2026-03-27 16:37 (UTC)
This comment from @AvacadoCookie should be pinned, IMO.
If anyone is getting errors about
Cythonorsetuptools, and they are usingConda, that comment has the answer.If anyone is getting errors about
Cythonorsetuptools, and they are usingpyenv, there are 2 possible ways to fix it:pyenv local systemto set Python back to the system installed Python for this session.pip install Cython setuptoolsto install the necessary packages to your preferred python installation.AvocadoCookie commented on 2025-12-14 16:22 (UTC)
For all users with
ModuleNotFoundError: No module named 'Cython'or'setuptools'reported, please try the following methods to address the problem:condaenvironment. Now afterwhich pythontyped in console, the output should be/usr/bin/python.pacman -S cython python-setuptools.