Software not compiling

[garcia-nacho]

I have tried to compile the source and I get this error:

make[2]: *** [pybindings/CMakeFiles/pyhdbscan.dir/build.make:63: pybindings/CMakeFiles/pyhdbscan.dir/pyhdbscan.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:191: pybindings/CMakeFiles/pyhdbscan.dir/all] Error 2
make: *** [Makefile:84: all] Error 2

[wangyiqiu]

Did you initialize the dependencies? See instructions here
If it still does not work for you, please share the commands, system, and architecture that you used.

[garcia-nacho]

Yes I did it.
I did it inside a conda environment since I don't want to install all the required packages on my base environment because of compatibility issues.

Same error on two different computers, the last one Ubuntu 19.04 (x86_64)
Commands:

conda create -n hdbscan
conda activate hdbscan 
conda install pip
git clone https://github.com/wangyiqiu/hdbscan.git
cd hdbscan
git submodule init
git submodule update
pip3 install -r pybindings/requirements.txt
mkdir build
cd build
cmake ..
make -j 

and again the last lines of the error:

In file included from /home/nacho/anaconda3/envs/hdbscan/include/python3.11/Python.h:42,
                 from /home/nacho/hdbscan/external/pybind11/include/pybind11/detail/common.h:124,
                 from /home/nacho/hdbscan/external/pybind11/include/pybind11/pytypes.h:12,
                 from /home/nacho/hdbscan/external/pybind11/include/pybind11/cast.h:13,
                 from /home/nacho/hdbscan/external/pybind11/include/pybind11/attr.h:13,
                 from /home/nacho/hdbscan/external/pybind11/include/pybind11/pybind11.h:45,
                 from /home/nacho/hdbscan/pybindings/pyhdbscan.cpp:6:
/home/nacho/anaconda3/envs/hdbscan/include/python3.11/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’}
   22 | typedef struct _frame PyFrameObject;
      |                ^~~~~~
make[2]: *** [pybindings/CMakeFiles/pyhdbscan.dir/build.make:63: pybindings/CMakeFiles/pyhdbscan.dir/pyhdbscan.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:187: pybindings/CMakeFiles/pyhdbscan.dir/all] Error 2
make: *** [Makefile:84: all] Error 2

[wangyiqiu]

I see, thanks. It's probably because of incompatibilities across Python and Pybind versions. Could you try installing under virtual environment in your base environment? I will try to replicate your error in Conda and will get back to you about it.

…

On Wed, Feb 15, 2023 at 5:19 PM Nacho Garcia ***@***.***> wrote: Yes I did it. I did it inside a conda environment since I don't want to install all the required packages on my base environment because of compatibility issues. Same error on two different computers, the last one Ubuntu 19.04 (x86_64) Commands: conda create -n hdbscan conda activate hdbscan conda install pip git clone https://github.com/wangyiqiu/hdbscan.git cd hdbscan git submodule init git submodule update pip3 install -r pybindings/requirements.txt mkdir build cd build cmake .. make -j and again the last lines of the error: In file included from /home/nacho/anaconda3/envs/hdbscan/include/python3.11/Python.h:42, from /home/nacho/hdbscan/external/pybind11/include/pybind11/detail/common.h:124, from /home/nacho/hdbscan/external/pybind11/include/pybind11/pytypes.h:12, from /home/nacho/hdbscan/external/pybind11/include/pybind11/cast.h:13, from /home/nacho/hdbscan/external/pybind11/include/pybind11/attr.h:13, from /home/nacho/hdbscan/external/pybind11/include/pybind11/pybind11.h:45, from /home/nacho/hdbscan/pybindings/pyhdbscan.cpp:6: /home/nacho/anaconda3/envs/hdbscan/include/python3.11/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 22 | typedef struct _frame PyFrameObject; | ^~~~~~ make[2]: *** [pybindings/CMakeFiles/pyhdbscan.dir/build.make:63: pybindings/CMakeFiles/pyhdbscan.dir/pyhdbscan.cpp.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:187: pybindings/CMakeFiles/pyhdbscan.dir/all] Error 2 make: *** [Makefile:84: all] Error 2 — Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACY5DHIM3IHM4DNE4WN4XTLWXVJA7ANCNFSM6AAAAAAU4QFFHA> . You are receiving this because you commented.Message ID: ***@***.***>