Why am I getting name mangling issues in cython when using a c++ header?

Question

I have a codebase where I use some hand-written C++ code. The C++-code includes the line

#include "gzstream.h"

It seems like the code in that header gets mangled, because when I try to run the code I get errors like:

ImportError: dlopen(/Users/endrebakkenstovner/anaconda3/lib/python3.8/site-packages/epic2-0.0.48-py3.8-macosx-10.9-x86_64.egg/epic2/src/cpp_read_files.cpython-38-darwin.so, 2): Symbol not found: __ZN12gzstreambaseD0Ev
  Referenced from: /Users/endrebakkenstovner/anaconda3/lib/python3.8/site-packages/epic2-0.0.48-py3.8-macosx-10.9-x86_64.egg/epic2/src/cpp_read_files.cpython-38-darwin.so
  Expected in: flat namespace

(Symbol not found: __ZN12*gzstreambaseD0Ev)

Is there a way to tell Cython about that header file to avoid name mangling?

Here is the line where I require gzstream.h: https://github.com/biocore-ntnu/epic2/blob/master/epic2/src/read_files.cpp#L202

Is there a way to make Cython aware of it in a pxd-file or something?

Related: https://stackoverflow.com/questions/48633172/renamed-c-files-to-cpp-importing-cython-library-fails — The Unfun Cat, Oct 26 '20 at 18:02
The gzstream.h is a header with all the required code. I am guessing no linking is required? — The Unfun Cat, Oct 26 '20 at 19:10
nope, `gzstream.h` has no implementation of `~gzstreambase()` which is the symbol in your error — Alan Birtles, Oct 26 '20 at 20:06
You are absolutely correct, I will need to find out how to link that file in Cython. — The Unfun Cat, Oct 26 '20 at 20:42

Why am I getting name mangling issues in cython when using a c++ header?

0 Answers0