libgap.so.0: No such file or directory

[DanieleMarchei]

I installed gappy-system using
pip3 install gappy-system
I also downloaded GAP from https://www.gap-system.org/Releases/4.12.2.html, ran ./configure && make, the BuildPackages.sh script and make install-libgap.
When I try to import gappy in python

from gappy import gap

I get the following error

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/daniele/.local/lib/python3.10/site-packages/gappy/__init__.py", line 2, in <module>
    from .core import gap, Gap
ImportError: libgap.so.0: cannot open shared object file: No such file or directory

I checked and my /usr/local/lib contains the file libgap.so, but not the libgap.so.0.
Creating a symbolic link using
ln -s libgap.so libgap.so.0
does not raise the error, but then if I try running

from gappy import gap
gap.SymmetricGroup(4)

it gives a segmentation fault.

I then tried cloning the repo and installing it from there with
pip3 install .
but I get the following error

Defaulting to user installation because normal site-packages is not writeable
Processing /home/daniele/Scrivania/polytime_algo/gappy
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: cysignals in /home/daniele/.local/lib/python3.10/site-packages (from gappy-system==0.1.0a4.dev5+ga0642c4) (1.11.4)
Requirement already satisfied: psutil in /home/daniele/.local/lib/python3.10/site-packages (from gappy-system==0.1.0a4.dev5+ga0642c4) (5.9.6)
Building wheels for collected packages: gappy-system
  Building wheel for gappy-system (pyproject.toml) ... error
  error: subprocess-exited-with-error
  × Building wheel for gappy-system (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [55 lines of output]
      /tmp/pip-build-env-bs5nmqmd/overlay/local/lib/python3.10/dist-packages/setuptools/dist.py:472: SetuptoolsDeprecationWarning: Invalid dash-separated options
      !!
              ********************************************************************************
              Usage of dash-separated 'author-email' will not be supported in future
              versions. Please use the underscore name 'author_email' instead.
              By 2024-Sep-26, you need to update your project and remove deprecated calls
              or your builds will no longer be supported.
              See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
              ********************************************************************************
      !!
        opt = self.warn_dash_deprecation(opt, section)
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.linux-x86_64-cpython-310
      creating build/lib.linux-x86_64-cpython-310/gappy
      copying gappy/conftest.py -> build/lib.linux-x86_64-cpython-310/gappy
      copying gappy/__init__.py -> build/lib.linux-x86_64-cpython-310/gappy
      copying gappy/gap_globals.py -> build/lib.linux-x86_64-cpython-310/gappy
      copying gappy/exceptions.py -> build/lib.linux-x86_64-cpython-310/gappy
      copying gappy/context_managers.py -> build/lib.linux-x86_64-cpython-310/gappy
      copying gappy/version.py -> build/lib.linux-x86_64-cpython-310/gappy
      copying gappy/gap_functions.py -> build/lib.linux-x86_64-cpython-310/gappy
      copying gappy/_version.py -> build/lib.linux-x86_64-cpython-310/gappy
      copying gappy/operations.py -> build/lib.linux-x86_64-cpython-310/gappy
      copying gappy/core.pxd -> build/lib.linux-x86_64-cpython-310/gappy
      copying gappy/gap_includes.pxd -> build/lib.linux-x86_64-cpython-310/gappy
      copying gappy/gmp.pxd -> build/lib.linux-x86_64-cpython-310/gappy
      copying gappy/gapobj.pxd -> build/lib.linux-x86_64-cpython-310/gappy
      copying gappy/core.pyx -> build/lib.linux-x86_64-cpython-310/gappy
      copying gappy/gapobj.pyx -> build/lib.linux-x86_64-cpython-310/gappy
      copying gappy/utils.pyx -> build/lib.linux-x86_64-cpython-310/gappy
      running build_ext
      Compiling gappy/core.pyx because it changed.
      Compiling gappy/gapobj.pyx because it changed.
      Compiling gappy/utils.pyx because it changed.
      [1/3] Cythonizing gappy/core.pyx
      [2/3] Cythonizing gappy/gapobj.pyx
      [3/3] Cythonizing gappy/utils.pyx
      building 'gappy.core' extension
      creating build/temp.linux-x86_64-cpython-310/gappy
      x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-bs5nmqmd/overlay/local/lib/python3.10/dist-packages/cysignals -Ibuild/temp.linux-x86_64-cpython-310/include -I/home/daniele/gap-4.12.2/gen -I/usr/include/python3.10 -c gappy/core.c -o build/temp.linux-x86_64-cpython-310/gappy/core.o
      gappy/core.c:810:23: error: conflicting types for ‘GAP_MakeStringWithLen’; have ‘struct OpaqueBag *(char *, size_t)’ {aka ‘struct OpaqueBag *(char *, long unsigned int)’}
        810 |     static inline Obj GAP_MakeStringWithLen(char *s, size_t len) {
            |                       ^~~~~~~~~~~~~~~~~~~~~
      In file included from gappy/core.c:776:
      build/temp.linux-x86_64-cpython-310/include/gap/libgap-api.h:521:5: note: previous declaration of ‘GAP_MakeStringWithLen’ with type ‘struct OpaqueBag *(const char *, UInt)’ {aka ‘struct OpaqueBag *(const char *, long unsigned int)’}
        521 | Obj GAP_MakeStringWithLen(const char * string, UInt len);
            |     ^~~~~~~~~~~~~~~~~~~~~
      error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
      [end of output]
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for gappy-system
Failed to build gappy-system
ERROR: Could not build wheels for gappy-system, which is required to install pyproject.toml-based projects

[embray]

If you install GAP from source it's best to make sure to set GAP_ROOT=... when installing, pointing to your GAP root.

That said , GAP 4.12 isn't supported yet. 4.11 is the highest supported version, probably hence the segfault (and possibly also the different soname)