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error: cannot repair "pynemo-0.0.0.dev0-cp311-cp311-linux_x86_64.whl" to "manylinux_2_28_x86_64" ABI because of the presence of too-recent versioned symbols. You'll need to compile the wheel on an older toolchain. #516

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mcleantom opened this issue Nov 6, 2024 · 0 comments
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error: cannot repair "pynemo-0.0.0.dev0-cp311-cp311-linux_x86_64.whl" to "manylinux_2_28_x86_64" ABI because of the presence of too-recent versioned symbols. You'll need to compile the wheel on an older toolchain. #516

mcleantom opened this issue Nov 6, 2024 · 0 comments

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@mcleantom
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mcleantom commented Nov 6, 2024 •
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I am trying to make my package both windows and linux compatible, the pyproject.toml for the package is:

[build-system]
requires = [
    "scikit-build-core",
    "pybind11"
]
build-backend = "scikit_build_core.build"

[project]
name = "pynemo"
version = "0.0.0dev0"
description = "Python bindings for nemo"
readme = "README.md"
authors = [
    { name = "Tom McLean",  email = "[email protected]" }
]
dependencies = [
  "fastapi",
  "click"
]

requires-python = ">=3.11"
classifiers = [
  "Development Status :: 4 - Beta",
  "License :: OSI Approved :: MIT License",
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
]

[tool.scikit-build]
cmake.verbose = true
logging.level = "DEBUG"
cmake.args = [
    "-DCMAKE_TOOLCHAIN_FILE=./vcpkg/scripts/buildsystems/vcpkg.cmake",
    "-DVCPKG_INSTALLED_DIR=../vcpkg_installed",
    "-DNEMO_BUILD_PYTHON_EXTENSION=ON",
    "-DCMAKE_POSITION_INDEPENDENT_CODE=ON"
]
backport.find-python = "0"

[tool.pytest.ini_options]
minversion = "6.0"
addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
xfail_strict = true
log_cli_level = "INFO"
filterwarnings = [
  "error",
]
testpaths = ["tests"]

[tool.cibuildwheel]
build = "cp*"
skip = ["cp*-musllinux*", "pp*"]
archs = ["x86_64", "AMD64", "arm64"]
manylinux-x86_64-image = "manylinux_2_28"
manylinux-i686-image = "manylinux_2_28"
manylinux-aarch64-image = "manylinux_2_28"
manylinux-ppc64le-image = "manylinux_2_28"
manylinux-s390x-image = "manylinux_2_28"
manylinux-pypy_x86_64-image = "manylinux_2_28"
manylinux-pypy_i686-image = "manylinux_2_28"
manylinux-pypy_aarch64-image = "manylinux_2_28"

[tool.cibuildwheel.linux]
before-all = '''
rm -rf vcpkg
rm -rf vcpkg_installed
yum -y install curl zip unzip tar autoconf automake libtool pkg-config perl-open python3.11-pip
python3.11 -m pip install jinja2
for python in /opt/python/*/bin/python3*; do
    if [ -x "$python" ]; then
        echo "Using Python: $python"
        $python -m pip install jinja2
    fi
done
ln -sf /usr/bin/python3.11 /usr/bin/python3
git clone https://github.com/microsoft/vcpkg.git
./vcpkg/bootstrap-vcpkg.sh
./vcpkg/vcpkg install
'''
archs = ['x86_64']

[tool.cibuildwheel.windows]
archs = ['AMD64']

I can create the wheel but when it gets to auditwheel repair it says:

auditwheel: error: cannot repair "pynemo-0.0.0.dev0-cp311-cp311-linux_x86_64.whl" to "manylinux_2_28_x86_64" ABI because of the presence of too-recent versioned symbols. You'll need to compile the wheel on an older toolchain.

I couldnt post the full debug logs as it was too long, but using auditwheel symbols I am getting

pynemo/_core.cpython-311-x86_64-linux-gnu.so is manylinux_2_28 compliant.
pynemo/ld-2.28.so is manylinux_2_28 compliant.
pynemo/ld-linux-x86-64.so.2 is manylinux_2_28 compliant.
pynemo/libc-2.28.so is manylinux_2_28 compliant.
pynemo/libc.so.6 is manylinux_2_28 compliant.
pynemo/libdl-2.28.so is not manylinux_2_28 compliant because it links the following forbidden libraries:
libc.so.6       offending symbols: _dl_signal_error@@GLIBC_PRIVATE, _dl_vsym@@GLIBC_PRIVATE, _dl_addr@@GLIBC_PRIVATE, _dl_sym@@GLIBC_PRIVATE, _dl_rtld_di_serinfo@@GLIBC_PRIVATE
pynemo/libdl.so.2 is not manylinux_2_28 compliant because it links the following forbidden libraries:
libc.so.6       offending symbols: _dl_signal_error@@GLIBC_PRIVATE, _dl_vsym@@GLIBC_PRIVATE, _dl_addr@@GLIBC_PRIVATE, _dl_sym@@GLIBC_PRIVATE, _dl_rtld_di_serinfo@@GLIBC_PRIVATE
pynemo/libgcc_s-8-20210514.so.1 is manylinux_2_28 compliant.
pynemo/libgcc_s.so.1 is manylinux_2_28 compliant.
pynemo/libm-2.28.so is not manylinux_2_28 compliant because it links the following forbidden libraries:
libc.so.6       offending versions: GLIBC_PRIVATE
pynemo/libm.so.6 is not manylinux_2_28 compliant because it links the following forbidden libraries:
libc.so.6       offending versions: GLIBC_PRIVATE
pynemo/libpthread-2.28.so is not manylinux_2_28 compliant because it links the following forbidden libraries:
libc.so.6       offending symbols: __libc_siglongjmp@@GLIBC_PRIVATE, __tsearch@@GLIBC_PRIVATE, __getrlimit@@GLIBC_PRIVATE, __libc_dlclose@@GLIBC_PRIVATE, __libc_fatal@@GLIBC_PRIVATE, __sigtimedwait@@GLIBC_PRIVATE, __mmap@@GLIBC_PRIVATE, __libc_system@@GLIBC_PRIVATE, __munmap@@GLIBC_PRIVATE, __libc_fork@@GLIBC_PRIVATE, _IO_enable_locks@@GLIBC_PRIVATE, __write_nocancel@@GLIBC_PRIVATE, _dl_deallocate_tls@@GLIBC_PRIVATE, __call_tls_dtors@@GLIBC_PRIVATE, __libc_thread_freeres@@GLIBC_PRIVATE, __mprotect@@GLIBC_PRIVATE, __clock_gettime@@GLIBC_PRIVATE, __libc_fcntl64@@GLIBC_PRIVATE, __nanosleep_nocancel@@GLIBC_PRIVATE, __libc_current_sigrtmax_private@@GLIBC_PRIVATE, __tdelete@@GLIBC_PRIVATE, __libc_dlopen_mode@@GLIBC_PRIVATE, __read_nocancel@@GLIBC_PRIVATE, _dl_make_stack_executable@@GLIBC_PRIVATE, __libc_pthread_init@@GLIBC_PRIVATE, __ctype_init@@GLIBC_PRIVATE, __libc_dlsym@@GLIBC_PRIVATE, __tfind@@GLIBC_PRIVATE, __open64_nocancel@@GLIBC_PRIVATE, __libc_current_sigrtmin_private@@GLIBC_PRIVATE, __madvise@@GLIBC_PRIVATE, __pause_nocancel@@GLIBC_PRIVATE, __mktemp@@GLIBC_PRIVATE, __twalk@@GLIBC_PRIVATE, _dl_allocate_tls@@GLIBC_PRIVATE, __tunable_get_val@@GLIBC_PRIVATE, _dl_get_tls_static_info@@GLIBC_PRIVATE, __libc_alloca_cutoff@@GLIBC_PRIVATE, _dl_allocate_tls_init@@GLIBC_PRIVATE, __close_nocancel@@GLIBC_PRIVATE, __libc_allocate_rtsig_private@@GLIBC_PRIVATE, __libc_longjmp@@GLIBC_PRIVATE
pynemo/libpthread.so.0 is not manylinux_2_28 compliant because it links the following forbidden libraries:
libc.so.6       offending symbols: __libc_siglongjmp@@GLIBC_PRIVATE, __tsearch@@GLIBC_PRIVATE, __getrlimit@@GLIBC_PRIVATE, __libc_dlclose@@GLIBC_PRIVATE, __libc_fatal@@GLIBC_PRIVATE, __sigtimedwait@@GLIBC_PRIVATE, __mmap@@GLIBC_PRIVATE, __libc_system@@GLIBC_PRIVATE, __munmap@@GLIBC_PRIVATE, __libc_fork@@GLIBC_PRIVATE, _IO_enable_locks@@GLIBC_PRIVATE, __write_nocancel@@GLIBC_PRIVATE, _dl_deallocate_tls@@GLIBC_PRIVATE, __call_tls_dtors@@GLIBC_PRIVATE, __libc_thread_freeres@@GLIBC_PRIVATE, __mprotect@@GLIBC_PRIVATE, __clock_gettime@@GLIBC_PRIVATE, __libc_fcntl64@@GLIBC_PRIVATE, __nanosleep_nocancel@@GLIBC_PRIVATE, __libc_current_sigrtmax_private@@GLIBC_PRIVATE, __tdelete@@GLIBC_PRIVATE, __libc_dlopen_mode@@GLIBC_PRIVATE, __read_nocancel@@GLIBC_PRIVATE, _dl_make_stack_executable@@GLIBC_PRIVATE, __libc_pthread_init@@GLIBC_PRIVATE, __ctype_init@@GLIBC_PRIVATE, __libc_dlsym@@GLIBC_PRIVATE, __tfind@@GLIBC_PRIVATE, __open64_nocancel@@GLIBC_PRIVATE, __libc_current_sigrtmin_private@@GLIBC_PRIVATE, __madvise@@GLIBC_PRIVATE, __pause_nocancel@@GLIBC_PRIVATE, __mktemp@@GLIBC_PRIVATE, __twalk@@GLIBC_PRIVATE, _dl_allocate_tls@@GLIBC_PRIVATE, __tunable_get_val@@GLIBC_PRIVATE, _dl_get_tls_static_info@@GLIBC_PRIVATE, __libc_alloca_cutoff@@GLIBC_PRIVATE, _dl_allocate_tls_init@@GLIBC_PRIVATE, __close_nocancel@@GLIBC_PRIVATE, __libc_allocate_rtsig_private@@GLIBC_PRIVATE, __libc_longjmp@@GLIBC_PRIVATE
pynemo/librt-2.28.so is not manylinux_2_28 compliant because it links the following forbidden libraries:
libc.so.6       offending symbols: __recv@@GLIBC_PRIVATE, __libc_pwrite@@GLIBC_PRIVATE, __libc_fatal@@GLIBC_PRIVATE, __libc_pread@@GLIBC_PRIVATE, __pthread_barrier_init@@GLIBC_PRIVATE, __pthread_unwind@@GLIBC_PRIVATE, __pthread_get_minstack@@GLIBC_PRIVATE, __libc_dlopen_mode@@GLIBC_PRIVATE, __pthread_barrier_wait@@GLIBC_PRIVATE, __libc_dlsym@@GLIBC_PRIVATE, __socket@@GLIBC_PRIVATE, __pthread_attr_copy@@GLIBC_PRIVATE, __shm_directory@@GLIBC_PRIVATE, __fortify_fail@@GLIBC_PRIVATE, __close_nocancel@@GLIBC_PRIVATE
libpthread.so.0 offending symbols: __recv@@GLIBC_PRIVATE, __libc_pwrite@@GLIBC_PRIVATE, __libc_fatal@@GLIBC_PRIVATE, __libc_pread@@GLIBC_PRIVATE, __pthread_barrier_init@@GLIBC_PRIVATE, __pthread_unwind@@GLIBC_PRIVATE, __pthread_get_minstack@@GLIBC_PRIVATE, __libc_dlopen_mode@@GLIBC_PRIVATE, __pthread_barrier_wait@@GLIBC_PRIVATE, __libc_dlsym@@GLIBC_PRIVATE, __socket@@GLIBC_PRIVATE, __pthread_attr_copy@@GLIBC_PRIVATE, __shm_directory@@GLIBC_PRIVATE, __fortify_fail@@GLIBC_PRIVATE, __close_nocancel@@GLIBC_PRIVATE
pynemo/librt.so.1 is not manylinux_2_28 compliant because it links the following forbidden libraries:
libpthread.so.0 offending symbols: __recv@@GLIBC_PRIVATE, __libc_pwrite@@GLIBC_PRIVATE, __libc_fatal@@GLIBC_PRIVATE, __libc_pread@@GLIBC_PRIVATE, __pthread_barrier_init@@GLIBC_PRIVATE, __pthread_unwind@@GLIBC_PRIVATE, __pthread_get_minstack@@GLIBC_PRIVATE, __libc_dlopen_mode@@GLIBC_PRIVATE, __pthread_barrier_wait@@GLIBC_PRIVATE, __libc_dlsym@@GLIBC_PRIVATE, __socket@@GLIBC_PRIVATE, __pthread_attr_copy@@GLIBC_PRIVATE, __shm_directory@@GLIBC_PRIVATE, __fortify_fail@@GLIBC_PRIVATE, __close_nocancel@@GLIBC_PRIVATE
libc.so.6       offending symbols: __recv@@GLIBC_PRIVATE, __libc_pwrite@@GLIBC_PRIVATE, __libc_fatal@@GLIBC_PRIVATE, __libc_pread@@GLIBC_PRIVATE, __pthread_barrier_init@@GLIBC_PRIVATE, __pthread_unwind@@GLIBC_PRIVATE, __pthread_get_minstack@@GLIBC_PRIVATE, __libc_dlopen_mode@@GLIBC_PRIVATE, __pthread_barrier_wait@@GLIBC_PRIVATE, __libc_dlsym@@GLIBC_PRIVATE, __socket@@GLIBC_PRIVATE, __pthread_attr_copy@@GLIBC_PRIVATE, __shm_directory@@GLIBC_PRIVATE, __fortify_fail@@GLIBC_PRIVATE, __close_nocancel@@GLIBC_PRIVATE
pynemo/libstdc++.so.6 is manylinux_2_28 compliant.
pynemo/libstdc++.so.6.0.25 is manylinux_2_28 compliant.

And the first bit of the output of the full logs:

DEBUG:auditwheel.wheel_abi:full_elftree:
{
    "pynemo/_core.cpython-311-x86_64-linux-gnu.so": {
        "interp": null,
        "path": "pynemo/_core.cpython-311-x86_64-linux-gnu.so",
        "realpath": "pynemo/_core.cpython-311-x86_64-linux-gnu.so",
        "needed": [
            "libpthread.so.0",
            "librt.so.1",
            "libdl.so.2",
            "libstdc++.so.6",
            "libm.so.6",
            "libgcc_s.so.1",
            "libc.so.6",
            "ld-linux-x86-64.so.2"
        ],
        "rpath": [],
        "runpath": [],
        "libs": {
            "libpthread.so.0": {
                "realpath": "/lib64/libpthread-2.28.so",
                "path": "/lib64/libpthread.so.0",
                "needed": [
                    "libc.so.6",
                    "ld-linux-x86-64.so.2"
                ]
            },
            "libc.so.6": {
                "realpath": "/lib64/libc-2.28.so",
                "path": "/lib64/libc.so.6",
                "needed": [
                    "ld-linux-x86-64.so.2"
                ]
            },
            "ld-linux-x86-64.so.2": {
                "realpath": "/lib64/ld-2.28.so",
                "path": "/lib64/ld-linux-x86-64.so.2",
                "needed": []
            },
            "librt.so.1": {
                "realpath": "/lib64/librt-2.28.so",
                "path": "/lib64/librt.so.1",
                "needed": [
                    "libpthread.so.0",
                    "libc.so.6"
                ]
            },
            "libdl.so.2": {
                "realpath": "/lib64/libdl-2.28.so",
                "path": "/lib64/libdl.so.2",
                "needed": [
                    "libc.so.6",
                    "ld-linux-x86-64.so.2"
                ]
            },
            "libstdc++.so.6": {
                "realpath": "/lib64/libstdc++.so.6.0.25",
                "path": "/lib64/libstdc++.so.6",
                "needed": [
                    "libm.so.6",
                    "libc.so.6",
                    "ld-linux-x86-64.so.2",
                    "libgcc_s.so.1"
                ]
            },
            "libm.so.6": {
                "realpath": "/lib64/libm-2.28.so",
                "path": "/lib64/libm.so.6",
                "needed": [
                    "libc.so.6",
                    "ld-linux-x86-64.so.2"
                ]
            },
            "libgcc_s.so.1": {
                "realpath": "/lib64/libgcc_s-8-20210514.so.1",
                "path": "/lib64/libgcc_s.so.1",
                "needed": [
                    "libc.so.6"
                ]
            }
        }
    },
    "pynemo/ld-2.28.so": {
        "interp": null,
        "path": "pynemo/ld-2.28.so",
        "realpath": "pynemo/ld-2.28.so",
        "needed": [],
        "rpath": [],
        "runpath": [],
        "libs": {}
    },
    "pynemo/libc-2.28.so": {
        "interp": "/lib64/ld-linux-x86-64.so.2",
        "path": "pynemo/libc-2.28.so",
        "realpath": "pynemo/libc-2.28.so",
        "needed": [
            "ld-linux-x86-64.so.2"
        ],
        "rpath": [],
        "runpath": [],
        "libs": {
            "ld-linux-x86-64.so.2": {
                "path": "/lib64/ld-linux-x86-64.so.2",
                "realpath": "/lib64/ld-2.28.so",
                "needed": []
            }
        }
    },
    "pynemo/libdl-2.28.so": {
        "interp": null,
        "path": "pynemo/libdl-2.28.so",
        "realpath": "pynemo/libdl-2.28.so",
        "needed": [
            "libc.so.6",
            "ld-linux-x86-64.so.2"
        ],
        "rpath": [],
        "runpath": [],
        "libs": {
            "libc.so.6": {
                "realpath": "/lib64/libc-2.28.so",
                "path": "/lib64/libc.so.6",
                "needed": [
                    "ld-linux-x86-64.so.2"
                ]
            },
            "ld-linux-x86-64.so.2": {
                "realpath": "/lib64/ld-2.28.so",
                "path": "/lib64/ld-linux-x86-64.so.2",
                "needed": []
            }
        }
    },
    "pynemo/libgcc_s-8-20210514.so.1": {
        "interp": null,
        "path": "pynemo/libgcc_s-8-20210514.so.1",
        "realpath": "pynemo/libgcc_s-8-20210514.so.1",
        "needed": [
            "libc.so.6"
        ],
        "rpath": [],
        "runpath": [],
        "libs": {
            "libc.so.6": {
                "realpath": "/lib64/libc-2.28.so",
                "path": "/lib64/libc.so.6",
                "needed": [
                    "ld-linux-x86-64.so.2"
                ]
            },
            "ld-linux-x86-64.so.2": {
                "realpath": "/lib64/ld-2.28.so",
                "path": "/lib64/ld-linux-x86-64.so.2",
                "needed": []
            }
        }
    },
    "pynemo/libm-2.28.so": {
        "interp": null,
        "path": "pynemo/libm-2.28.so",
        "realpath": "pynemo/libm-2.28.so",
        "needed": [
            "libc.so.6",
            "ld-linux-x86-64.so.2"
        ],
        "rpath": [],
        "runpath": [],
        "libs": {
            "libc.so.6": {
                "realpath": "/lib64/libc-2.28.so",
                "path": "/lib64/libc.so.6",
                "needed": [
                    "ld-linux-x86-64.so.2"
                ]
            },
            "ld-linux-x86-64.so.2": {
                "realpath": "/lib64/ld-2.28.so",
                "path": "/lib64/ld-linux-x86-64.so.2",
                "needed": []
            }
        }
    },
    "pynemo/libpthread-2.28.so": {
        "interp": "/lib64/ld-linux-x86-64.so.2",
        "path": "pynemo/libpthread-2.28.so",
        "realpath": "pynemo/libpthread-2.28.so",
        "needed": [
            "libc.so.6",
            "ld-linux-x86-64.so.2"
        ],
        "rpath": [],
        "runpath": [],
        "libs": {
            "ld-linux-x86-64.so.2": {
                "path": "/lib64/ld-linux-x86-64.so.2",
                "realpath": "/lib64/ld-2.28.so",
                "needed": []
            },
            "libc.so.6": {
                "realpath": "/lib64/libc-2.28.so",
                "path": "/lib64/libc.so.6",
                "needed": [
                    "ld-linux-x86-64.so.2"
                ]
            }
        }
    },
    "pynemo/librt-2.28.so": {
        "interp": null,
        "path": "pynemo/librt-2.28.so",
        "realpath": "pynemo/librt-2.28.so",
        "needed": [
            "libpthread.so.0",
            "libc.so.6"
        ],
        "rpath": [],
        "runpath": [],
        "libs": {
            "libpthread.so.0": {
                "realpath": "/lib64/libpthread-2.28.so",
                "path": "/lib64/libpthread.so.0",
                "needed": [
                    "libc.so.6",
                    "ld-linux-x86-64.so.2"
                ]
            },
            "libc.so.6": {
                "realpath": "/lib64/libc-2.28.so",
                "path": "/lib64/libc.so.6",
                "needed": [
                    "ld-linux-x86-64.so.2"
                ]
            },
            "ld-linux-x86-64.so.2": {
                "realpath": "/lib64/ld-2.28.so",
                "path": "/lib64/ld-linux-x86-64.so.2",
                "needed": []
            }
        }
    },
    "pynemo/libstdc++.so.6.0.25": {
        "interp": null,
        "path": "pynemo/libstdc++.so.6.0.25",
        "realpath": "pynemo/libstdc++.so.6.0.25",
        "needed": [
            "libm.so.6",
            "libc.so.6",
            "ld-linux-x86-64.so.2",
            "libgcc_s.so.1"
        ],
        "rpath": [],
        "runpath": [],
        "libs": {
            "libm.so.6": {
                "realpath": "/lib64/libm-2.28.so",
                "path": "/lib64/libm.so.6",
                "needed": [
                    "libc.so.6",
                    "ld-linux-x86-64.so.2"
                ]
            },
            "libc.so.6": {
                "realpath": "/lib64/libc-2.28.so",
                "path": "/lib64/libc.so.6",
                "needed": [
                    "ld-linux-x86-64.so.2"
                ]
            },
            "ld-linux-x86-64.so.2": {
                "realpath": "/lib64/ld-2.28.so",
                "path": "/lib64/ld-linux-x86-64.so.2",
                "needed": []
            },
            "libgcc_s.so.1": {
                "realpath": "/lib64/libgcc_s-8-20210514.so.1",
                "path": "/lib64/libgcc_s.so.1",
                "needed": [
                    "libc.so.6"
                ]
            }
        }
    }
}

I am not sure why I am getting a too-recent versioned error as I am building my library inside a manylinux_2_28 container. How can I fix this issue? Thanks
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@mcleantom