在新环境中构建cython扩展:找不到/lib/libpthread.so.0
在新环境中构建cython扩展:找不到/lib/libpthread.so.0
提问于 2020-02-19 10:20:47
我正在尝试部署一个使用一些cython扩展的包。我已经编写了以下设置脚本：
import os
import sys
from setuptools import setup, Extension
# factory function
def my_build_ext(pars):
# import delayed:
from setuptools.command.build_ext import build_ext as _build_ext
# include_dirs adjusted:
class build_ext(_build_ext):
def finalize_options(self):
_build_ext.finalize_options(self)
# Prevent numpy from thinking it is still in its setup process:
__builtins__.__NUMPY_SETUP__ = False
import numpy
self.include_dirs.append(numpy.get_include())
#object returned:
return build_ext(pars)
# cython c++ extensions
extnames = [
'npextc',
'intquickheapdict',
'FixedOrderedIntDict'
]
...
PATHADD = 'vemomoto_core/npcollections/'
PACKAGEADD = PATHADD.replace("/", ".")
ext = '.pyx'
extensions = [Extension(PACKAGEADD+name, [PATHADD+name+ext],
extra_compile_args=['-std=c++11', '-O3']+parcompileargs,
extra_link_args=parlinkargs,
)
for name in extnames]
for e in extensions:
e.language_level = 3
e.language = 'c++'
setup(
name="vemomoto_core_npcollections",
version="0.9.0.a7",
cmdclass={'build_ext' : my_build_ext},
setup_requires=['numpy', 'setuptools>=18.0'],
install_requires=['numpy', 'scipy'],
python_requires='>=3.6',
packages=['vemomoto_core', PACKAGEADD[:-1]],
ext_modules=extensions,
package_data={
'': ['*.pxd', '*.pyx', '*.c', '*.cpp'],
},
zip_safe=False,
)当我通过在setup.py目录中执行pip install .来构建包时，只要我在我的默认环境中工作，一切都可以正常工作。然而，当我在一个新的测试环境中测试这个过程时，我得到了错误
/home/user/anaconda3/envs/test37/compiler_compat/ld: cannot find /lib/libpthread.so.0
/home/user/anaconda3/envs/test37/compiler_compat/ld: cannot find /usr/lib/libpthread_nonshared.a
collect2: error: ld returned 1 exit status
error: command 'g++' failed with exit status 1(完整输出如下所示。)
我假设这里缺少一些依赖项，但我不知道如何找出它是什么，从而如何解决这个错误。我能做些什么？
完整错误消息：
Building wheels for collected packages: vemomoto-core-npcollections [76/1898]
Building wheel for vemomoto-core-npcollections (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /home/user/anaconda3/envs/test37/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-0_ns61r9/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-0_ns61r9/se
tup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-4zeu
yeay
cwd: /tmp/pip-req-build-0_ns61r9/
Complete output (49 lines):
/home/user/anaconda3/envs/test37/lib/python3.7/site-packages/setuptools/dist.py:476: UserWarning: Normalizing '0.9.0.a1' to '0.9.0a1'
normalized_version,
running bdist_wheel
running build
running build_py
package init file 'vemomoto_core/__init__.py' not found (or not a regular file)
creating build
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/vemomoto_core
creating build/lib.linux-x86_64-3.7/vemomoto_core/npcollections
copying vemomoto_core/npcollections/_setup_npextc.py -> build/lib.linux-x86_64-3.7/vemomoto_core/npcollections
copying vemomoto_core/npcollections/sparse3d.py -> build/lib.linux-x86_64-3.7/vemomoto_core/npcollections
copying vemomoto_core/npcollections/_setup_FixedOrderedIntDict.py -> build/lib.linux-x86_64-3.7/vemomoto_core/npcollections
copying vemomoto_core/npcollections/_FixedOrderedIntDict_reduce.py -> build/lib.linux-x86_64-3.7/vemomoto_core/npcollections
copying vemomoto_core/npcollections/__init__.py -> build/lib.linux-x86_64-3.7/vemomoto_core/npcollections copying vemomoto_core/npcollections/_setup_intquickheapdict.py -> build/lib.linux-x86_64-3.7/vemomoto_core/npcollections copying vemomoto_core/npcollections/npext.py -> build/lib.linux-x86_64-3.7/vemomoto_core/npcollections
copying vemomoto_core/npcollections/_npextc_utils.py -> build/lib.linux-x86_64-3.7/vemomoto_core/npcollections
copying vemomoto_core/__init__.pxd -> build/lib.linux-x86_64-3.7/vemomoto_core
copying vemomoto_core/npcollections/FixedOrderedIntDict.pxd -> build/lib.linux-x86_64-3.7/vemomoto_core/npcollections
copying vemomoto_core/npcollections/npextc.pxd -> build/lib.linux-x86_64-3.7/vemomoto_core/npcollections
copying vemomoto_core/npcollections/intquickheapdict.pxd -> build/lib.linux-x86_64-3.7/vemomoto_core/npcollections
copying vemomoto_core/npcollections/intquickheapdict.pyx -> build/lib.linux-x86_64-3.7/vemomoto_core/npcollections copying vemomoto_core/npcollections/npextc.pyx -> build/lib.linux-x86_64-3.7/vemomoto_core/npcollections
copying vemomoto_core/npcollections/FixedOrderedIntDict.pyx -> build/lib.linux-x86_64-3.7/vemomoto_core/npcollections
copying vemomoto_core/npcollections/heapoperations_c.c -> build/lib.linux-x86_64-3.7/vemomoto_core/npcollections
copying vemomoto_core/npcollections/sectionsum.c -> build/lib.linux-x86_64-3.7/vemomoto_core/npcollections copying vemomoto_core/npcollections/intquickheapdict.cpp -> build/lib.linux-x86_64-3.7/vemomoto_core/npcollections copying vemomoto_core/npcollections/FixedOrderedIntDict.cpp -> build/lib.linux-x86_64-3.7/vemomoto_core/npcollections
copying vemomoto_core/npcollections/npextc.cpp -> build/lib.linux-x86_64-3.7/vemomoto_core/npcollections
running build_ext
building 'vemomoto_core.npcollections.npextc' extension
creating build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/vemomoto_core
creating build/temp.linux-x86_64-3.7/vemomoto_core/npcollections gcc -pthread -B /home/user/anaconda3/envs/test37/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/user/anaconda3/envs/test37/include/python3.7m -I/home/user/anaconda3/envs/test37/lib/python3.7/site-packages/numpy/core/include -c vemomoto_core/npcollections/npextc.cpp -o build/temp.linux-x86_64-3.7/vemomoto_core/npcollections/npextc.o -std=c++11 -O3 -fopenmp
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
In file included from /home/user/anaconda3/envs/test37/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:0,
from /home/user/anaconda3/envs/test37/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/user/anaconda3/envs/test37/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from vemomoto_core/npcollections/npextc.cpp:636:
/home/user/anaconda3/envs/test37/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEP
RECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it with " \
^~~~~~~
g++ -pthread -shared -B /home/user/anaconda3/envs/test37/compiler_compat -L/home/user/anaconda3/envs/test37/lib -Wl,-rpath=/home/user/anaconda3/envs/test37/lib -Wl,--no-as-needed -Wl,--sysroot=
/ -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections build/temp.linux-x86_64-3.7/vemomoto_core/npcollections/npextc.o -o build/lib.linux-x86_64-3.7/ve
momoto_core/npcollections/npextc.cpython-37m-x86_64-linux-gnu.so -fopenmp
/home/user/anaconda3/envs/test37/compiler_compat/ld: cannot find /lib/libpthread.so.0
/home/user/anaconda3/envs/test37/compiler_compat/ld: cannot find /usr/lib/libpthread_nonshared.a
collect2: error: ld returned 1 exit status
error: command 'g++' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for vemomoto-core-npcollections
Running setup.py clean for vemomoto-core-npcollections
Failed to build vemomoto-core-npcollections回答 1
Stack Overflow用户
发布于 2020-02-20 04:34:34
为了解决这个问题，我比较了新的anaconda环境和我使用的环境。为此，我使用了
conda list在旧的和新的安装中，并比较输出。然后，我寻找那些包含在旧环境中但不包含在新环境中的包，这些包的名称表明它们可能包含正确的文件。
在安装了候选程序并重新尝试构建后，我发现gxx_linux-64 (对于另一个包cmake)是构建的必要要求。由于这些包在PyPI上似乎不可用，因此我将要求最终用户使用anaconda命令
conda install gxx_linux-64
conda install cmake在安装我的软件包之前。如果能在设置脚本中包含这个依赖项就好了，但这是另一个问题……
页面原文内容由Stack Overflow提供。腾讯云小微IT领域专用引擎提供翻译支持
原文链接：
https://stackoverflow.com/questions/60292082
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