最近的Python用户，我正在尝试使用fcm模块来分析流式细胞术数据( https://pythonhosted.org/fcm/ )。我在 pip 安装期间发现与“gcc”相关的错误。
尝试更新pip和setuptools，还按照How to fix gcc error produced by pip install?中的建议安装了brew和openssl ，仍然发现同样的错误。
终端输出如下:
Collecting fcm
Downloading https://files.pythonhosted.org/packages/b8/50/92e6fcf82b3411def7c5c08a1b9be5fc4d5f4a4ae8eb7c95ee4b0485fbdd/fcm-0.9.1.tar.gz (1.1MB)
100% |████████████████████████████████| 1.1MB 12.9MB/s
Installing collected packages: fcm
Running setup.py install for fcm ... error
Complete output from command /anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/kt/54_zwpj929b852yth43_hj440000gn/T/pip-install-424k_8e4/fcm/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/kt/54_zwpj929b852yth43_hj440000gn/T/pip-record-43efnrvl/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
creating build
creating build/lib.macosx-10.7-x86_64-3.7
creating build/lib.macosx-10.7-x86_64-3.7/fcm
copying src/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm
creating build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/transforms.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/tree.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/annotation.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/fcmdata.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/logicle.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/compensate.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/gate.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/fcmcollection.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/fcmexceptions.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/subsample.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
creating build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/plot.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/experimental.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/plot_gate.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/util.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/dimechart.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
creating build/lib.macosx-10.7-x86_64-3.7/fcm/gui
copying src/gui/mpl_qgate.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/gui
copying src/gui/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/gui
copying src/gui/mpl_gate.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/gui
creating build/lib.macosx-10.7-x86_64-3.7/fcm/io
copying src/io/flowjoxml.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/io
copying src/io/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/io
copying src/io/export_to_fcs.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/io
copying src/io/readfcs.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/io
creating build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/mvnpdf.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/partition.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/util.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/modelresult.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/kmeans.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/dime.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/distributions.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/cluster.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/dp_cluster.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/component.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
running build_ext
building 'fcm.core._logicle' extension
creating build/temp.macosx-10.7-x86_64-3.7
creating build/temp.macosx-10.7-x86_64-3.7/src
creating build/temp.macosx-10.7-x86_64-3.7/src/core
creating build/temp.macosx-10.7-x86_64-3.7/src/core/logicle_ext
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/anaconda3/include -arch x86_64 -I/anaconda3/include -arch x86_64 -I/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/anaconda3/include/python3.7m -c src/core/logicle_ext/Logicle.cpp -o build/temp.macosx-10.7-x86_64-3.7/src/core/logicle_ext/Logicle.o
warning: include path for stdlibc++ headers not found; pass '-stdlib=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
src/core/logicle_ext/Logicle.cpp:3:10: fatal error: 'cstring' file not found
#include <cstring>
^~~~~~~~~
1 warning and 1 error generated.
error: command 'gcc' failed with exit status 1
----------------------------------------
Command "/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/kt/54_zwpj929b852yth43_hj440000gn/T/pip-install-424k_8e4/fcm/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/kt/54_zwpj929b852yth43_hj440000gn/T/pip-record-43efnrvl/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/kt/54_zwpj929b852yth43_hj440000gn/T/pip-install-424k_8e4/fcm/
感谢任何进一步的建议
编辑:安装命令行工具并导出 -stdlib=libc++
Downloading https://files.pythonhosted.org/packages/b8/50/92e6fcf82b3411def7c5c08a1b9be5fc4d5f4a4ae8eb7c95ee4b0485fbdd/fcm-0.9.1.tar.gz (1.1MB)
100% |████████████████████████████████| 1.1MB 13.3MB/s
Installing collected packages: fcm
Running setup.py install for fcm ... error
Complete output from command /anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/kt/54_zwpj929b852yth43_hj440000gn/T/pip-install-p_ehtvg8/fcm/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/kt/54_zwpj929b852yth43_hj440000gn/T/pip-record-4xk1zm47/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
creating build
creating build/lib.macosx-10.7-x86_64-3.7
creating build/lib.macosx-10.7-x86_64-3.7/fcm
copying src/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm
creating build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/transforms.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/tree.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/annotation.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/fcmdata.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/logicle.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/compensate.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/gate.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/fcmcollection.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/fcmexceptions.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/subsample.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
creating build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/plot.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/experimental.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/plot_gate.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/util.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/dimechart.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
creating build/lib.macosx-10.7-x86_64-3.7/fcm/gui
copying src/gui/mpl_qgate.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/gui
copying src/gui/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/gui
copying src/gui/mpl_gate.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/gui
creating build/lib.macosx-10.7-x86_64-3.7/fcm/io
copying src/io/flowjoxml.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/io
copying src/io/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/io
copying src/io/export_to_fcs.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/io
copying src/io/readfcs.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/io
creating build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/mvnpdf.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/partition.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/util.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/modelresult.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/kmeans.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/dime.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/distributions.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/cluster.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/dp_cluster.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/component.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
running build_ext
building 'fcm.core._logicle' extension
creating build/temp.macosx-10.7-x86_64-3.7
creating build/temp.macosx-10.7-x86_64-3.7/src
creating build/temp.macosx-10.7-x86_64-3.7/src/core
creating build/temp.macosx-10.7-x86_64-3.7/src/core/logicle_ext
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/anaconda3/include/python3.7m -c src/core/logicle_ext/Logicle.cpp -o build/temp.macosx-10.7-x86_64-3.7/src/core/logicle_ext/Logicle.o
src/core/logicle_ext/Logicle.cpp:290:4: warning: add explicit braces to avoid dangling else [-Wdangling-else]
else
^
1 warning generated.
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/anaconda3/include/python3.7m -c src/core/logicle_ext/my_logicle.cpp -o build/temp.macosx-10.7-x86_64-3.7/src/core/logicle_ext/my_logicle.o
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/anaconda3/include/python3.7m -c src/core/logicle_ext/my_logicle_wrapper.cpp -o build/temp.macosx-10.7-x86_64-3.7/src/core/logicle_ext/my_logicle_wrapper.o
src/core/logicle_ext/my_logicle_wrapper.cpp:788:3: error: no matching function for call to 'PyBytes_AsStringAndSize'
PyBytes_AsStringAndSize(str, &cstr, &len);
^~~~~~~~~~~~~~~~~~~~~~~
/anaconda3/include/python3.7m/bytesobject.h:103:17: note: candidate function not viable: no known conversion from 'int *' to 'Py_ssize_t *' (aka 'long *') for 3rd argument
PyAPI_FUNC(int) PyBytes_AsStringAndSize(
^
src/core/logicle_ext/my_logicle_wrapper.cpp:2229:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
res = SWIG_AddCast(res);
~~~ ^ ~~~
src/core/logicle_ext/my_logicle_wrapper.cpp:2232:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
res = SWIG_AddCast(res);
~~~ ^ ~~~
src/core/logicle_ext/my_logicle_wrapper.cpp:2454:20: error: use of undeclared identifier 'PyCObject_Import'; did you mean 'PyObject_Init'?
type_pointer = PyCObject_Import((char*)"swig_runtime_data" SWIG_RUNTIME_VERSION,
^~~~~~~~~~~~~~~~
PyObject_Init
/anaconda3/include/python3.7m/objimpl.h:130:24: note: 'PyObject_Init' declared here
PyAPI_FUNC(PyObject *) PyObject_Init(PyObject *, PyTypeObject *);
^
src/core/logicle_ext/my_logicle_wrapper.cpp:2454:37: error: cannot initialize a parameter of type 'PyObject *' (aka '_object *') with an rvalue of type 'char *'
type_pointer = PyCObject_Import((char*)"swig_runtime_data" SWIG_RUNTIME_VERSION,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/anaconda3/include/python3.7m/objimpl.h:130:48: note: passing argument to parameter here
PyAPI_FUNC(PyObject *) PyObject_Init(PyObject *, PyTypeObject *);
^
src/core/logicle_ext/my_logicle_wrapper.cpp:2524:23: error: use of undeclared identifier 'PyCObject_FromVoidPtr'
PyObject *pointer = PyCObject_FromVoidPtr((void *) swig_module, SWIG_Python_DestroyModule);
^
src/core/logicle_ext/my_logicle_wrapper.cpp:2547:37: error: use of undeclared identifier 'PyCObject_AsVoidPtr'
descriptor = (swig_type_info *) PyCObject_AsVoidPtr(obj);
^
src/core/logicle_ext/my_logicle_wrapper.cpp:2552:13: error: use of undeclared identifier 'PyCObject_FromVoidPtr'
obj = PyCObject_FromVoidPtr(descriptor, NULL);
^
In file included from src/core/logicle_ext/my_logicle_wrapper.cpp:2800:
In file included from /anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1824:
/anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
^
src/core/logicle_ext/my_logicle_wrapper.cpp:2919:9: error: use of undeclared identifier 'PyString_Check'; did you mean 'PyMapping_Check'?
if (PyString_Check( py_obj)) return "string" ;
^~~~~~~~~~~~~~
PyMapping_Check
/anaconda3/include/python3.7m/abstract.h:1006:17: note: 'PyMapping_Check' declared here
PyAPI_FUNC(int) PyMapping_Check(PyObject *o);
^
src/core/logicle_ext/my_logicle_wrapper.cpp:2925:9: error: use of undeclared identifier 'PyFile_Check'
if (PyFile_Check( py_obj)) return "file" ;
^
src/core/logicle_ext/my_logicle_wrapper.cpp:2927:9: error: use of undeclared identifier 'PyInstance_Check'; did you mean 'PySequence_Check'?
if (PyInstance_Check(py_obj)) return "instance" ;
^~~~~~~~~~~~~~~~
PySequence_Check
/anaconda3/include/python3.7m/abstract.h:838:17: note: 'PySequence_Check' declared here
PyAPI_FUNC(int) PySequence_Check(PyObject *o);
^
src/core/logicle_ext/my_logicle_wrapper.cpp:3435:14: warning: explicitly assigning value of variable of type 'void *' to itself [-Wself-assign]
clientdata = clientdata;
~~~~~~~~~~ ^ ~~~~~~~~~~
4 warnings and 9 errors generated.
error: command 'gcc' failed with exit status 1
----------------------------------------
Command "/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/kt/54_zwpj929b852yth43_hj440000gn/T/pip-install-p_ehtvg8/fcm/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/kt/54_zwpj929b852yth43_hj440000gn/T/pip-record-4xk1zm47/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/kt/54_zwpj929b852yth43_hj440000gn/T/pip-install-p_ehtvg8/fcm/
最佳答案
如果您尝试为“django”安装“fcm”，那么您可以这样做
pip install django-fcm
关于python - 如何修复 python 3.7 中软件包安装 (fcm) 期间的 gcc 错误，我们在Stack Overflow上找到一个类似的问题： https://stackoverflow.com/questions/57075128/