jfrelinger / fcm Goto Github PK
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a python library for working with flow cytometry data.
How about including informations about installation (and not just necessary libraries)? Can we install it with pip? Or is it necessary to use setup.py?
I don't understand the point of making a page on installation just to list third party libraries that are nessesary..
I can build and install from this repo just fine under Py2, once dpmix
and all its associated dependencies were installed. However, I get the following when trying to build with the Ubuntu 16.04 version of Python 3.5.1+:
$ python3 setup.py build
running build
running build_py
running build_ext
building 'fcm.core._logicle' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/lib/python3.5/dist-packages/numpy/core/include -I/usr/include/python3.5m -c src/core/logicle_ext/Logicle.cpp -o build/temp.linux-x86_64-3.5/src/core/logicle_ext/Logicle.o
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
src/core/logicle_ext/Logicle.cpp: In member function ‘virtual double Logicle::scale(double) const’:
src/core/logicle_ext/Logicle.cpp:286:6: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
if (std::abs(delta) < tolerance)
^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/lib/python3.5/dist-packages/numpy/core/include -I/usr/include/python3.5m -c src/core/logicle_ext/my_logicle.cpp -o build/temp.linux-x86_64-3.5/src/core/logicle_ext/my_logicle.o
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/lib/python3.5/dist-packages/numpy/core/include -I/usr/include/python3.5m -c src/core/logicle_ext/my_logicle_wrapper.cpp -o build/temp.linux-x86_64-3.5/src/core/logicle_ext/my_logicle_wrapper.o
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
In file included from /usr/local/lib/python3.5/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1777:0,
from /usr/local/lib/python3.5/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /usr/local/lib/python3.5/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
from src/core/logicle_ext/my_logicle_wrapper.cpp:2800:
/usr/local/lib/python3.5/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
src/core/logicle_ext/my_logicle_wrapper.cpp: In function ‘char* SWIG_Python_str_AsChar(PyObject*)’:
src/core/logicle_ext/my_logicle_wrapper.cpp:788:43: error: cannot convert ‘int*’ to ‘Py_ssize_t* {aka long int*}’ for argument ‘3’ to ‘int PyBytes_AsStringAndSize(PyObject*, char**, Py_ssize_t*)’
PyBytes_AsStringAndSize(str, &cstr, &len);
^
src/core/logicle_ext/my_logicle_wrapper.cpp: In function ‘swig_module_info* SWIG_Python_GetModule()’:
src/core/logicle_ext/my_logicle_wrapper.cpp:2455:51: error: ‘PyCObject_Import’ was not declared in this scope
(char*)"type_pointer" SWIG_TYPE_TABLE_NAME);
^
src/core/logicle_ext/my_logicle_wrapper.cpp: In function ‘void SWIG_Python_SetModule(swig_module_info*)’:
src/core/logicle_ext/my_logicle_wrapper.cpp:2524:92: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope
PyObject *pointer = PyCObject_FromVoidPtr((void *) swig_module, SWIG_Python_DestroyModule);
^
src/core/logicle_ext/my_logicle_wrapper.cpp:2515:22: warning: unused variable ‘swig_empty_runtime_method_table’ [-Wunused-variable]
static PyMethodDef swig_empty_runtime_method_table[] = { {NULL, NULL, 0, NULL} };/* Sentinel */
^
src/core/logicle_ext/my_logicle_wrapper.cpp: In function ‘swig_type_info* SWIG_Python_TypeQuery(const char*)’:
src/core/logicle_ext/my_logicle_wrapper.cpp:2547:60: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope
descriptor = (swig_type_info *) PyCObject_AsVoidPtr(obj);
^
src/core/logicle_ext/my_logicle_wrapper.cpp:2552:51: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope
obj = PyCObject_FromVoidPtr(descriptor, NULL);
^
src/core/logicle_ext/my_logicle_wrapper.cpp: In function ‘const char* pytype_string(PyObject*)’:
src/core/logicle_ext/my_logicle_wrapper.cpp:2919:32: error: ‘PyString_Check’ was not declared in this scope
if (PyString_Check( py_obj)) return "string" ;
^
src/core/logicle_ext/my_logicle_wrapper.cpp:2925:32: error: ‘PyFile_Check’ was not declared in this scope
if (PyFile_Check( py_obj)) return "file" ;
^
src/core/logicle_ext/my_logicle_wrapper.cpp:2927:32: error: ‘PyInstance_Check’ was not declared in this scope
if (PyInstance_Check(py_obj)) return "instance" ;
^
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
Here's my GCC info:
$ x86_64-linux-gnu-gcc --version
x86_64-linux-gnu-gcc (Ubuntu 5.3.1-14ubuntu2.1) 5.3.1 20160413
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
I have all the Python 3 headers installed, so that's not the issue (and the errors would likely be different if it was).
Unfortunately, I don't know C++, so I don't have the slightest idea how to fix this error. I really like this package, and I would love to get it working with Py3 (as I'm sure many other people would as well). Any help you could provide would be fantastic.
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