Hi all,

I am trying to run imp_sampcon exhaust from the actin tutorial and pyRMSD is required. I tried pip installation and git cloned the repository but got the following issue on installation.

"""

/cm/shared/apps/python-3.7.7/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'install_requires'

warnings.warn(msg)

running install

running build

running build_py

running build_ext

building 'pyRMSD.pdbReader' extension

gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/cm/shared/apps/python-3.7.7/lib/python3.7/site-packages/numpy/core/include -I/cm/shared/apps/python-3.7.7/include/python3.7m -I/cm/shared/apps/python-3.7.7/include/python3.7m -c src/pdbreaderlite/PDBReader.cpp -o build/temp.linux-x86_64-3.7/src/pdbreaderlite/PDBReader.o

gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/cm/shared/apps/python-3.7.7/lib/python3.7/site-packages/numpy/core/include -I/cm/shared/apps/python-3.7.7/include/python3.7m -I/cm/shared/apps/python-3.7.7/include/python3.7m -c src/pdbreaderlite/PDBReaderObject.cpp -o build/temp.linux-x86_64-3.7/src/pdbreaderlite/PDBReaderObject.o

In file included from /cm/shared/apps/python-3.7.7/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:0,

from /cm/shared/apps/python-3.7.7/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,

from /cm/shared/apps/python-3.7.7/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,

from src/pdbreaderlite/PDBReaderObject.cpp:3:

/cm/shared/apps/python-3.7.7/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_DEPRECATED_API NPY_1_7_API_VERSION" -Wcpp]

#warning "Using deprecated NumPy API, disable it with " \

^~~~~~~

src/pdbreaderlite/PDBReaderObject.cpp: In function ‘PyObject* pdbreader_read(pdbreader*, PyObject*)’:

src/pdbreaderlite/PDBReaderObject.cpp:87:55: warning: narrowing conversion of ‘self->pdbreader::reader->PDBReader::all_coordinates.std::vector<_Tp, _Alloc>::size<double, std::allocator<double> >()’ from ‘std::vector<double>::size_type {aka long unsigned int}’ to ‘npy_intp {aka long int}’ inside { } [-Wnarrowing]

npy_intp dims[] = {self->reader->all_coordinates.size()};

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~

src/pdbreaderlite/PDBReaderObject.cpp: At global scope:

src/pdbreaderlite/PDBReaderObject.cpp:142:1: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t {aka long int}’ [-fpermissive]

};

^

src/pdbreaderlite/PDBReaderObject.cpp:108:5: error: invalid conversion from ‘destructor {aka void (*)(_object*)}’ to ‘printfunc {aka int (*)(_object*, _IO_FILE*, int)}’ [-fpermissive]

(destructor)pdbreader_dealloc, /*tp_dealloc*/

^~~~~~~~~~~~~~~~~~~~~~~~~~~~~

src/pdbreaderlite/PDBReaderObject.cpp:123:23: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive]

Py_TPFLAGS_DEFAULT| Py_TPFLAGS_BASETYPE , /*tp_flags*/

src/pdbreaderlite/PDBReaderObject.cpp:142:1: error: cannot convert ‘const char*’ to ‘traverseproc {aka int (*)(_object*, int (*)(_object*, void*), void*)}’ in initialization

};

^

src/pdbreaderlite/PDBReaderObject.cpp:142:1: error: cannot convert ‘PyMethodDef*’ to ‘PyMemberDef*’ in initialization

src/pdbreaderlite/PDBReaderObject.cpp:142:1: error: cannot convert ‘PyMemberDef*’ to ‘PyGetSetDef*’ in initialization

src/pdbreaderlite/PDBReaderObject.cpp:139:2: error: invalid conversion from ‘initproc {aka int (*)(_object*, _object*, _object*)}’ to ‘allocfunc {aka _object* (*)(_typeobject*, long int)}’ [-fpermissive]

(initproc)pdbreader_init, /* tp_init */

^~~~~~~~~~~~~~~~~~~~~~~~

src/pdbreaderlite/PDBReaderObject.cpp:142:1: error: invalid conversion from ‘PyObject* (*)(PyTypeObject*, PyObject*, PyObject*) {aka _object* (*)(_typeobject*, _object*, _object*)}’ to ‘freefunc {aka void (*)(void*)}’ [-fpermissiv]

};

^

src/pdbreaderlite/PDBReaderObject.cpp: In function ‘PyObject* initpdbReader()’:

src/pdbreaderlite/PDBReaderObject.cpp:153:9: error: return-statement with no value, in function returning ‘PyObject* {aka _object*}’ [-fpermissive]

return;

^~~~~~

src/pdbreaderlite/PDBReaderObject.cpp:155:67: error: ‘Py_InitModule3’ was not declared in this scope

module = Py_InitModule3("pdbReader", NULL,"Simple pdb reading");

^

src/pdbreaderlite/PDBReaderObject.cpp:157:11: error: return-statement with no value, in function returning ‘PyObject* {aka _object*}’ [-fpermissive]

return;

^~~~~~

src/pdbreaderlite/PDBReaderObject.cpp:163:1: warning: control reaches end of non-void function [-Wreturn-type]

}

^

error: command 'gcc' failed with exit status 1

"""

Has anyone encountered this error before? Any help would be greatly appreciated.

All the best,

Jose Gorbea