尝试安装mirnylib时出现GCC错误

Question

I am trying to install mirnylib in my Ubuntu machine. https://bitbucket.org/mirnylab/mirnylib

I believe all of the required and optional dependencies are installed. However when I run the following command,

pip install https://bitbucket.org/mirnylab/mirnylib/get/tip.tar.gz

I get the following error (sorry for its length. I don't know how to format it better such that it breaks down into parragraphs)

> Collecting https://bitbucket.org/mirnylab/mirnylib/get/tip.tar.gz
  Using cached https://bitbucket.org/mirnylab/mirnylib/get/tip.tar.gz
Requirement already satisfied (use --upgrade to upgrade): biopython in ./anaconda2/lib/python2.7/site-packages (from mirnylib==0.0.0)
Requirement already satisfied (use --upgrade to upgrade): joblib>=0.6.3 in ./anaconda2/lib/python2.7/site-packages (from mirnylib==0.0.0)
Requirement already satisfied (use --upgrade to upgrade): h5py in ./anaconda2/lib/python2.7/site-packages (from mirnylib==0.0.0)
Requirement already satisfied (use --upgrade to upgrade): numpy>=1.6.1 in ./anaconda2/lib/python2.7/site-packages (from h5py->mirnylib==0.0.0)
Requirement already satisfied (use --upgrade to upgrade): six in ./anaconda2/lib/python2.7/site-packages (from h5py->mirnylib==0.0.0)
Installing collected packages: mirnylib
  Running setup.py install for mirnylib ... error
    Complete output from command /home/pau/anaconda2/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-Pg5CY9-build/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-90GRYK-record/install-record.txt --single-version-externally-managed --compile:
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-2.7
    creating build/lib.linux-x86_64-2.7/mirnylib
    copying mirnylib/genome.py -> build/lib.linux-x86_64-2.7/mirnylib
    copying mirnylib/h5dict.py -> build/lib.linux-x86_64-2.7/mirnylib
    copying mirnylib/plotting.py -> build/lib.linux-x86_64-2.7/mirnylib
    copying mirnylib/systemutils.py -> build/lib.linux-x86_64-2.7/mirnylib
    copying mirnylib/__init__.py -> build/lib.linux-x86_64-2.7/mirnylib
    copying mirnylib/numutils.py -> build/lib.linux-x86_64-2.7/mirnylib
    creating build/lib.linux-x86_64-2.7/mirnylib/h5dictUtils
    copying mirnylib/h5dictUtils/h5dictToTxt.py -> build/lib.linux-x86_64-2.7/mirnylib/h5dictUtils
    copying mirnylib/h5dictUtils/__init__.py -> build/lib.linux-x86_64-2.7/mirnylib/h5dictUtils
    copying mirnylib/h5dictUtils/h5dictToMat.py -> build/lib.linux-x86_64-2.7/mirnylib/h5dictUtils
    running build_ext
    cythoning mirnylib/numutils_new.pyx to mirnylib/numutils_new.cpp
    building 'mirnylib.numutils_new' extension
    creating build/temp.linux-x86_64-2.7
    creating build/temp.linux-x86_64-2.7/mirnylib
    gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include -I/home/pau/anaconda2/include/python2.7 -c mirnylib/numutils_new.cpp -o build/temp.linux-x86_64-2.7/mirnylib/numutils_new.o
    cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
    In file included from /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1781:0,
                     from /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from mirnylib/numutils_new.cpp:251:
    /home/pau/anaconda2/lib/python2.7/site-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 " \
      ^
    In file included from /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:27:0,
                     from /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from mirnylib/numutils_new.cpp:251:
    /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1634:1: warning: ‘int _import_array()’ defined but not used [-Wunused-function]
     _import_array(void)
     ^
    mirnylib/numutils_new.cpp:35493:18: warning: ‘PyObject* __pyx_memview_get___pyx_t_double_complex(const char*)’ defined but not used [-Wunused-function]
     static PyObject *__pyx_memview_get___pyx_t_double_complex(const char *itemp) {
                      ^
    mirnylib/numutils_new.cpp:35496:12: warning: ‘int __pyx_memview_set___pyx_t_double_complex(const char*, PyObject*)’ defined but not used [-Wunused-function]
     static int __pyx_memview_set___pyx_t_double_complex(const char *itemp, PyObject *obj) {
                ^
    g++ -pthread -shared -L/home/pau/anaconda2/lib -Wl,-rpath=/home/pau/anaconda2/lib,--no-as-needed build/temp.linux-x86_64-2.7/mirnylib/numutils_new.o -L/home/pau/anaconda2/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/mirnylib/numutils_new.so
    skipping 'mirnylib/fastExtensions/fastExtensionspy.cpp' Cython extension (up-to-date)
    building 'mirnylib.fastExtensions' extension
    creating build/temp.linux-x86_64-2.7/mirnylib/fastExtensions
    gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include -I/home/pau/anaconda2/include/python2.7 -c mirnylib/fastExtensions/fastExtensionspy.cpp -o build/temp.linux-x86_64-2.7/mirnylib/fastExtensions/fastExtensionspy.o -march=native -Ofast -fopenmp
    cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
    In file included from /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1781:0,
                     from /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from mirnylib/fastExtensions/fastExtensionspy.cpp:251:
    /home/pau/anaconda2/lib/python2.7/site-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 " \
      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp: In function ‘PyObject* __pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_openmmArraySum(PyObject*, PyObject*, PyObject*, PyObject*, PyObject*)’:
    mirnylib/fastExtensions/fastExtensionspy.cpp:2302:7: error: redeclaration of ‘int __pyx_v_unsigned_int_is_signed’
       int __pyx_v_unsigned_int_is_signed;
           ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2298:7: error: ‘int __pyx_v_unsigned_int_is_signed’ previously declared here
       int __pyx_v_unsigned_int_is_signed;
           ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2303:7: error: redeclaration of ‘int __pyx_v_long_is_signed’
       int __pyx_v_long_is_signed;
           ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2296:7: error: ‘int __pyx_v_long_is_signed’ previously declared here
       int __pyx_v_long_is_signed;
           ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2305:7: error: redeclaration of ‘int __pyx_v_unsigned_char_is_signed’
       int __pyx_v_unsigned_char_is_signed;
           ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2295:7: error: ‘int __pyx_v_unsigned_char_is_signed’ previously declared here
       int __pyx_v_unsigned_char_is_signed;
           ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2306:7: error: redeclaration of ‘int __pyx_v_int_is_signed’
       int __pyx_v_int_is_signed;
           ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2297:7: error: ‘int __pyx_v_int_is_signed’ previously declared here
       int __pyx_v_int_is_signed;
           ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2370:23: error: cannot convert ‘PyObject* {aka _object*}’ to ‘PyTypeObject* {aka _typeobject*}’ in assignment
           __pyx_v_ndarray = ((PyObject*)__pyx_t_1);
                           ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2443:85: error: ‘__Pyx_PyDict_Contains’ was not declared in this scope
       __pyx_t_3 = (__Pyx_PyDict_Contains(__pyx_n_s_a, ((PyObject*)__pyx_v_kwargs), Py_EQ)); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                                                                         ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2486:58: error: comparison between distinct pointer types ‘PyTypeObject* {aka _typeobject*}’ and ‘PyObject* {aka _object*}’ lacks a cast
           __pyx_t_2 = (__pyx_v_ndarray != ((PyObject*)Py_None));
                                                              ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2541:43: error: ‘__pyx_builtin_ord’ was not declared in this scope
               __pyx_t_8 = __Pyx_PyObject_Call(__pyx_builtin_ord, __pyx_t_9, NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                               ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2865:11: error: case label ‘'f'’ not within a switch statement
               case 'f':
               ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2901:11: error: case label ‘'c'’ not within a switch statement
               case 'c':
               ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2903:11: error: case label ‘'O'’ not within a switch statement
               case 'O':
               ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2905:11: error: case label not within a switch statement
               default: break;
               ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:3048:14: error: label ‘__pyx_L84’ used but not defined
             goto __pyx_L84;
                  ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:3077:14: error: label ‘__pyx_L88’ used but not defined
             goto __pyx_L88;
                  ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:3106:14: error: label ‘__pyx_L92’ used but not defined
             goto __pyx_L92;
                  ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:3135:14: error: label ‘__pyx_L96’ used but not defined
             goto __pyx_L96;
                  ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:3164:14: error: label ‘__pyx_L100’ used but not defined
             goto __pyx_L100;
                  ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:3193:14: error: label ‘__pyx_L104’ used but not defined
             goto __pyx_L104;
                  ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:3222:14: error: label ‘__pyx_L108’ used but not defined
             goto __pyx_L108;
                  ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:3385:14: error: label ‘__pyx_L120_unpacking_done’ used but not defined
             goto __pyx_L120_unpacking_done;
                  ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:3391:9: warning: label ‘__pyx_L121_unpacking_done’ defined but not used [-Wunused-label]
             __pyx_L121_unpacking_done:;
             ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:3419:12: error: label ‘__pyx_L124’ used but not defined
           goto __pyx_L124;
                ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2572:20: error: label ‘__pyx_L17_break’ used but not defined
                   goto __pyx_L17_break;
                        ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2839:18: error: label ‘__pyx_L16_break’ used but not defined
                 goto __pyx_L16_break;
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2932:14: error: label ‘__pyx_L68’ used but not defined
             goto __pyx_L68;
                  ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2961:14: error: label ‘__pyx_L72’ used but not defined
             goto __pyx_L72;
                  ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2990:14: error: label ‘__pyx_L76’ used but not defined
             goto __pyx_L76;
                  ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:3019:14: error: label ‘__pyx_L80’ used but not defined
             goto __pyx_L80;
                  ^
    mirnylib/fastExtensions/fastExtensionspy.cpp: At global scope:
    mirnylib/fastExtensions/fastExtensionspy.cpp:19243:49: error: ‘__pyx_k_net_levsha_home_libraries_mirny’ was not declared in this scope
       {&__pyx_kp_s_net_levsha_home_libraries_mirny, __pyx_k_net_levsha_home_libraries_mirny, sizeof(__pyx_k_net_levsha_home_libraries_mirny), 0, 0, 1, 0},
                                                     ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:19243:97: error: ‘__pyx_k_net_levsha_home_libraries_mirny’ was not declared in this scope
       {&__pyx_kp_s_net_levsha_home_libraries_mirny, __pyx_k_net_levsha_home_libraries_mirny, sizeof(__pyx_k_net_levsha_home_libraries_mirny), 0, 0, 1, 0},
                                                                                                     ^
    mirnylib/fastExtensions/fastExtensionspy.cpp: In function ‘int __Pyx_InitCachedBuiltins()’:
    mirnylib/fastExtensions/fastExtensionspy.cpp:19287:3: error: ‘__pyx_builtin_ord’ was not declared in this scope
       __pyx_builtin_ord = __Pyx_GetBuiltinName(__pyx_n_s_ord); if (!__pyx_builtin_ord) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:19287:44: error: ‘__pyx_n_s_ord’ was not declared in this scope
       __pyx_builtin_ord = __Pyx_GetBuiltinName(__pyx_n_s_ord); if (!__pyx_builtin_ord) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                                ^
    mirnylib/fastExtensions/fastExtensionspy.cpp: In function ‘int __Pyx_InitCachedConstants()’:
    mirnylib/fastExtensions/fastExtensionspy.cpp:19548:3: error: ‘__pyx_codeobj__26’ was not declared in this scope
       __pyx_codeobj__26 = (PyObject*)__Pyx_PyCode_New(1, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__25, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_magus_HiC2011_libraries_mi, __pyx_n_s_openmmArraySum, 35, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__26)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:19557:3: error: ‘__pyx_tuple__27’ was not declared in this scope
       __pyx_tuple__27 = PyTuple_Pack(11, __pyx_n_s_filename, __pyx_n_s_data, __pyx_n_s_chromCount, __pyx_n_s_useX, __pyx_n_s_useY, __pyx_n_s_useM, __pyx_n_s_Xnum, __pyx_n_s_Ynum, __pyx_n_s_Mnum, __pyx_n_s_Mkb, __pyx_n_s_resolution); if (unlikely(!__pyx_tuple__27)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:19560:3: error: ‘__pyx_codeobj__28’ was not declared in this scope
       __pyx_codeobj__28 = (PyObject*)__Pyx_PyCode_New(11, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__27, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_magus_HiC2011_libraries_mi, __pyx_n_s_readWigFile, 40, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__28)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
       ^
    mirnylib/fastExtensions/fastExtensionspy.cpp: In function ‘void initfastExtensionspy()’:
    mirnylib/fastExtensions/fastExtensionspy.cpp:19796:229: error: ‘__pyx_codeobj__26’ was not declared in this scope
       __pyx_t_2 = __pyx_FusedFunction_NewEx(&__pyx_fuse_0__pyx_mdef_8mirnylib_14fastExtensions_16fastExtensionspy_5openmmArraySum, 0, __pyx_n_s_openmmArraySum, NULL, __pyx_n_s_mirnylib_fastExtensions_fastExte, __pyx_d, ((PyObject *)__pyx_codeobj__26)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                                                                                                                                                                                                                         ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:1354:102: note: in definition of macro ‘__pyx_FusedFunction_NewEx’
             __pyx_FusedFunction_New(__pyx_FusedFunctionType, ml, flags, qualname, self, module, globals, code)
                                                                                                          ^
    In file included from /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:27:0,
                     from /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from mirnylib/fastExtensions/fastExtensionspy.cpp:251:
    /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h: At global scope:
    /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1634:1: warning: ‘int _import_array()’ defined but not used [-Wunused-function]
     _import_array(void)
     ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:20679:13: warning: ‘long int __Pyx__PyObject_Ord(PyObject*)’ defined but not used [-Wunused-function]
     static long __Pyx__PyObject_Ord(PyObject* c) {
                 ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2102:18: warning: ‘PyObject* __pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_28openmmArraySum(PyObject*, __Pyx_memviewslice)’ declared ‘static’ but never defined [-Wunused-function]
     static PyObject *__pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_28openmmArraySum(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_a); /* proto */
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2103:18: warning: ‘PyObject* __pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_2coverageSum(PyObject*, PyObject*, PyObject*, PyObject*, PyObject*)’ declared ‘static’ but never defined [-Wunused-function]
     static PyObject *__pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_2coverageSum(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_signatures, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs, CYTHON_UNUSED PyObject *__pyx_v_defaults); /* proto */
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2104:18: warning: ‘PyObject* __pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_32coverageSum(PyObject*, __Pyx_memviewslice, int)’ declared ‘static’ but never defined [-Wunused-function]
     static PyObject *__pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_32coverageSum(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_a, int __pyx_v_N); /* proto */
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2105:18: warning: ‘PyObject* __pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_34coverageSum(PyObject*, __Pyx_memviewslice, int)’ declared ‘static’ but never defined [-Wunused-function]
     static PyObject *__pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_34coverageSum(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_a, int __pyx_v_N); /* proto */
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2106:18: warning: ‘PyObject* __pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_36coverageSum(PyObject*, __Pyx_memviewslice, int)’ declared ‘static’ but never defined [-Wunused-function]
     static PyObject *__pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_36coverageSum(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_a, int __pyx_v_N); /* proto */
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2107:18: warning: ‘PyObject* __pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_38coverageSum(PyObject*, __Pyx_memviewslice, int)’ declared ‘static’ but never defined [-Wunused-function]
     static PyObject *__pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_38coverageSum(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_a, int __pyx_v_N); /* proto */
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2108:18: warning: ‘PyObject* __pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_40coverageSum(PyObject*, __Pyx_memviewslice, int)’ declared ‘static’ but never defined [-Wunused-function]
     static PyObject *__pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_40coverageSum(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_a, int __pyx_v_N); /* proto */
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2109:18: warning: ‘PyObject* __pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_42coverageSum(PyObject*, __Pyx_memviewslice, int)’ declared ‘static’ but never defined [-Wunused-function]
     static PyObject *__pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_42coverageSum(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_a, int __pyx_v_N); /* proto */
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2110:18: warning: ‘PyObject* __pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_44coverageSum(PyObject*, __Pyx_memviewslice, int)’ declared ‘static’ but never defined [-Wunused-function]
     static PyObject *__pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_44coverageSum(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_a, int __pyx_v_N); /* proto */
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2111:18: warning: ‘PyObject* __pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_46coverageSum(PyObject*, __Pyx_memviewslice, int)’ declared ‘static’ but never defined [-Wunused-function]
     static PyObject *__pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_46coverageSum(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_a, int __pyx_v_N); /* proto */
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2112:18: warning: ‘PyObject* __pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_48coverageSum(PyObject*, __Pyx_memviewslice, int)’ declared ‘static’ but never defined [-Wunused-function]
     static PyObject *__pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_48coverageSum(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_a, int __pyx_v_N); /* proto */
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2113:18: warning: ‘PyObject* __pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_50coverageSum(PyObject*, __Pyx_memviewslice, int)’ declared ‘static’ but never defined [-Wunused-function]
     static PyObject *__pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_50coverageSum(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_a, int __pyx_v_N); /* proto */
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2114:18: warning: ‘PyObject* __pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_52coverageSum(PyObject*, __Pyx_memviewslice, int)’ declared ‘static’ but never defined [-Wunused-function]
     static PyObject *__pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_52coverageSum(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_a, int __pyx_v_N); /* proto */
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2115:18: warning: ‘PyObject* __pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_54coverageSum(PyObject*, __Pyx_memviewslice, int)’ declared ‘static’ but never defined [-Wunused-function]
     static PyObject *__pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_54coverageSum(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_a, int __pyx_v_N); /* proto */
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2116:18: warning: ‘PyObject* __pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_4readWigFile(PyObject*, char*, __Pyx_memviewslice, int, PyBoolObject*, PyBoolObject*, PyBoolObject*, int, int, int, int, int)’ declared ‘static’ but never defined [-Wunused-function]
     static PyObject *__pyx_pf_8mirnylib_14fastExtensions_16fastExtensionspy_4readWigFile(CYTHON_UNUSED PyObject *__pyx_self, char *__pyx_v_filename, __Pyx_memviewslice __pyx_v_data, int __pyx_v_chromCount, PyBoolObject *__pyx_v_useX, PyBoolObject *__pyx_v_useY, PyBoolObject *__pyx_v_useM, int __pyx_v_Xnum, int __pyx_v_Ynum, int __pyx_v_Mnum, int __pyx_v_Mkb, int __pyx_v_resolution); /* proto */
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2162:18: warning: ‘__pyx_tuple__7’ defined but not used [-Wunused-variable]
     static PyObject *__pyx_tuple__7;
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2163:18: warning: ‘__pyx_tuple__8’ defined but not used [-Wunused-variable]
     static PyObject *__pyx_tuple__8;
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2164:18: warning: ‘__pyx_tuple__9’ defined but not used [-Wunused-variable]
     static PyObject *__pyx_tuple__9;
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2168:18: warning: ‘__pyx_tuple__10’ defined but not used [-Wunused-variable]
     static PyObject *__pyx_tuple__10;
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2185:18: warning: ‘__pyx_tuple__30’ defined but not used [-Wunused-variable]
     static PyObject *__pyx_tuple__30;
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2186:18: warning: ‘__pyx_tuple__32’ defined but not used [-Wunused-variable]
     static PyObject *__pyx_tuple__32;
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2187:18: warning: ‘__pyx_tuple__34’ defined but not used [-Wunused-variable]
     static PyObject *__pyx_tuple__34;
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2193:18: warning: ‘__pyx_codeobj__31’ defined but not used [-Wunused-variable]
     static PyObject *__pyx_codeobj__31;
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2194:18: warning: ‘__pyx_codeobj__33’ defined but not used [-Wunused-variable]
     static PyObject *__pyx_codeobj__33;
                      ^
    mirnylib/fastExtensions/fastExtensionspy.cpp:2195:18: warning: ‘__pyx_codeobj__35’ defined but not used [-Wunused-variable]
     static PyObject *__pyx_codeobj__35;
                      ^
>    error: command 'gcc' failed with exit status 1

>    ----------------------------------------
>Command "/home/pau/anaconda2/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-Pg5CY9-build/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-90GRYK-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-Pg5CY9-build

Thank you

Answer 1

From a quick glance at the bitbucket repository you linked, I think you need to install the libhdf5-dev package.

For the h5py package to install properly, you need to have the shared library and development headers for HDF5 1.8.4 or newer installed (libhdf5-dev or similar). See the h5py docs for more information.

Answer 2

You need to install biopython by typing 'conda install biopython', and you properly have to check if you have installed all required dependencies and then retry it. Hopefully it works for you.