python - GCC error when trying to install mirnylib -
i trying install mirnylib in ubuntu machine. https://bitbucket.org/mirnylab/mirnylib
i believe of required , optional dependencies installed. when run following command,
pip install https://bitbucket.org/mirnylab/mirnylib/get/tip.tar.gz i following error (sorry length. don't know how format better such breaks down parragraphs)
> collecting https://bitbucket.org/mirnylab/mirnylib/get/tip.tar.gz using cached https://bitbucket.org/mirnylab/mirnylib/get/tip.tar.gz requirement satisfied (use --upgrade upgrade): biopython in ./anaconda2/lib/python2.7/site-packages (from mirnylib==0.0.0) requirement satisfied (use --upgrade upgrade): joblib>=0.6.3 in ./anaconda2/lib/python2.7/site-packages (from mirnylib==0.0.0) requirement satisfied (use --upgrade upgrade): h5py in ./anaconda2/lib/python2.7/site-packages (from mirnylib==0.0.0) requirement satisfied (use --upgrade upgrade): numpy>=1.6.1 in ./anaconda2/lib/python2.7/site-packages (from h5py->mirnylib==0.0.0) requirement satisfied (use --upgrade upgrade): 6 in ./anaconda2/lib/python2.7/site-packages (from h5py->mirnylib==0.0.0) installing collected packages: mirnylib running setup.py install mirnylib ... error complete output 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 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’ valid c/objc not c++ [enabled default] in file included /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1781:0, /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, 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 " "#defining npy_no_deprecated_api npy_1_7_api_version" [-wcpp] #warning "using deprecated numpy api, disable " \ ^ in file included /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:27:0, /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, 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 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 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 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’ valid c/objc not c++ [enabled default] in file included /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1781:0, /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, 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 " "#defining npy_no_deprecated_api npy_1_7_api_version" [-wcpp] #warning "using deprecated numpy api, disable " \ ^ 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’ 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’ 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’ 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’ declared here int __pyx_v_int_is_signed; ^ mirnylib/fastextensions/fastextensionspy.cpp:2370:23: error: cannot convert ‘pyobject* {aka _object*}’ ‘pytypeobject* {aka _typeobject*}’ in assignment __pyx_v_ndarray = ((pyobject*)__pyx_t_1); ^ mirnylib/fastextensions/fastextensionspy.cpp:2443:85: error: ‘__pyx_pydict_contains’ not declared in 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*}’ , ‘pyobject* {aka _object*}’ lacks cast __pyx_t_2 = (__pyx_v_ndarray != ((pyobject*)py_none)); ^ mirnylib/fastextensions/fastextensionspy.cpp:2541:43: error: ‘__pyx_builtin_ord’ not declared in 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 switch statement case 'f': ^ mirnylib/fastextensions/fastextensionspy.cpp:2901:11: error: case label ‘'c'’ not within switch statement case 'c': ^ mirnylib/fastextensions/fastextensionspy.cpp:2903:11: error: case label ‘'o'’ not within switch statement case 'o': ^ mirnylib/fastextensions/fastextensionspy.cpp:2905:11: error: case label not within switch statement default: break; ^ mirnylib/fastextensions/fastextensionspy.cpp:3048:14: error: label ‘__pyx_l84’ used not defined goto __pyx_l84; ^ mirnylib/fastextensions/fastextensionspy.cpp:3077:14: error: label ‘__pyx_l88’ used not defined goto __pyx_l88; ^ mirnylib/fastextensions/fastextensionspy.cpp:3106:14: error: label ‘__pyx_l92’ used not defined goto __pyx_l92; ^ mirnylib/fastextensions/fastextensionspy.cpp:3135:14: error: label ‘__pyx_l96’ used not defined goto __pyx_l96; ^ mirnylib/fastextensions/fastextensionspy.cpp:3164:14: error: label ‘__pyx_l100’ used not defined goto __pyx_l100; ^ mirnylib/fastextensions/fastextensionspy.cpp:3193:14: error: label ‘__pyx_l104’ used not defined goto __pyx_l104; ^ mirnylib/fastextensions/fastextensionspy.cpp:3222:14: error: label ‘__pyx_l108’ used not defined goto __pyx_l108; ^ mirnylib/fastextensions/fastextensionspy.cpp:3385:14: error: label ‘__pyx_l120_unpacking_done’ used not defined goto __pyx_l120_unpacking_done; ^ mirnylib/fastextensions/fastextensionspy.cpp:3391:9: warning: label ‘__pyx_l121_unpacking_done’ defined not used [-wunused-label] __pyx_l121_unpacking_done:; ^ mirnylib/fastextensions/fastextensionspy.cpp:3419:12: error: label ‘__pyx_l124’ used not defined goto __pyx_l124; ^ mirnylib/fastextensions/fastextensionspy.cpp:2572:20: error: label ‘__pyx_l17_break’ used not defined goto __pyx_l17_break; ^ mirnylib/fastextensions/fastextensionspy.cpp:2839:18: error: label ‘__pyx_l16_break’ used not defined goto __pyx_l16_break; ^ mirnylib/fastextensions/fastextensionspy.cpp:2932:14: error: label ‘__pyx_l68’ used not defined goto __pyx_l68; ^ mirnylib/fastextensions/fastextensionspy.cpp:2961:14: error: label ‘__pyx_l72’ used not defined goto __pyx_l72; ^ mirnylib/fastextensions/fastextensionspy.cpp:2990:14: error: label ‘__pyx_l76’ used not defined goto __pyx_l76; ^ mirnylib/fastextensions/fastextensionspy.cpp:3019:14: error: label ‘__pyx_l80’ used not defined goto __pyx_l80; ^ mirnylib/fastextensions/fastextensionspy.cpp: @ global scope: mirnylib/fastextensions/fastextensionspy.cpp:19243:49: error: ‘__pyx_k_net_levsha_home_libraries_mirny’ not declared in 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’ not declared in 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’ not declared in 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’ not declared in 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’ not declared in 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’ not declared in 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’ not declared in 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’ not declared in 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 /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:27:0, /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, mirnylib/fastextensions/fastextensionspy.cpp:251: /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h: @ global scope: /home/pau/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1634:1: warning: ‘int _import_array()’ defined not used [-wunused-function] _import_array(void) ^ mirnylib/fastextensions/fastextensionspy.cpp:20679:13: warning: ‘long int __pyx__pyobject_ord(pyobject*)’ defined 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’ 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’ 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’ 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’ 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’ 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’ 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’ 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’ 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’ 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’ 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’ 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’ 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’ 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’ 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’ 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 not used [-wunused-variable] static pyobject *__pyx_tuple__7; ^ mirnylib/fastextensions/fastextensionspy.cpp:2163:18: warning: ‘__pyx_tuple__8’ defined not used [-wunused-variable] static pyobject *__pyx_tuple__8; ^ mirnylib/fastextensions/fastextensionspy.cpp:2164:18: warning: ‘__pyx_tuple__9’ defined not used [-wunused-variable] static pyobject *__pyx_tuple__9; ^ mirnylib/fastextensions/fastextensionspy.cpp:2168:18: warning: ‘__pyx_tuple__10’ defined not used [-wunused-variable] static pyobject *__pyx_tuple__10; ^ mirnylib/fastextensions/fastextensionspy.cpp:2185:18: warning: ‘__pyx_tuple__30’ defined not used [-wunused-variable] static pyobject *__pyx_tuple__30; ^ mirnylib/fastextensions/fastextensionspy.cpp:2186:18: warning: ‘__pyx_tuple__32’ defined not used [-wunused-variable] static pyobject *__pyx_tuple__32; ^ mirnylib/fastextensions/fastextensionspy.cpp:2187:18: warning: ‘__pyx_tuple__34’ defined not used [-wunused-variable] static pyobject *__pyx_tuple__34; ^ mirnylib/fastextensions/fastextensionspy.cpp:2193:18: warning: ‘__pyx_codeobj__31’ defined not used [-wunused-variable] static pyobject *__pyx_codeobj__31; ^ mirnylib/fastextensions/fastextensionspy.cpp:2194:18: warning: ‘__pyx_codeobj__33’ defined not used [-wunused-variable] static pyobject *__pyx_codeobj__33; ^ mirnylib/fastextensions/fastextensionspy.cpp:2195:18: warning: ‘__pyx_codeobj__35’ defined not used [-wunused-variable] static pyobject *__pyx_codeobj__35; ^ > error: command 'gcc' failed 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 error code 1 in /tmp/pip-pg5cy9-build thank you
from quick glance @ bitbucket repository linked, think need install libhdf5-dev package.
for h5py package install properly, need have shared library , development headers hdf5 1.8.4 or newer installed (libhdf5-dev or similar). see h5py docs more information.
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