x86_64-apple-darwin13.4.0-clang -bundle -undefined dynamic_lookup -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/bpeng/anaconda3/envs/ictr/lib -L/Users/bpeng/anaconda3/envs/ictr/lib -flto -Wl,-export_dynamic -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/bpeng/anaconda3/envs/ictr/lib -L/Users/bpeng/anaconda3/envs/ictr/lib -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/bpeng/anaconda3/envs/ictr/lib -L/Users/bpeng/anaconda3/envs/ictr/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/bpeng/anaconda3/envs/ictr/include -D_FORTIFY_SOURCE=2 -isystem /Users/bpeng/anaconda3/envs/ictr/include -arch x86_64 build/temp.macosx-10.9-x86_64-3.8/pydigree/cydigree/vcfparse.o -o build/lib.macosx-10.9-x86_64-3.8/pydigree/cydigree/vcfparse.cpython-38-darwin.so
ld: warning: -pie being ignored. It is only used when linking a main executable
building 'pydigree.cydigree.sparsearray' extension
x86_64-apple-darwin13.4.0-clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/bpeng/anaconda3/envs/ictr=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/bpeng/anaconda3/envs/ictr/include -D_FORTIFY_SOURCE=2 -isystem /Users/bpeng/anaconda3/envs/ictr/include -I/Users/bpeng/anaconda3/envs/ictr/include/python3.8 -c pydigree/cydigree/sparsearray.cpp -o build/temp.macosx-10.9-x86_64-3.8/pydigree/cydigree/sparsearray.o -Wno-unused-function
clang-11: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]
In file included from pydigree/cydigree/sparsearray.cpp:23:
/Users/bpeng/anaconda3/envs/ictr/include/python3.8/Python.h:14:2: error: "Something's broken. UCHAR_MAX should be defined in limits.h."
#error "Something's broken. UCHAR_MAX should be defined in limits.h."
^
/Users/bpeng/anaconda3/envs/ictr/include/python3.8/Python.h:18:2: error: "Python's source code assumes C's unsigned char is an 8-bit type."
#error "Python's source code assumes C's unsigned char is an 8-bit type."
^
/Users/bpeng/anaconda3/envs/ictr/include/python3.8/Python.h:27:5: error: "Python.h requires that stdio.h define NULL."
# error "Python.h requires that stdio.h define NULL."
^
In file included from pydigree/cydigree/sparsearray.cpp:23:
In file included from /Users/bpeng/anaconda3/envs/ictr/include/python3.8/Python.h:30:
/Users/bpeng/anaconda3/envs/ictr/bin/../include/c++/v1/string.h:73:64: error: use of undeclared identifier 'strchr'
char* __libcpp_strchr(const char* __s, int __c) {return (char*)strchr(__s, __c);}
^
/Users/bpeng/anaconda3/envs/ictr/bin/../include/c++/v1/string.h:80:75: error: use of undeclared identifier 'strpbrk'
char* __libcpp_strpbrk(const char* __s1, const char* __s2) {return (char*)strpbrk(__s1, __s2);}
^
/Users/bpeng/anaconda3/envs/ictr/bin/../include/c++/v1/string.h:87:65: error: use of undeclared identifier 'strrchr'; did you mean 'strchr'?
char* __libcpp_strrchr(const char* __s, int __c) {return (char*)strrchr(__s, __c);}
/Users/bpeng/anaconda3/envs/ictr/bin/../include/c++/v1/math.h:772:46: note: candidate function
inline _LIBCPP_INLINE_VISIBILITY long double acos(long double __lcpp_x) _NOEXCEPT {return ::acosl(__lcpp_x);}
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
error: command 'x86_64-apple-darwin13.4.0-clang' failed with exit status 1
Running
gives me error messages such as
Is this project on
conda-forgeorbioconda(so that I do not have to install from source)?