Python package installs globally but fails within virtual environment-CodePudding

The

The main error is:

ERROR: Failed building wheel for fdasrsf Successfully built hdbscan Failed to build fdasrsf ERROR: Could not build wheels for fdasrsf, which is required to install pyproject.toml-based projects

How is it possible that I can install globally, but not within the virtual environment via the terminal in Visual Studio Code?

EDIT I used pip3 as suggested. I still get the same error. Heres are more. Here are more logs of the errors:

_Nonnull /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:83:53: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness] int pthread_sigmask(int, const sigset_t *, sigset_t *) __DARWIN_ALIAS(pthread_sigmask); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:83:53: note: insert '_Nullable' if the pointer may be null int pthread_sigmask(int, const sigset_t *, sigset_t *) __DARWIN_ALIAS(pthread_sigmask); ^ _Nullable /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:83:53: note: insert '_Nonnull' if the pointer should never be null int pthread_sigmask(int, const sigset_t *, sigset_t *) __DARWIN_ALIAS(pthread_sigmask); ^ _Nonnull /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:84:43: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness] int sigaction(int, const struct sigaction * __restrict, ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:84:43: note: insert '_Nullable' if the pointer may be null int sigaction(int, const struct sigaction * __restrict, ^ _Nullable /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:84:43: note: insert '_Nonnull' if the pointer should never be null int sigaction(int, const struct sigaction * __restrict, ^ _Nonnull /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:85:23: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness] struct sigaction * __restrict); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:85:23: note: insert '_Nullable' if the pointer may be null struct sigaction * __restrict); ^ _Nullable /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:85:23: note: insert '_Nonnull' if the pointer should never be null struct sigaction * __restrict); ^ _Nonnull /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:86:24: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness] int sigaddset(sigset_t *, int); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:86:24: note: insert '_Nullable' if the pointer may be null int sigaddset(sigset_t *, int); ^ _Nullable /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:86:24: note: insert '_Nonnull' if the pointer should never be null int sigaddset(sigset_t *, int); ^ _Nonnull /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:87:31: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness] int sigaltstack(const stack_t * __restrict, stack_t * __restrict) __DARWIN_ALIAS(sigaltstack) __WATCHOS_PROHIBITED __TVOS_PROHIBITED; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:87:31: note: insert '_Nullable' if the pointer may be null int sigaltstack(const stack_t * __restrict, stack_t * __restrict) __DARWIN_ALIAS(sigaltstack) __WATCHOS_PROHIBITED __TVOS_PROHIBITED; ^ _Nullable /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:87:31: note: insert '_Nonnull' if the pointer should never be null int sigaltstack(const stack_t * __restrict, stack_t * __restrict) __DARWIN_ALIAS(sigaltstack) __WATCHOS_PROHIBITED __TVOS_PROHIBITED; ^ _Nonnull /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:87:53: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness] int sigaltstack(const stack_t * __restrict, stack_t * __restrict) __DARWIN_ALIAS(sigaltstack) __WATCHOS_PROHIBITED __TVOS_PROHIBITED; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:87:53: note: insert '_Nullable' if the pointer may be null int sigaltstack(const stack_t * __restrict, stack_t * __restrict) __DARWIN_ALIAS(sigaltstack) __WATCHOS_PROHIBITED __TVOS_PROHIBITED; ^ _Nullable /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:87:53: note: insert '_Nonnull' if the pointer should never be null int sigaltstack(const stack_t * __restrict, stack_t * __restrict) __DARWIN_ALIAS(sigaltstack) __WATCHOS_PROHIBITED __TVOS_PROHIBITED; ^ _Nonnull /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:88:24: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness] int sigdelset(sigset_t *, int); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:88:24: note: insert '_Nullable' if the pointer may be null int sigdelset(sigset_t *, int); ^ _Nullable /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:88:24: note: insert '_Nonnull' if the pointer should never be null int sigdelset(sigset_t *, int); ^ _Nonnull /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:89:26: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness] int sigemptyset(sigset_t *); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:89:26: note: insert '_Nullable' if the pointer may be null int sigemptyset(sigset_t *); ^ _Nullable /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:89:26: note: insert '_Nonnull' if the pointer should never be null int sigemptyset(sigset_t *); ^ _Nonnull /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:90:25: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness] int sigfillset(sigset_t *); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:90:25: note: insert '_Nullable' if the pointer may be null int sigfillset(sigset_t *); ^ _Nullable /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:90:25: note: insert '_Nonnull' if the pointer should never be null int sigfillset(sigset_t *); ^ _Nonnull /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:94:32: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness] int sigismember(const sigset_t *, int); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:94:32: note: insert '_Nullable' if the pointer may be null int sigismember(const sigset_t *, int); ^ _Nullable /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:94:32: note: insert '_Nonnull' if the pointer should never be null int sigismember(const sigset_t *, int); ^ _Nonnull /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:96:25: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness] int sigpending(sigset_t *); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:96:25: note: insert '_Nullable' if the pointer may be null int sigpending(sigset_t *); ^ _Nullable /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:96:25: note: insert '_Nonnull' if the pointer should never be null int sigpending(sigset_t *); ^ _Nonnull /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:97:37: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness] int sigprocmask(int, const sigset_t * __restrict, sigset_t * __restrict); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:97:37: note: insert '_Nullable' if the pointer may be null int sigprocmask(int, const sigset_t * __restrict, sigset_t * __restrict); ^ _Nullable /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:97:37: note: insert '_Nonnull' if the pointer should never be null int sigprocmask(int, const sigset_t * __restrict, sigset_t * __restrict); ^ _Nonnull /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:97:60: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness] int sigprocmask(int, const sigset_t * __restrict, sigset_t * __restrict); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:97:60: note: insert '_Nullable' if the pointer may be null int sigprocmask(int, const sigset_t * __restrict, sigset_t * __restrict); ^ _Nullable /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:97:60: note: insert '_Nonnull' if the pointer should never be null int sigprocmask(int, const sigset_t * __restrict, sigset_t * __restrict); ^ _Nonnull /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:100:31: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness] int sigsuspend(const sigset_t *) __DARWIN_ALIAS_C(sigsuspend); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:100:31: note: insert '_Nullable' if the pointer may be null int sigsuspend(const sigset_t *) __DARWIN_ALIAS_C(sigsuspend); ^ _Nullable /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:100:31: note: insert '_Nonnull' if the pointer should never be null int sigsuspend(const sigset_t *) __DARWIN_ALIAS_C(sigsuspend); ^ _Nonnull /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:101:28: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness] int sigwait(const sigset_t * __restrict, int * __restrict) __DARWIN_ALIAS_C(sigwait); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:101:28: note: insert '_Nullable' if the pointer may be null int sigwait(const sigset_t * __restrict, int * __restrict) __DARWIN_ALIAS_C(sigwait); ^ _Nullable /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:101:28: note: insert '_Nonnull' if the pointer should never be null int sigwait(const sigset_t * __restrict, int * __restrict) __DARWIN_ALIAS_C(sigwait); ^ _Nonnull /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:101:46: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness] int sigwait(const sigset_t * __restrict, int * __restrict) __DARWIN_ALIAS_C(sigwait); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:101:46: note: insert '_Nullable' if the pointer may be null int sigwait(const sigset_t * __restrict, int * __restrict) __DARWIN_ALIAS_C(sigwait); ^ _Nullable /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:101:46: note: insert '_Nonnull' if the pointer should never be null int sigwait(const sigset_t * __restrict, int * __restrict) __DARWIN_ALIAS_C(sigwait); ^ _Nonnull /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:103:39: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness] void psignal(unsigned int, const char *); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:103:39: note: insert '_Nullable' if the pointer may be null void psignal(unsigned int, const char *); ^ _Nullable /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:103:39: note: insert '_Nonnull' if the pointer should never be null void psignal(unsigned int, const char *); ^ _Nonnull /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:106:31: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness] int sigvec(int, struct sigvec *, struct sigvec *); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:106:31: note: insert '_Nullable' if the pointer may be null int sigvec(int, struct sigvec *, struct sigvec *); ^ _Nullable /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:106:31: note: insert '_Nonnull' if the pointer should never be null int sigvec(int, struct sigvec *, struct sigvec *); ^ _Nonnull /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:106:48: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness] int sigvec(int, struct sigvec *, struct sigvec *); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:106:48: note: insert '_Nullable' if the pointer may be null int sigvec(int, struct sigvec *, struct sigvec *); ^ _Nullable /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/signal.h:106:48: note: insert '_Nonnull' if the pointer should never be null int sigvec(int, struct sigvec *, struct sigvec *); ^ _Nonnull 220 warnings generated. clang -bundle -undefined dynamic_lookup -L/usr/local/opt/readline/lib -L/usr/local/opt/readline/lib -L/Users/markkelly/.pyenv/versions/3.8.0/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/readline/lib -L/Users/markkelly/.pyenv/versions/3.8.0/lib build/temp.macosx-10.15-x86_64-3.8/src/DP.o build/temp.macosx-10.15-x86_64-3.8/src/optimum_reparam_N.o -o build/lib.macosx-10.15-x86_64-3.8/optimum_reparam_N.cpython-38-darwin.so clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/private/var/folders/pg/g0n4w9955m7ff1rsj6b6tpz40000gn/T/pip-build-env-vgswf17a/overlay/lib/python3.8/site-packages/numpy/core/include -I/Users/markkelly/RedMatter/repos/new_version/cytopy/.venv/include -I/Users/markkelly/.pyenv/versions/3.8.0/include/python3.8 -c src/bayesian.cpp -o build/temp.macosx-10.15-x86_64-3.8/src/bayesian.o In file included from src/bayesian.cpp:1: In file included from src/armadillo:26: /Library/Developer/CommandLineTools/usr/bin/../include/c /v1/cmath:317:9: error: no member named 'signbit' in the global namespace using ::signbit; ~~^ /Library/Developer/CommandLineTools/usr/bin/../include/c /v1/cmath:318:9: error: no member named 'fpclassify' in the global namespace using ::fpclassify; ~~^ /Library/Developer/CommandLineTools/usr/bin/../include/c /v1/cmath:319:9: error: no member named 'isfinite' in the global namespace; did you mean 'finite'? using ::isfinite; ~~^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/math.h:752:12: note: 'finite' declared here extern int finite(double) ^ In file included from src/bayesian.cpp:1: In file included from src/armadillo:26: /Library/Developer/CommandLineTools/usr/bin/../include/c /v1/cmath:320:9: error: no member named 'isinf' in the global namespace using ::isinf; ~~^ /Library/Developer/CommandLineTools/usr/bin/../include/c /v1/cmath:321:9: error: no member named 'isnan' in the global namespace using ::isnan; ~~^ /Library/Developer/CommandLineTools/usr/bin/../include/c /v1/cmath:322:9: error: no member named 'isnormal' in the global namespace using ::isnormal; ~~^ /Library/Developer/CommandLineTools/usr/bin/../include/c /v1/cmath:323:9: error: no member named 'isgreater' in the global namespace using ::isgreater; ~~^ /Library/Developer/CommandLineTools/usr/bin/../include/c /v1/cmath:324:9: error: no member named 'isgreaterequal' in the global namespace using ::isgreaterequal; ~~^ /Library/Developer/CommandLineTools/usr/bin/../include/c /v1/cmath:325:9: error: no member named 'isless' in the global namespace using ::isless; ~~^ /Library/Developer/CommandLineTools/usr/bin/../include/c /v1/cmath:326:9: error: no member named 'islessequal' in the global namespace using ::islessequal; ~~^ /Library/Developer/CommandLineTools/usr/bin/../include/c /v1/cmath:327:9: error: no member named 'islessgreater' in the global namespace using ::islessgreater; ~~^ /Library/Developer/CommandLineTools/usr/bin/../include/c /v1/cmath:328:9: error: no member named 'isunordered' in the global namespace using ::isunordered; ~~^ /Library/Developer/CommandLineTools/usr/bin/../include/c /v1/cmath:329:9: error: no member named 'isunordered' in the global namespace using ::isunordered; ~~^ /Library/Developer/CommandLineTools/usr/bin/../include/c /v1/cmath:640:26: error: no template named 'numeric_limits' bool _FloatBigger = (numeric_limits<_FloatT>::digits > numeric_limits<_IntT>::digits), ^ /Library/Developer/CommandLineTools/usr/bin/../include/c /v1/cmath:640:60: error: no template named 'numeric_limits' bool _FloatBigger = (numeric_limits<_FloatT>::digits > numeric_limits<_IntT>::digits), ^ /Library/Developer/CommandLineTools/usr/bin/../include/c /v1/cmath:641:18: error: no template named 'numeric_limits' int _Bits = (numeric_limits<_IntT>::digits - numeric_limits<_FloatT>::digits)> ^ /Library/Developer/CommandLineTools/usr/bin/../include/c /v1/cmath:641:50: error: no template named 'numeric_limits' int _Bits = (numeric_limits<_IntT>::digits - numeric_limits<_FloatT>::digits)> ^ /Library/Developer/CommandLineTools/usr/bin/../include/c /v1/cmath:646:17: error: no template named 'numeric_limits' static_assert(numeric_limits<_FloatT>::radix == 2, "FloatT has incorrect radix"); ^ /Library/Developer/CommandLineTools/usr/bin/../include/c /v1/cmath:649:25: error: no template named 'numeric_limits' return _FloatBigger ? numeric_limits<_IntT>::max() : (numeric_limits<_IntT>::max() >> _Bits << _Bits); ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. setup.py:47: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. mac_ver = str(LooseVersion(get_config_var('MACOSX_DEPLOYMENT_TARGET'))) not modified: 'build/_DP.c'

It seems to be something to do with CommandLineTools

EDIT

To follow on from a comment below by Alan, when I go to Visual Studio Code > Command Palette > Python: Select Interpreter, I see this:

CodePudding user response：

I think the library you are trying to use is supported on python3.6 and python3.7. I think your default global python version is 2.7, but your venv was created with python3.8, hence error.

Try creating venv with one of 2.7, 3.6 or 3.7 python and try again.

I found that: python<version optionally> -m pip install <sth> always uses proper pip and saves me a lot of head scratching and hair pulling.

CodePudding user response：

Your env is python3 and pip on mac is python2. I think. Try and use pip3 for the install or run your env in python2. Might be using different python verions.