argkh
Reputation: 21
What's wrong with installing scipy via pip, py39 under FreeBSD 13.1?
I'm triyng to install scipy via pip in an virtual environment but it ends with an error.
$ uname -a FreeBSD BSD-13 13.1-RELEASE-p3 FreeBSD 13.1-RELEASE-p3 GENERIC amd64
Venv is with python 3.9
What I do:
(env)$ pip install scipy
What I get: ` note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed
× Encountered error while generating package metadata. ╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.`
From output:
(env) $ pip install scipy
error: subprocess-exited-with-error
× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [1115 lines of output]
The Meson build system
Version: 1.1.1
Source dir: /tmp/pip-install-5z2e6tci/scipy_ad2046d2ded14815af222ec7dbe3dd66
Build dir: /tmp/pip-install-5z2e6tci/scipy_ad2046d2ded14815af222ec7dbe3dd66/.mesonpy-rx7e0be7/build
Build type: native build
Project name: SciPy
Project version: 1.10.1
C compiler for the host machine: cc (clang 13.0.0 "FreeBSD clang version 13.0.0 ([email protected]:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303)")
C linker for the host machine: cc ld.lld 13.0.0
C++ compiler for the host machine: c++ (clang 13.0.0 "FreeBSD clang version 13.0.0 ([email protected]:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303)")
C++ linker for the host machine: c++ ld.lld 13.0.0
Cython compiler for the host machine: cython (cython 0.29.35)
Host machine cpu family: x86_64
Host machine cpu: x86_64
Compiler for C supports arguments -Wno-unused-but-set-variable: YES
Compiler for C supports arguments -Wno-unused-function: YES
Compiler for C supports arguments -Wno-conversion: YES
Compiler for C supports arguments -Wno-misleading-indentation: YES
Compiler for C supports arguments -Wno-incompatible-pointer-types: YES
Library m found: YES
Fortran compiler for the host machine: gfortran (gcc 12.2.0 "GNU Fortran (FreeBSD Ports Collection) 12.2.0")
Fortran linker for the host machine: gfortran ld.bfd 2.40
Compiler for Fortran supports arguments -Wno-conversion: YES
Checking if "-Wl,--version-script" : links: YES
Program cython found: YES (/tmp/pip-build-env-cfphp0hs/overlay/bin/cython)
Program python found: YES (/usr/home/argkh/PyVenv/env/bin/python3)
Found pkg-config: /usr/local/bin/pkg-config (1.8.1)
Program pythran found: YES (/tmp/pip-build-env-cfphp0hs/overlay/bin/pythran)
Run-time dependency threads found: YES
Library npymath found: YES
Library npyrandom found: YES
Run-time dependency openblas found: YES 0.3.20
Dependency openblas found: YES 0.3.20 (cached)
Compiler for C supports arguments -Wno-maybe-uninitialized: NO
Compiler for C supports arguments -Wno-discarded-qualifiers: NO
Compiler for C supports arguments -Wno-empty-body: YES
Compiler for C supports arguments -Wno-implicit-function-declaration: YES
Compiler for C supports arguments -Wno-parentheses: YES
Compiler for C supports arguments -Wno-switch: YES
Compiler for C supports arguments -Wno-unused-label: YES
Compiler for C supports arguments -Wno-unused-variable: YES
Compiler for C++ supports arguments -Wno-cpp: YES
Compiler for C++ supports arguments -Wno-deprecated-declarations: YES
Compiler for C++ supports arguments -Wno-class-memaccess: NO
Compiler for C++ supports arguments -Wno-format-truncation: NO
Compiler for C++ supports arguments -Wno-non-virtual-dtor: YES
Compiler for C++ supports arguments -Wno-sign-compare: YES
Compiler for C++ supports arguments -Wno-switch: YES
Compiler for C++ supports arguments -Wno-terminate: NO
Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES
Compiler for C++ supports arguments -Wno-unused-function: YES
Compiler for C++ supports arguments -Wno-unused-local-typedefs: YES
Compiler for C++ supports arguments -Wno-unused-variable: YES
Compiler for C++ supports arguments -Wno-int-in-bool-context: YES
Compiler for Fortran supports arguments -Wno-argument-mismatch: YES
Compiler for Fortran supports arguments -Wno-conversion: YES (cached)
Compiler for Fortran supports arguments -Wno-intrinsic-shadow: YES
Compiler for Fortran supports arguments -Wno-maybe-uninitialized: YES
Compiler for Fortran supports arguments -Wno-surprising: YES
Compiler for Fortran supports arguments -Wno-uninitialized: YES
Compiler for Fortran supports arguments -Wno-unused-dummy-argument: YES
Compiler for Fortran supports arguments -Wno-unused-label: YES
Compiler for Fortran supports arguments -Wno-unused-variable: YES
Compiler for Fortran supports arguments -Wno-tabs: YES
Compiler for Fortran supports arguments -Wno-argument-mismatch: YES (cached)
Compiler for Fortran supports arguments -Wno-conversion: YES (cached)
Compiler for Fortran supports arguments -Wno-maybe-uninitialized: YES (cached)
Compiler for Fortran supports arguments -Wno-unused-dummy-argument: YES (cached)
Compiler for Fortran supports arguments -Wno-unused-label: YES (cached)
Compiler for Fortran supports arguments -Wno-unused-variable: YES (cached)
Compiler for Fortran supports arguments -Wno-tabs: YES (cached)
Checking if "Check atomic builtins without -latomic" : links: YES
Configuring __config__.py using configuration
Checking for function "open_memstream" : YES
Configuring messagestream_config.h using configuration
Compiler for Fortran supports arguments -w: YES
Checking for size of "void*" : 8
Compiler for C supports arguments -Wno-unused-variable: YES (cached)
Compiler for C supports arguments -Wno-parentheses: YES (cached)
Compiler for C supports arguments -Wno-unused-label: YES (cached)
Compiler for C supports arguments -Wno-implicit-function-declaration: YES (cached)
Compiler for C supports arguments -Wno-switch: YES (cached)
Compiler for Fortran supports arguments -w: YES (cached)
Checking for size of "void*" : 8 (cached)
Build targets in project: 252
NOTICE: Future-deprecated features used:
* 1.1.0: {'"boolean option" keyword argument "value" of type str'}
SciPy 1.10.1
User defined options
Native files: /tmp/pip-install-5z2e6tci/scipy_ad2046d2ded14815af222ec7dbe3dd66/.mesonpy-native-file.ini
debug : false
optimization: 2
prefix : /usr/local
Found ninja-1.11.1.git.kitware.jobserver-1 at /tmp/pip-build-env-cfphp0hs/normal/bin/ninja
......................................................
[819/1619] Linking target scipy/stats/_qmc_cy.cpython-39.so
[820/1619] Compiling C++ object scipy/stats/_stats_pythran.cpython-39.so.p/meson-generated_..__stats_pythran.cpp.o
FAILED: scipy/stats/_stats_pythran.cpython-39.so.p/meson-generated_..__stats_pythran.cpp.o
c++ -Iscipy/stats/_stats_pythran.cpython-39.so.p -Iscipy/stats -I../../scipy/stats -I/tmp/pip-build-env-cfphp0hs/overlay/lib/python3.9/site-packages/pythran -I/tmp/pip-buil d-env-cfphp0hs/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -fvisibility=hidden -fvisibility-inlines-hidden -fcolor-diagnostics -D_FILE_O
FFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O2 -fPIC -DENABLE_PYTHON_MODULE -D__PYTHRAN__=3 -DPYTHRAN_BLAS_NONE -Wno-cpp -Wno-deprecated-declarations -Wno-unused-but-set-variable -Wno-unused-function -Wno-unused-variable -Wno-int-in-bool-context -MD -MQ scipy/stats/_stats_pythran.cpython-39.so.p/meson-generated_..__stats_pythran.cpp.o -MF scipy/stats/_stats_pythran.cpython-39.so.p/meson-generated_..__stats_pythran.cpp.o.d -o scipy/stats/_stats_pythran.cpython-39.so.p/meson-generated_..__stats_pythran.cpp.o -c scipy/stats/_stats_pythran.cpp
In file included from scipy/stats/_stats_pythran.cpp:34:
In file included from /tmp/pip-build-env-cfphp0hs/overlay/lib/python3.9/site-packages/pythran/pythonic/include/numpy/ceil.hpp:8:
In file included from /tmp/pip-build-env-cfphp0hs/overlay/lib/python3.9/site-packages/pythran/xsimd/xsimd.hpp:55:
/tmp/pip-build-env-cfphp0hs/overlay/lib/python3.9/site-packages/pythran/xsimd/arch/xsimd_scalar.hpp:447:16: error: no member named 'exp10f' in the global namespace; did you mean 'exp10'?
return ::exp10f(x);
^~~~~~~~
exp10
/tmp/pip-build-env-cfphp0hs/overlay/lib/python3.9/site-packages/pythran/xsimd/arch/xsimd_scalar.hpp:445:18: note: 'exp10' declared here
inline float exp10(const float& x) noexcept
^
/tmp/pip-build-env-cfphp0hs/overlay/lib/python3.9/site-packages/pythran/xsimd/arch/xsimd_scalar.hpp:451:16: error: no member named 'exp10' in the global namespace; did you mean simply 'exp10'?
return ::exp10(x);
^~~~~~~
exp10
/tmp/pip-build-env-cfphp0hs/overlay/lib/python3.9/site-packages/pythran/xsimd/arch/xsimd_scalar.hpp:449:19: note: 'exp10' declared here
inline double exp10(const double& x) noexcept
^
2 errors generated.
[821/1619] Generating 'scipy/stats/_boost/binom_ufunc.cpython-39.so.p/binom_ufunc.cpp'.
[822/1619] Compiling C object scipy/stats/_sobol.cpython-39.so.p/meson-generated__sobol.c.o
[823/1619] Compiling C object scipy/stats/_stats.cpython-39.so.p/meson-generated__stats.c.o
[824/1619] Compiling C++ object scipy/sparse/sparsetools/_sparsetools.cpython-39.so.p/csr.cxx.o
[825/1619] Compiling C++ object scipy/sparse/sparsetools/_sparsetools.cpython-39.so.p/bsr.cxx.o
ninja: build stopped: subcommand failed.
INFO: autodetecting backend as ninja
INFO: calculating backend command to run: /tmp/pip-build-env-cfphp0hs/normal/bin/ninja
+ meson setup --prefix=/usr/local /tmp/pip-install-5z2e6tci/scipy_ad2046d2ded14815af222ec7dbe3dd66 /tmp/pip-install-5z2e6tci/scipy_ad2046d2ded14815af222ec7dbe3dd66/.mesonpy-rx7e0be7/build --native-file=/tmp/pip-install-5z2e6tci/scipy_ad2046d2ded14815af222ec7dbe3dd66/.mesonpy-native-file.ini -Ddebug=false -Doptimization=2
+ meson compile
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details
Upvotes: 0
Views: 674
Answers (1)
Valery S.
Reputation: 636
Like it is said here:
In file included from /tmp/pip-build-env-cfphp0hs/overlay/lib/python3.9/site-packages/pythran/xsimd/xsimd.hpp:55:
/tmp/pip-build-env-cfphp0hs/overlay/lib/python3.9/site-packages/pythran/xsimd/arch/xsimd_scalar.hpp:447:16: error: no member named 'exp10f' in the global namespace; did you mean 'exp10'?
return ::exp10f(x);
^~~~~~~~
exp10
::exp10f is not found ; so, it is related to pythran, which is required by scipy ; this bug has a workaround here :
FreeBSD-13.1-pythran-issues-2070
Or you could try to install it through the ports collection in science/py-scipy, which is better than pip because any bug found have their patches already. What you get with pip is compiling from the the source tree which could lead to some bug because it is generally made (or designed) under Linux.
Upvotes: 2