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BUG: Cannot install from source on macOS 12.1 with ld: library not found for -lSystem #20677
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00 - Bug57 - Close?Issues which may be closable unless discussion continuedIssues which may be closable unless discussion continued
Description
Describe the issue:
I'm trying to contribute and thus build from source but I can't get it to work.
I get the following error:
ld: library not found for -lSystem
clang-11: error: linker command failed with exit code 1 (use -v to see invocation)
I created a conda environment using
conda env create -n numpydev
and this seems to be where ld was installed:
- ld64 530 hd2e7500_21 installed
- ld64_osx-64 530 he8994da_21 installed
- ldid 2.1.2 h6a69015_3 installed
❯ which ld
/usr/local/Caskroom/mambaforge/base/envs/numpydev/bin/ld
❯ ld -v
@(#)PROGRAM:ld PROJECT:ld64-530
BUILD 16:51:25 Apr 5 2021
configured to support archs: armv6 armv7 armv7s arm64 arm64e arm64_32 i386 x86_64 x86_64h armv6m armv7k armv7m armv7em (tvOS)
LTO support using: LLVM version 11.1.0 (static support for 27, runtime is 27)
TAPI support using: TAPI version 11.0.0 (tapi-1100.0.11)
❯ gcc --version
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 13.0.0 (clang-1300.0.29.30)
Target: x86_64-apple-darwin21.2.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
Reproduce the code example:
python runtests.py -vvError message:
This is the full stack trace:
Full stack trace
python runtests.py -vv
Building, see build.log...
Running from numpy source directory.
numpy/random/_bounded_integers.pxd.in has not changed
numpy/random/_philox.pyx has not changed
numpy/random/_bounded_integers.pyx.in has not changed
numpy/random/_sfc64.pyx has not changed
numpy/random/_mt19937.pyx has not changed
numpy/random/bit_generator.pyx has not changed
numpy/random/_bounded_integers.pyx has not changed
numpy/random/mtrand.pyx has not changed
numpy/random/_generator.pyx has not changed
numpy/random/_pcg64.pyx has not changed
numpy/random/_common.pyx has not changed
Cythonizing sources
INFO: blas_opt_info:
INFO: blas_armpl_info:
INFO: customize UnixCCompiler
INFO: libraries armpl_lp64_mp not found in ['/usr/local/Caskroom/mambaforge/base/envs/numpydev/lib', '/usr/local/lib', '/usr/lib']
INFO: NOT AVAILABLE
INFO:
INFO: blas_mkl_info:
INFO: libraries not found in ['']
INFO: NOT AVAILABLE
INFO:
INFO: blis_info:
INFO: libraries blis not found in ['']
INFO: NOT AVAILABLE
INFO:
INFO: openblas_info:
INFO: libraries not found in ['']
INFO: NOT AVAILABLE
INFO:
INFO: accelerate_info:
INFO: libraries accelerate not found in ['/usr/local/Caskroom/mambaforge/base/envs/numpydev/lib', '/usr/local/lib', '/usr/lib']
INFO: Library accelerate was not found. Ignoring
INFO: libraries veclib not found in ['/usr/local/Caskroom/mambaforge/base/envs/numpydev/lib', '/usr/local/lib', '/usr/lib']
INFO: Library veclib was not found. Ignoring
INFO: FOUND:
INFO: extra_compile_args = ['-msse3', '-I/System/Library/Frameworks/vecLib.framework/Headers']
INFO: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
INFO: define_macros = [('NO_ATLAS_INFO', 3), ('HAVE_CBLAS', None)]
INFO:
INFO: FOUND:
INFO: extra_compile_args = ['-msse3', '-I/System/Library/Frameworks/vecLib.framework/Headers']
INFO: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
INFO: define_macros = [('NO_ATLAS_INFO', 3), ('HAVE_CBLAS', None)]
INFO:
INFO: lapack_opt_info:
INFO: lapack_armpl_info:
INFO: libraries armpl_lp64_mp not found in ['/usr/local/Caskroom/mambaforge/base/envs/numpydev/lib', '/usr/local/lib', '/usr/lib']
INFO: NOT AVAILABLE
INFO:
INFO: lapack_mkl_info:
INFO: libraries not found in ['']
INFO: NOT AVAILABLE
INFO:
INFO: openblas_lapack_info:
INFO: libraries not found in ['']
INFO: NOT AVAILABLE
INFO:
INFO: openblas_clapack_info:
INFO: libraries not found in ['']
INFO: NOT AVAILABLE
INFO:
INFO: flame_info:
INFO: libraries not found in ['']
INFO: NOT AVAILABLE
INFO:
INFO: FOUND:
INFO: extra_compile_args = ['-msse3', '-I/System/Library/Frameworks/vecLib.framework/Headers']
INFO: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
INFO: define_macros = [('NO_ATLAS_INFO', 3), ('HAVE_CBLAS', None)]
INFO:
Warning: attempted relative import with no known parent package
/usr/local/Caskroom/mambaforge/base/envs/numpydev/lib/python3.10/distutils/dist.py:274: UserWarning: Unknown distribution option: 'define_macros'
warnings.warn(msg)
running build
running config_cc
INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
INFO: build_src
INFO: building py_modules sources
INFO: building library "npymath" sources
ld: library not found for -lSystem
clang-11: error: linker command failed with exit code 1 (use -v to see invocation)
Traceback (most recent call last):
File "/Users/cr/code/numpy/setup.py", line 455, in <module>
setup_package()
File "/Users/cr/code/numpy/setup.py", line 447, in setup_package
setup(**metadata)
File "/Users/cr/code/numpy/numpy/distutils/core.py", line 169, in setup
return old_setup(**new_attr)
File "/usr/local/Caskroom/mambaforge/base/envs/numpydev/lib/python3.10/site-packages/setuptools/__init__.py", line 153, in setup
return distutils.core.setup(**attrs)
File "/usr/local/Caskroom/mambaforge/base/envs/numpydev/lib/python3.10/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/local/Caskroom/mambaforge/base/envs/numpydev/lib/python3.10/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/usr/local/Caskroom/mambaforge/base/envs/numpydev/lib/python3.10/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/Users/cr/code/numpy/numpy/distutils/command/build.py", line 62, in run
old_build.run(self)
File "/usr/local/Caskroom/mambaforge/base/envs/numpydev/lib/python3.10/distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/usr/local/Caskroom/mambaforge/base/envs/numpydev/lib/python3.10/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/local/Caskroom/mambaforge/base/envs/numpydev/lib/python3.10/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/Users/cr/code/numpy/numpy/distutils/command/build_src.py", line 144, in run
self.build_sources()
File "/Users/cr/code/numpy/numpy/distutils/command/build_src.py", line 155, in build_sources
self.build_library_sources(*libname_info)
File "/Users/cr/code/numpy/numpy/distutils/command/build_src.py", line 288, in build_library_sources
sources = self.generate_sources(sources, (lib_name, build_info))
File "/Users/cr/code/numpy/numpy/distutils/command/build_src.py", line 378, in generate_sources
source = func(extension, build_dir)
File "/Users/cr/code/numpy/numpy/core/setup.py", line 702, in get_mathlib_info
raise RuntimeError(
RuntimeError: Broken toolchain: cannot link a simple C program.
Build failed!NumPy/Python version information:
Not applicable
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