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Debugging NumPy development build in conda env
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| $ conda list | |
| # packages in environment at /home/lg/.miniconda3/envs/dev-numpy: | |
| # | |
| # Name Version Build Channel | |
| alabaster 0.7.12 py37_0 | |
| asn1crypto 0.24.0 py37_0 | |
| asv 0.3.1 py37hfc679d8_0 conda-forge | |
| atomicwrites 1.2.1 py37_0 | |
| attrs 18.2.0 py37h28b3542_0 | |
| babel 2.6.0 py37_0 | |
| backcall 0.1.0 py37_0 | |
| blas 1.0 mkl | |
| ca-certificates 2018.03.07 0 | |
| certifi 2018.11.29 py37_0 | |
| cffi 1.11.5 py37he75722e_1 | |
| chardet 3.0.4 py37_1 | |
| coverage 4.5.2 py37h7b6447c_0 | |
| cryptography 2.4.2 py37h1ba5d50_0 | |
| cython 0.29.2 py37he6710b0_0 | |
| decorator 4.3.0 py37_0 | |
| docutils 0.14 py37_0 | |
| idna 2.8 py37_0 | |
| imagesize 1.1.0 py37_0 | |
| intel-openmp 2019.1 144 | |
| ipython 7.2.0 py37h39e3cac_0 | |
| ipython_genutils 0.2.0 py37_0 | |
| jedi 0.13.2 py37_0 | |
| jinja2 2.10 py37_0 | |
| libedit 3.1.20170329 h6b74fdf_2 | |
| libffi 3.2.1 hd88cf55_4 | |
| libgcc-ng 8.2.0 hdf63c60_1 | |
| libgfortran-ng 7.3.0 hdf63c60_0 | |
| libstdcxx-ng 8.2.0 hdf63c60_1 | |
| line_profiler 2.1.2 py37h14c3975_0 | |
| markupsafe 1.1.0 py37h7b6447c_0 | |
| mkl 2019.1 144 | |
| mkl_fft 1.0.6 py37hd81dba3_0 | |
| mkl_random 1.0.2 py37hd81dba3_0 | |
| more-itertools 4.3.0 py37_0 | |
| ncurses 6.1 he6710b0_1 | |
| numpydoc 0.8.0 py37_0 | |
| openssl 1.1.1a h7b6447c_0 | |
| packaging 18.0 py37_0 | |
| parso 0.3.1 py37_0 | |
| pexpect 4.6.0 py37_0 | |
| pickleshare 0.7.5 py37_0 | |
| pip 18.1 py37_0 | |
| pluggy 0.8.0 py37_0 | |
| prompt_toolkit 2.0.7 py37_0 | |
| ptyprocess 0.6.0 py37_0 | |
| py 1.7.0 py37_0 | |
| pycparser 2.19 py37_0 | |
| pygments 2.3.1 py37_0 | |
| pyopenssl 18.0.0 py37_0 | |
| pyparsing 2.3.0 py37_0 | |
| pysocks 1.6.8 py37_0 | |
| pytest 4.0.2 py37_0 | |
| python 3.7.2 h0371630_0 | |
| pytz 2018.7 py37_0 | |
| readline 7.0 h7b6447c_5 | |
| requests 2.21.0 py37_0 | |
| setuptools 40.6.3 py37_0 | |
| six 1.12.0 py37_0 | |
| snowballstemmer 1.2.1 py37_0 | |
| sphinx 1.8.2 py37_0 | |
| sphinxcontrib 1.0 py37_1 | |
| sphinxcontrib-websupport 1.1.0 py37_1 | |
| sqlite 3.26.0 h7b6447c_0 | |
| tk 8.6.8 hbc83047_0 | |
| traitlets 4.3.2 py37_0 | |
| urllib3 1.24.1 py37_0 | |
| wcwidth 0.1.7 py37_0 | |
| wheel 0.32.3 py37_0 | |
| xz 5.2.4 h14c3975_4 | |
| zlib 1.2.11 h7b6447c_3 | |
| $ python setup.py build_ext --inplace | |
| Running from numpy source directory. | |
| Cythonizing sources | |
| Processing numpy/random/mtrand/randint_helpers.pxi.in | |
| Processing numpy/random/mtrand/mtrand.pyx | |
| blas_opt_info: | |
| blas_mkl_info: | |
| customize UnixCCompiler | |
| FOUND: | |
| libraries = ['mkl_rt', 'pthread'] | |
| library_dirs = ['/home/lg/.miniconda3/envs/dev-numpy/lib'] | |
| define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)] | |
| include_dirs = ['/usr/local/include', '/usr/include', '/home/lg/.miniconda3/envs/dev-numpy/include'] | |
| FOUND: | |
| libraries = ['mkl_rt', 'pthread'] | |
| library_dirs = ['/home/lg/.miniconda3/envs/dev-numpy/lib'] | |
| define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)] | |
| include_dirs = ['/usr/local/include', '/usr/include', '/home/lg/.miniconda3/envs/dev-numpy/include'] | |
| non-existing path in 'numpy/distutils': 'site.cfg' | |
| lapack_opt_info: | |
| lapack_mkl_info: | |
| customize UnixCCompiler | |
| FOUND: | |
| libraries = ['mkl_rt', 'pthread'] | |
| library_dirs = ['/home/lg/.miniconda3/envs/dev-numpy/lib'] | |
| define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)] | |
| include_dirs = ['/usr/local/include', '/usr/include', '/home/lg/.miniconda3/envs/dev-numpy/include'] | |
| FOUND: | |
| libraries = ['mkl_rt', 'pthread'] | |
| library_dirs = ['/home/lg/.miniconda3/envs/dev-numpy/lib'] | |
| define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)] | |
| include_dirs = ['/usr/local/include', '/usr/include', '/home/lg/.miniconda3/envs/dev-numpy/include'] | |
| /home/lg/.miniconda3/envs/dev-numpy/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'define_macros' | |
| warnings.warn(msg) | |
| running build_ext | |
| running build_src | |
| build_src | |
| building py_modules sources | |
| building library "npymath" sources | |
| creating build | |
| creating build/src.linux-x86_64-3.7 | |
| get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']' | |
| customize Gnu95FCompiler | |
| Found executable /usr/bin/gfortran | |
| customize Gnu95FCompiler | |
| customize Gnu95FCompiler using config | |
| C compiler: gcc -pthread -B /home/lg/.miniconda3/envs/dev-numpy/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC | |
| compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/home/lg/.miniconda3/envs/dev-numpy/include/python3.7m -c' | |
| gcc: _configtest.c | |
| gcc -pthread -B /home/lg/.miniconda3/envs/dev-numpy/compiler_compat -Wl,--sysroot=/ _configtest.o -o _configtest | |
| /home/lg/.miniconda3/envs/dev-numpy/compiler_compat/ld: _configtest.o: unable to initialize decompress status for section .debug_info | |
| /home/lg/.miniconda3/envs/dev-numpy/compiler_compat/ld: _configtest.o: unable to initialize decompress status for section .debug_info | |
| /home/lg/.miniconda3/envs/dev-numpy/compiler_compat/ld: _configtest.o: unable to initialize decompress status for section .debug_info | |
| /home/lg/.miniconda3/envs/dev-numpy/compiler_compat/ld: _configtest.o: unable to initialize decompress status for section .debug_info | |
| _configtest.o: file not recognized: file format not recognized | |
| collect2: error: ld returned 1 exit status | |
| failure. | |
| removing: _configtest.c _configtest.o _configtest.o.d | |
| Traceback (most recent call last): | |
| File "setup.py", line 409, in <module> | |
| setup_package() | |
| File "setup.py", line 401, in setup_package | |
| setup(**metadata) | |
| File "/home/lg/Projects/numpy/numpy/distutils/core.py", line 171, in setup | |
| return old_setup(**new_attr) | |
| File "/home/lg/.miniconda3/envs/dev-numpy/lib/python3.7/site-packages/setuptools/__init__.py", line 143, in setup | |
| return distutils.core.setup(**attrs) | |
| File "/home/lg/.miniconda3/envs/dev-numpy/lib/python3.7/distutils/core.py", line 148, in setup | |
| dist.run_commands() | |
| File "/home/lg/.miniconda3/envs/dev-numpy/lib/python3.7/distutils/dist.py", line 966, in run_commands | |
| self.run_command(cmd) | |
| File "/home/lg/.miniconda3/envs/dev-numpy/lib/python3.7/distutils/dist.py", line 985, in run_command | |
| cmd_obj.run() | |
| File "/home/lg/Projects/numpy/numpy/distutils/command/build_ext.py", line 79, in run | |
| self.run_command('build_src') | |
| File "/home/lg/.miniconda3/envs/dev-numpy/lib/python3.7/distutils/cmd.py", line 313, in run_command | |
| self.distribution.run_command(command) | |
| File "/home/lg/.miniconda3/envs/dev-numpy/lib/python3.7/distutils/dist.py", line 985, in run_command | |
| cmd_obj.run() | |
| File "/home/lg/Projects/numpy/numpy/distutils/command/build_src.py", line 148, in run | |
| self.build_sources() | |
| File "/home/lg/Projects/numpy/numpy/distutils/command/build_src.py", line 159, in build_sources | |
| self.build_library_sources(*libname_info) | |
| File "/home/lg/Projects/numpy/numpy/distutils/command/build_src.py", line 292, in build_library_sources | |
| sources = self.generate_sources(sources, (lib_name, build_info)) | |
| File "/home/lg/Projects/numpy/numpy/distutils/command/build_src.py", line 375, in generate_sources | |
| source = func(extension, build_dir) | |
| File "numpy/core/setup.py", line 667, in get_mathlib_info | |
| raise RuntimeError("Broken toolchain: cannot link a simple C program") | |
| RuntimeError: Broken toolchain: cannot link a simple C program |
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