macos build log

conda_forge_compilers_macos_buildlog.txt

(conda-forge-compilers) 0 [~/code/scikit-learn (master)]$ pip install -e . -v
Created temporary directory: /private/var/folders/69/7jxl92h50w10b4v998qt4tj00000gn/T/pip-ephem-wheel-cache-cn0u3xn5
Created temporary directory: /private/var/folders/69/7jxl92h50w10b4v998qt4tj00000gn/T/pip-req-tracker-7xtixh31
Created requirements tracker '/private/var/folders/69/7jxl92h50w10b4v998qt4tj00000gn/T/pip-req-tracker-7xtixh31'
Created temporary directory: /private/var/folders/69/7jxl92h50w10b4v998qt4tj00000gn/T/pip-install-q8mggn78
Obtaining file:///Users/ogrisel/code/scikit-learn
  Added file:///Users/ogrisel/code/scikit-learn to build tracker '/private/var/folders/69/7jxl92h50w10b4v998qt4tj00000gn/T/pip-req-tracker-7xtixh31'
    Running setup.py (path:/Users/ogrisel/code/scikit-learn/setup.py) egg_info for package from file:///Users/ogrisel/code/scikit-learn
    Running command python setup.py egg_info
    running egg_info
    writing scikit_learn.egg-info/PKG-INFO
    writing dependency_links to scikit_learn.egg-info/dependency_links.txt
    writing requirements to scikit_learn.egg-info/requires.txt
    writing top-level names to scikit_learn.egg-info/top_level.txt
    reading manifest file 'scikit_learn.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    writing manifest file 'scikit_learn.egg-info/SOURCES.txt'
    Partial import of sklearn during the build process.
  Source in /Users/ogrisel/code/scikit-learn has version 0.22.dev0, which satisfies requirement scikit-learn==0.22.dev0 from file:///Users/ogrisel/code/scikit-learn
  Removed scikit-learn==0.22.dev0 from file:///Users/ogrisel/code/scikit-learn from build tracker '/private/var/folders/69/7jxl92h50w10b4v998qt4tj00000gn/T/pip-req-tracker-7xtixh31'
Requirement already satisfied: numpy>=1.11.0 in /Users/ogrisel/miniconda3/envs/conda-forge-compilers/lib/python3.7/site-packages (from scikit-learn==0.22.dev0) (1.17.2)
Requirement already satisfied: scipy>=0.17.0 in /Users/ogrisel/miniconda3/envs/conda-forge-compilers/lib/python3.7/site-packages (from scikit-learn==0.22.dev0) (1.3.1)
Requirement already satisfied: joblib>=0.11 in /Users/ogrisel/miniconda3/envs/conda-forge-compilers/lib/python3.7/site-packages (from scikit-learn==0.22.dev0) (0.13.2)
Installing collected packages: scikit-learn
  Running setup.py develop for scikit-learn
    Running command /Users/ogrisel/miniconda3/envs/conda-forge-compilers/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/Users/ogrisel/code/scikit-learn/setup.py'"'"'; __file__='"'"'/Users/ogrisel/code/scikit-learn/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps
    C compiler: 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/ogrisel/miniconda3/envs/conda-forge-compilers=/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 -I/Users/ogrisel/miniconda3/envs/conda-forge-compilers/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9

    compile options: '-c'
    extra options: '-fopenmp'
    x86_64-apple-darwin13.4.0-clang: test_openmp.c
    clang-4.0: warning: -Wl,-export_dynamic: 'linker' input unused [-Wunused-command-line-argument]
    x86_64-apple-darwin13.4.0-clang -arch x86_64 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -L/Users/ogrisel/miniconda3/envs/conda-forge-compilers/lib -Wl,-rpath,/Users/ogrisel/miniconda3/envs/conda-forge-compilers/lib objects/test_openmp.o -o test_openmp -fopenmp
    ld: warning: ignoring file /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd
    undef: _printf
    Undefined symbols for architecture x86_64:
      "_printf", referenced from:
          _.omp_outlined. in lto.o
    ld: symbol(s) not found for architecture x86_64
    clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation)
    Partial import of sklearn during the build process.
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/Users/ogrisel/code/scikit-learn/setup.py", line 290, in <module>
        setup_package()
      File "/Users/ogrisel/code/scikit-learn/setup.py", line 286, in setup_package
        setup(**metadata)
      File "/Users/ogrisel/miniconda3/envs/conda-forge-compilers/lib/python3.7/site-packages/numpy/distutils/core.py", line 137, in setup
        config = configuration()
      File "/Users/ogrisel/code/scikit-learn/setup.py", line 174, in configuration
        config.add_subpackage('sklearn')
      File "/Users/ogrisel/miniconda3/envs/conda-forge-compilers/lib/python3.7/site-packages/numpy/distutils/misc_util.py", line 1035, in add_subpackage
        caller_level = 2)
      File "/Users/ogrisel/miniconda3/envs/conda-forge-compilers/lib/python3.7/site-packages/numpy/distutils/misc_util.py", line 1004, in get_subpackage
        caller_level = caller_level + 1)
      File "/Users/ogrisel/miniconda3/envs/conda-forge-compilers/lib/python3.7/site-packages/numpy/distutils/misc_util.py", line 941, in _get_configuration_from_setup_py
        config = setup_module.configuration(*args)
      File "sklearn/setup.py", line 76, in configuration
        maybe_cythonize_extensions(top_path, config)
      File "/Users/ogrisel/code/scikit-learn/sklearn/_build_utils/__init__.py", line 43, in maybe_cythonize_extensions
        with_openmp = check_openmp_support()
      File "/Users/ogrisel/code/scikit-learn/sklearn/_build_utils/openmp_helpers.py", line 140, in check_openmp_support
        raise CompileError(err_message)
    distutils.errors.CompileError:
                        ***

    It seems that scikit-learn cannot be built with OpenMP support.

    - Make sure you have followed the installation instructions:

        https://scikit-learn.org/dev/developers/advanced_installation.html

    - If your compiler supports OpenMP but the build still fails, please
      submit a bug report at:

        https://github.com/scikit-learn/scikit-learn/issues

    - If you want to build scikit-learn without OpenMP support, you can set
      the environment variable SKLEARN_NO_OPENMP and rerun the build
      command. Note however that some estimators will run in sequential
      mode and their `n_jobs` parameter will have no effect anymore.

                        ***

Cleaning up...
Removed build tracker '/private/var/folders/69/7jxl92h50w10b4v998qt4tj00000gn/T/pip-req-tracker-7xtixh31'
ERROR: Command errored out with exit status 1: /Users/ogrisel/miniconda3/envs/conda-forge-compilers/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/Users/ogrisel/code/scikit-learn/setup.py'"'"'; __file__='"'"'/Users/ogrisel/code/scikit-learn/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps Check the logs for full command output.
Exception information:
Traceback (most recent call last):
  File "/Users/ogrisel/miniconda3/envs/conda-forge-compilers/lib/python3.7/site-packages/pip/_internal/cli/base_command.py", line 188, in main
    status = self.run(options, args)
  File "/Users/ogrisel/miniconda3/envs/conda-forge-compilers/lib/python3.7/site-packages/pip/_internal/commands/install.py", line 407, in run
    use_user_site=options.use_user_site,
  File "/Users/ogrisel/miniconda3/envs/conda-forge-compilers/lib/python3.7/site-packages/pip/_internal/req/__init__.py", line 58, in install_given_reqs
    **kwargs
  File "/Users/ogrisel/miniconda3/envs/conda-forge-compilers/lib/python3.7/site-packages/pip/_internal/req/req_install.py", line 918, in install
    install_options, global_options, prefix=prefix,
  File "/Users/ogrisel/miniconda3/envs/conda-forge-compilers/lib/python3.7/site-packages/pip/_internal/req/req_install.py", line 774, in install_editable
    cwd=self.setup_py_dir,
  File "/Users/ogrisel/miniconda3/envs/conda-forge-compilers/lib/python3.7/site-packages/pip/_internal/utils/misc.py", line 931, in call_subprocess
    raise InstallationError(exc_msg)
pip._internal.exceptions.InstallationError: Command errored out with exit status 1: /Users/ogrisel/miniconda3/envs/conda-forge-compilers/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/Users/ogrisel/code/scikit-learn/setup.py'"'"'; __file__='"'"'/Users/ogrisel/code/scikit-learn/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps Check the logs for full command output.
(conda-forge-compilers) 1 [~/code/scikit-learn (master)]$ echo $CFLAGS
-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/ogrisel/miniconda3/envs/conda-forge-compilers/include
(conda-forge-compilers) 0 [~/code/scikit-learn (master)]$ echo $LDFLAGS
-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -L/Users/ogrisel/miniconda3/envs/conda-forge-compilers/lib -Wl,-rpath,/Users/ogrisel/miniconda3/envs/conda-forge-compilers/lib
(conda-forge-compilers) 0 [~/code/scikit-learn (master)]$ conda list
# packages in environment at /Users/ogrisel/miniconda3/envs/conda-forge-compilers:
#
# Name                    Version                   Build  Channel
binutils-meta             1.0.2                         0    conda-forge
c-compiler                1.0.2                h01d97ff_0    conda-forge
ca-certificates           2019.5.15                     1
cctools                   895                           1
certifi                   2019.6.16                py37_1
clang                     4.0.1                         1
clang_osx-64              4.0.1               h1ce6c1d_18
clangxx                   4.0.1                         1
clangxx_osx-64            4.0.1               h22b1bf0_18
compiler-rt               4.0.1                hcfea43d_1
compilers                 1.0.2                         0    conda-forge
cxx-compiler              1.0.2                h770b8ee_0    conda-forge
cython                    0.29.13          py37h0a44026_0
fortran-compiler          1.0.2                he991be0_0    conda-forge
gfortran_impl_osx-64      7.3.0                h6351b9e_0    conda-forge
gfortran_osx-64           7.3.0                h22b1bf0_4    conda-forge
gmp                       6.1.2                hb37e062_1
isl                       0.19                          0    conda-forge
joblib                    0.13.2                   pypi_0    pypi
ld64                      274.2                         1
libblas                   3.8.0               12_openblas    conda-forge
libcblas                  3.8.0               12_openblas    conda-forge
libcxx                    4.0.1                hcfea43d_1
libcxxabi                 4.0.1                hcfea43d_1
libedit                   3.1.20181209         hb402a30_0
libffi                    3.2.1                h475c297_4
libgfortran               4.0.0                         2    conda-forge
libiconv                  1.15                 hdd342a3_7
liblapack                 3.8.0               12_openblas    conda-forge
libopenblas               0.3.7                h4bb4525_1    conda-forge
llvm                      4.0.1                         1
llvm-lto-tapi             4.0.1                         1
llvm-openmp               8.0.1                h770b8ee_0    conda-forge
mpc                       1.1.0                h6ef4df4_1
mpfr                      4.0.1                h3018a27_3
ncurses                   6.1                  h0a44026_1
numpy                     1.17.2           py37h6b0580a_0    conda-forge
openssl                   1.1.1d               h1de35cc_1
pip                       19.2.2                   py37_0
python                    3.7.4                h359304d_1
readline                  7.0                  h1de35cc_5
scipy                     1.3.1            py37h7e0e109_2    conda-forge
setuptools                41.0.1                   py37_0
sqlite                    3.29.0               ha441bb4_0
tk                        8.6.8                ha441bb4_0
wheel                     0.33.4                   py37_0
xz                        5.2.4                h1de35cc_4
zlib                      1.2.11               h1de35cc_3