Windows 10 Miniconda - hddm install issue
202 views
Skip to first unread message
Andrew
Jun 7, 2022, 1:51:45 AM6/7/22
to hddm-users
Hi all,
Apologies if there has been a previous post i have missed but im having issues installing both HDDM 0.9 and 0.8 in my conda environment.
For 0.9. I am able to, under a new conda environment pip install cython, pymc, and kabuki. But get errors when attempting to pip install hddm. I have tried this in multiple environment conditions with different versions of python (3.5, 3.6, 3.8) and in a completely clean environment. When attempting the pip install for hddm I get the following error:
ERROR: Command errored out with exit status 1:
command: 'C:\Users\amcka\miniconda3\envs\hddm\python.exe' -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\amcka\\AppData\\Local\\Temp\\pip-req-build-hlnl3t9p\\setup.py'"'"'; __file__='"'"'C:\\Users\\amcka\\AppData\\Local\\Temp\\pip-req-build-hlnl3t9p\\setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base 'C:\Users\amcka\AppData\Local\Temp\pip-pip-egg-info-f3cij_33'
cwd: C:\Users\amcka\AppData\Local\Temp\pip-req-build-hlnl3t9p\
Complete output (228 lines):
Compiling src/wfpt.pyx because it changed.
Compiling src/cddm_data_simulation.pyx because it changed.
[1/2] Cythonizing src/cddm_data_simulation.pyx
[2/2] Cythonizing src/wfpt.pyx
C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\setuptools\installer.py:27: SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer.
warnings.warn(
ERROR: Command errored out with exit status 1:
command: 'C:\Users\amcka\miniconda3\envs\hddm\python.exe' -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\amcka\\AppData\\Local\\Temp\\pip-wheel-woc7_qlu\\pymc_57401977b71e415f944e4810a04b93e6\\setup.py'"'"'; __file__='"'"'C:\\Users\\amcka\\AppData\\Local\\Temp\\pip-wheel-woc7_qlu\\pymc_57401977b71e415f944e4810a04b93e6\\setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d 'C:\Users\amcka\AppData\Local\Temp\pip-wheel-lb8ycukv'
cwd: C:\Users\amcka\AppData\Local\Temp\pip-wheel-woc7_qlu\pymc_57401977b71e415f944e4810a04b93e6\
Complete output (185 lines):
WARN: Could not locate executable g77
WARN: Could not locate executable f77
WARN: Could not locate executable ifort
WARN: Could not locate executable ifl
WARN: Could not locate executable f90
WARN: Could not locate executable DF
WARN: Could not locate executable efl
WARN: Could not locate executable gfortran
WARN: Could not locate executable f95
WARN: Could not locate executable g95
WARN: Could not locate executable efort
WARN: Could not locate executable efc
WARN: Could not locate executable flang
WARN: don't know how to compile Fortran code on platform 'nt'
C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\numpy\distutils\system_info.py:1902: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
return getattr(self, '_calc_info_{}'.format(name))()
C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\numpy\distutils\system_info.py:1902: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
return getattr(self, '_calc_info_{}'.format(name))()
C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\numpy\distutils\system_info.py:585: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
return cl().get_info(notfound_action)
No optimized BLAS or Lapack libraries found, building from source. This may take a while...
No optimized BLAS or Lapack libraries found, building from source. This may take a while...
running bdist_wheel
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 extension "pymc.flib" sources
INFO: f2py options: []
INFO: adding 'build\src.win-amd64-3.10\build\src.win-amd64-3.10\pymc\fortranobject.c' to sources.
INFO: adding 'build\src.win-amd64-3.10\build\src.win-amd64-3.10\pymc' to include_dirs.
INFO: adding 'build\src.win-amd64-3.10\pymc\flib-f2pywrappers.f' to sources.
INFO: building extension "pymc.LazyFunction" sources
INFO: building extension "pymc.Container_values" sources
INFO: building extension "pymc.gp.linalg_utils" sources
INFO: f2py options: []
INFO: adding 'build\src.win-amd64-3.10\build\src.win-amd64-3.10\pymc\gp\fortranobject.c' to sources.
INFO: adding 'build\src.win-amd64-3.10\build\src.win-amd64-3.10\pymc\gp' to include_dirs.
INFO: adding 'build\src.win-amd64-3.10\pymc\gp\linalg_utils-f2pywrappers.f' to sources.
INFO: building extension "pymc.gp.incomplete_chol" sources
INFO: f2py options: []
INFO: adding 'build\src.win-amd64-3.10\build\src.win-amd64-3.10\pymc\gp\fortranobject.c' to sources.
INFO: adding 'build\src.win-amd64-3.10\build\src.win-amd64-3.10\pymc\gp' to include_dirs.
INFO: adding 'build\src.win-amd64-3.10\pymc\gp\incomplete_chol-f2pywrappers.f' to sources.
INFO: building extension "pymc.gp.cov_funs.isotropic_cov_funs" sources
INFO: f2py options: []
INFO: adding 'build\src.win-amd64-3.10\build\src.win-amd64-3.10\pymc\gp\cov_funs\fortranobject.c' to sources.
INFO: adding 'build\src.win-amd64-3.10\build\src.win-amd64-3.10\pymc\gp\cov_funs' to include_dirs.
INFO: adding 'build\src.win-amd64-3.10\pymc\gp\cov_funs\isotropic_cov_funs-f2pywrappers.f' to sources.
INFO: building extension "pymc.gp.cov_funs.distances" sources
INFO: f2py options: []
INFO: adding 'build\src.win-amd64-3.10\build\src.win-amd64-3.10\pymc\gp\cov_funs\fortranobject.c' to sources.
INFO: adding 'build\src.win-amd64-3.10\build\src.win-amd64-3.10\pymc\gp\cov_funs' to include_dirs.
INFO: build_src: building npy-pkg config files
C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\setuptools\command\install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build_py
creating build\lib.win-amd64-3.10
creating build\lib.win-amd64-3.10\pymc
copying pymc\calc_utils.py -> build\lib.win-amd64-3.10\pymc
copying pymc\CircularStochastic.py -> build\lib.win-amd64-3.10\pymc
copying pymc\CommonDeterministics.py -> build\lib.win-amd64-3.10\pymc
copying pymc\Container.py -> build\lib.win-amd64-3.10\pymc
copying pymc\datatypes.py -> build\lib.win-amd64-3.10\pymc
copying pymc\decorators.py -> build\lib.win-amd64-3.10\pymc
copying pymc\diagnostics.py -> build\lib.win-amd64-3.10\pymc
copying pymc\distributions.py -> build\lib.win-amd64-3.10\pymc
copying pymc\graph.py -> build\lib.win-amd64-3.10\pymc
copying pymc\InstantiationDecorators.py -> build\lib.win-amd64-3.10\pymc
copying pymc\Matplot.py -> build\lib.win-amd64-3.10\pymc
copying pymc\MCMC.py -> build\lib.win-amd64-3.10\pymc
copying pymc\Model.py -> build\lib.win-amd64-3.10\pymc
copying pymc\Node.py -> build\lib.win-amd64-3.10\pymc
copying pymc\NormalApproximation.py -> build\lib.win-amd64-3.10\pymc
copying pymc\NumpyDeterministics.py -> build\lib.win-amd64-3.10\pymc
copying pymc\progressbar.py -> build\lib.win-amd64-3.10\pymc
copying pymc\PyMCObjects.py -> build\lib.win-amd64-3.10\pymc
copying pymc\ScipyDistributions.py -> build\lib.win-amd64-3.10\pymc
copying pymc\six.py -> build\lib.win-amd64-3.10\pymc
copying pymc\StepMethods.py -> build\lib.win-amd64-3.10\pymc
copying pymc\threadpool.py -> build\lib.win-amd64-3.10\pymc
copying pymc\utils.py -> build\lib.win-amd64-3.10\pymc
copying pymc\__init__.py -> build\lib.win-amd64-3.10\pymc
creating build\lib.win-amd64-3.10\pymc\database
copying pymc/database\base.py -> build\lib.win-amd64-3.10\pymc/database
copying pymc/database\hdf5.py -> build\lib.win-amd64-3.10\pymc/database
copying pymc/database\hdf5ea.py -> build\lib.win-amd64-3.10\pymc/database
copying pymc/database\no_trace.py -> build\lib.win-amd64-3.10\pymc/database
copying pymc/database\pickle.py -> build\lib.win-amd64-3.10\pymc/database
copying pymc/database\ram.py -> build\lib.win-amd64-3.10\pymc/database
copying pymc/database\sqlite.py -> build\lib.win-amd64-3.10\pymc/database
copying pymc/database\txt.py -> build\lib.win-amd64-3.10\pymc/database
copying pymc/database\__init__.py -> build\lib.win-amd64-3.10\pymc/database
creating build\lib.win-amd64-3.10\pymc\examples
copying pymc/examples\custom_step.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\disaster_model.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\disaster_model_gof.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\disaster_model_linear.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\disaster_model_missing.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\disaster_model_null.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\gelman_bioassay.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\melanoma.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\melanoma_data.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\weibull_fit.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\weibull_fit_gof.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\zip.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\__init__.py -> build\lib.win-amd64-3.10\pymc/examples
creating build\lib.win-amd64-3.10\pymc\examples\gp
copying pymc/examples/gp\basiscov.py -> build\lib.win-amd64-3.10\pymc/examples/gp
copying pymc/examples/gp\cov.py -> build\lib.win-amd64-3.10\pymc/examples/gp
copying pymc/examples/gp\covparams.py -> build\lib.win-amd64-3.10\pymc/examples/gp
copying pymc/examples/gp\MCMC.py -> build\lib.win-amd64-3.10\pymc/examples/gp
copying pymc/examples/gp\mean.py -> build\lib.win-amd64-3.10\pymc/examples/gp
copying pymc/examples/gp\mesh_choice.py -> build\lib.win-amd64-3.10\pymc/examples/gp
copying pymc/examples/gp\observation.py -> build\lib.win-amd64-3.10\pymc/examples/gp
copying pymc/examples/gp\PyMCmodel.py -> build\lib.win-amd64-3.10\pymc/examples/gp
copying pymc/examples/gp\realizations.py -> build\lib.win-amd64-3.10\pymc/examples/gp
copying pymc/examples/gp\__init__.py -> build\lib.win-amd64-3.10\pymc/examples/gp
creating build\lib.win-amd64-3.10\pymc\tests
copying pymc/tests\objectmodel.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_adaptive.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_AM.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_basiscov.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_binary_step.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_container.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_convergence.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_cov.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_database.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_distributions.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_GP_MCMC.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_gradients.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_graph.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_instantiation.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_interactive.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_MCMCSampler.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_mean.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_missing.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_norm_approx.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_observation.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_realization.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_slice.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_special_methods.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_utils.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\__init__.py -> build\lib.win-amd64-3.10\pymc/tests
creating build\lib.win-amd64-3.10\pymc\gp
copying pymc/gp\BasisCovariance.py -> build\lib.win-amd64-3.10\pymc/gp
copying pymc/gp\Covariance.py -> build\lib.win-amd64-3.10\pymc/gp
copying pymc/gp\FullRankCovariance.py -> build\lib.win-amd64-3.10\pymc/gp
copying pymc/gp\gpplots.py -> build\lib.win-amd64-3.10\pymc/gp
copying pymc/gp\GPutils.py -> build\lib.win-amd64-3.10\pymc/gp
copying pymc/gp\gp_submodel.py -> build\lib.win-amd64-3.10\pymc/gp
copying pymc/gp\Mean.py -> build\lib.win-amd64-3.10\pymc/gp
copying pymc/gp\NearlyFullRankCovariance.py -> build\lib.win-amd64-3.10\pymc/gp
copying pymc/gp\Realization.py -> build\lib.win-amd64-3.10\pymc/gp
copying pymc/gp\step_methods.py -> build\lib.win-amd64-3.10\pymc/gp
copying pymc/gp\__init__.py -> build\lib.win-amd64-3.10\pymc/gp
creating build\lib.win-amd64-3.10\pymc\gp\cov_funs
copying pymc/gp/cov_funs\bases.py -> build\lib.win-amd64-3.10\pymc/gp/cov_funs
copying pymc/gp/cov_funs\brownian.py -> build\lib.win-amd64-3.10\pymc/gp/cov_funs
copying pymc/gp/cov_funs\cov_utils.py -> build\lib.win-amd64-3.10\pymc/gp/cov_funs
copying pymc/gp/cov_funs\nsmatern.py -> build\lib.win-amd64-3.10\pymc/gp/cov_funs
copying pymc/gp/cov_funs\wrapped_distances.py -> build\lib.win-amd64-3.10\pymc/gp/cov_funs
copying pymc/gp/cov_funs\__init__.py -> build\lib.win-amd64-3.10\pymc/gp/cov_funs
running build_ext
INFO: No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
INFO: customize MSVCCompiler
INFO: customize MSVCCompiler using build_ext
INFO: CCompilerOpt.cc_test_flags[1021] : testing flags (/O2)
error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/
INFO: CCompilerOpt.cache_flush[817] : write cache to path -> C:\Users\amcka\AppData\Local\Temp\pip-wheel-woc7_qlu\pymc_57401977b71e415f944e4810a04b93e6\build\temp.win-amd64-3.10\Release\ccompiler_opt_cache_ext.py
----------------------------------------
ERROR: Failed building wheel for PyMC
ERROR: Failed to build one or more wheels
Traceback (most recent call last):
File "C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\setuptools\installer.py", line 82, in fetch_build_egg
subprocess.check_call(cmd)
File "C:\Users\amcka\miniconda3\envs\hddm\lib\subprocess.py", line 369, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['C:\\Users\\amcka\\miniconda3\\envs\\hddm\\python.exe', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', 'C:\\Users\\amcka\\AppData\\Local\\Temp\\tmp9o4i4de9', '--quiet', 'PyMC<3.0.0,>=2.3.3']' returned non-zero exit status 1.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "C:\Users\amcka\AppData\Local\Temp\pip-req-build-hlnl3t9p\setup.py", line 19, in <module>
setup(
File "C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\setuptools\__init__.py", line 86, in setup
_install_setup_requires(attrs)
File "C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\setuptools\__init__.py", line 80, in _install_setup_requires
dist.fetch_build_eggs(dist.setup_requires)
File "C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\setuptools\dist.py", line 861, in fetch_build_eggs
resolved_dists = pkg_resources.working_set.resolve(
File "C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\pkg_resources\__init__.py", line 777, in resolve
dist = best[req.key] = env.best_match(
File "C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\pkg_resources\__init__.py", line 1062, in best_match
return self.obtain(req, installer)
File "C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\pkg_resources\__init__.py", line 1074, in obtain
return installer(requirement)
File "C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\setuptools\dist.py", line 941, in fetch_build_egg
return fetch_build_egg(self, req)
File "C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\setuptools\installer.py", line 84, in fetch_build_egg
raise DistutilsError(str(e)) from e
distutils.errors.DistutilsError: Command '['C:\\Users\\amcka\\miniconda3\\envs\\hddm\\python.exe', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', 'C:\\Users\\amcka\\AppData\\Local\\Temp\\tmp9o4i4de9', '--quiet', 'PyMC<3.0.0,>=2.3.3']' returned non-zero exit status 1.
----------------------------------------
WARNING: Discarding git+https://github.com/hddm-devs/hddm. Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
command: 'C:\Users\amcka\miniconda3\envs\hddm\python.exe' -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\amcka\\AppData\\Local\\Temp\\pip-req-build-hlnl3t9p\\setup.py'"'"'; __file__='"'"'C:\\Users\\amcka\\AppData\\Local\\Temp\\pip-req-build-hlnl3t9p\\setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base 'C:\Users\amcka\AppData\Local\Temp\pip-pip-egg-info-f3cij_33'
cwd: C:\Users\amcka\AppData\Local\Temp\pip-req-build-hlnl3t9p\
Complete output (228 lines):
Compiling src/wfpt.pyx because it changed.
Compiling src/cddm_data_simulation.pyx because it changed.
[1/2] Cythonizing src/cddm_data_simulation.pyx
[2/2] Cythonizing src/wfpt.pyx
C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\setuptools\installer.py:27: SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer.
warnings.warn(
ERROR: Command errored out with exit status 1:
command: 'C:\Users\amcka\miniconda3\envs\hddm\python.exe' -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\amcka\\AppData\\Local\\Temp\\pip-wheel-woc7_qlu\\pymc_57401977b71e415f944e4810a04b93e6\\setup.py'"'"'; __file__='"'"'C:\\Users\\amcka\\AppData\\Local\\Temp\\pip-wheel-woc7_qlu\\pymc_57401977b71e415f944e4810a04b93e6\\setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d 'C:\Users\amcka\AppData\Local\Temp\pip-wheel-lb8ycukv'
cwd: C:\Users\amcka\AppData\Local\Temp\pip-wheel-woc7_qlu\pymc_57401977b71e415f944e4810a04b93e6\
Complete output (185 lines):
WARN: Could not locate executable g77
WARN: Could not locate executable f77
WARN: Could not locate executable ifort
WARN: Could not locate executable ifl
WARN: Could not locate executable f90
WARN: Could not locate executable DF
WARN: Could not locate executable efl
WARN: Could not locate executable gfortran
WARN: Could not locate executable f95
WARN: Could not locate executable g95
WARN: Could not locate executable efort
WARN: Could not locate executable efc
WARN: Could not locate executable flang
WARN: don't know how to compile Fortran code on platform 'nt'
C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\numpy\distutils\system_info.py:1902: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
return getattr(self, '_calc_info_{}'.format(name))()
C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\numpy\distutils\system_info.py:1902: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
return getattr(self, '_calc_info_{}'.format(name))()
C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\numpy\distutils\system_info.py:585: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
return cl().get_info(notfound_action)
No optimized BLAS or Lapack libraries found, building from source. This may take a while...
No optimized BLAS or Lapack libraries found, building from source. This may take a while...
running bdist_wheel
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 extension "pymc.flib" sources
INFO: f2py options: []
INFO: adding 'build\src.win-amd64-3.10\build\src.win-amd64-3.10\pymc\fortranobject.c' to sources.
INFO: adding 'build\src.win-amd64-3.10\build\src.win-amd64-3.10\pymc' to include_dirs.
INFO: adding 'build\src.win-amd64-3.10\pymc\flib-f2pywrappers.f' to sources.
INFO: building extension "pymc.LazyFunction" sources
INFO: building extension "pymc.Container_values" sources
INFO: building extension "pymc.gp.linalg_utils" sources
INFO: f2py options: []
INFO: adding 'build\src.win-amd64-3.10\build\src.win-amd64-3.10\pymc\gp\fortranobject.c' to sources.
INFO: adding 'build\src.win-amd64-3.10\build\src.win-amd64-3.10\pymc\gp' to include_dirs.
INFO: adding 'build\src.win-amd64-3.10\pymc\gp\linalg_utils-f2pywrappers.f' to sources.
INFO: building extension "pymc.gp.incomplete_chol" sources
INFO: f2py options: []
INFO: adding 'build\src.win-amd64-3.10\build\src.win-amd64-3.10\pymc\gp\fortranobject.c' to sources.
INFO: adding 'build\src.win-amd64-3.10\build\src.win-amd64-3.10\pymc\gp' to include_dirs.
INFO: adding 'build\src.win-amd64-3.10\pymc\gp\incomplete_chol-f2pywrappers.f' to sources.
INFO: building extension "pymc.gp.cov_funs.isotropic_cov_funs" sources
INFO: f2py options: []
INFO: adding 'build\src.win-amd64-3.10\build\src.win-amd64-3.10\pymc\gp\cov_funs\fortranobject.c' to sources.
INFO: adding 'build\src.win-amd64-3.10\build\src.win-amd64-3.10\pymc\gp\cov_funs' to include_dirs.
INFO: adding 'build\src.win-amd64-3.10\pymc\gp\cov_funs\isotropic_cov_funs-f2pywrappers.f' to sources.
INFO: building extension "pymc.gp.cov_funs.distances" sources
INFO: f2py options: []
INFO: adding 'build\src.win-amd64-3.10\build\src.win-amd64-3.10\pymc\gp\cov_funs\fortranobject.c' to sources.
INFO: adding 'build\src.win-amd64-3.10\build\src.win-amd64-3.10\pymc\gp\cov_funs' to include_dirs.
INFO: build_src: building npy-pkg config files
C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\setuptools\command\install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build_py
creating build\lib.win-amd64-3.10
creating build\lib.win-amd64-3.10\pymc
copying pymc\calc_utils.py -> build\lib.win-amd64-3.10\pymc
copying pymc\CircularStochastic.py -> build\lib.win-amd64-3.10\pymc
copying pymc\CommonDeterministics.py -> build\lib.win-amd64-3.10\pymc
copying pymc\Container.py -> build\lib.win-amd64-3.10\pymc
copying pymc\datatypes.py -> build\lib.win-amd64-3.10\pymc
copying pymc\decorators.py -> build\lib.win-amd64-3.10\pymc
copying pymc\diagnostics.py -> build\lib.win-amd64-3.10\pymc
copying pymc\distributions.py -> build\lib.win-amd64-3.10\pymc
copying pymc\graph.py -> build\lib.win-amd64-3.10\pymc
copying pymc\InstantiationDecorators.py -> build\lib.win-amd64-3.10\pymc
copying pymc\Matplot.py -> build\lib.win-amd64-3.10\pymc
copying pymc\MCMC.py -> build\lib.win-amd64-3.10\pymc
copying pymc\Model.py -> build\lib.win-amd64-3.10\pymc
copying pymc\Node.py -> build\lib.win-amd64-3.10\pymc
copying pymc\NormalApproximation.py -> build\lib.win-amd64-3.10\pymc
copying pymc\NumpyDeterministics.py -> build\lib.win-amd64-3.10\pymc
copying pymc\progressbar.py -> build\lib.win-amd64-3.10\pymc
copying pymc\PyMCObjects.py -> build\lib.win-amd64-3.10\pymc
copying pymc\ScipyDistributions.py -> build\lib.win-amd64-3.10\pymc
copying pymc\six.py -> build\lib.win-amd64-3.10\pymc
copying pymc\StepMethods.py -> build\lib.win-amd64-3.10\pymc
copying pymc\threadpool.py -> build\lib.win-amd64-3.10\pymc
copying pymc\utils.py -> build\lib.win-amd64-3.10\pymc
copying pymc\__init__.py -> build\lib.win-amd64-3.10\pymc
creating build\lib.win-amd64-3.10\pymc\database
copying pymc/database\base.py -> build\lib.win-amd64-3.10\pymc/database
copying pymc/database\hdf5.py -> build\lib.win-amd64-3.10\pymc/database
copying pymc/database\hdf5ea.py -> build\lib.win-amd64-3.10\pymc/database
copying pymc/database\no_trace.py -> build\lib.win-amd64-3.10\pymc/database
copying pymc/database\pickle.py -> build\lib.win-amd64-3.10\pymc/database
copying pymc/database\ram.py -> build\lib.win-amd64-3.10\pymc/database
copying pymc/database\sqlite.py -> build\lib.win-amd64-3.10\pymc/database
copying pymc/database\txt.py -> build\lib.win-amd64-3.10\pymc/database
copying pymc/database\__init__.py -> build\lib.win-amd64-3.10\pymc/database
creating build\lib.win-amd64-3.10\pymc\examples
copying pymc/examples\custom_step.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\disaster_model.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\disaster_model_gof.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\disaster_model_linear.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\disaster_model_missing.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\disaster_model_null.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\gelman_bioassay.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\melanoma.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\melanoma_data.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\weibull_fit.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\weibull_fit_gof.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\zip.py -> build\lib.win-amd64-3.10\pymc/examples
copying pymc/examples\__init__.py -> build\lib.win-amd64-3.10\pymc/examples
creating build\lib.win-amd64-3.10\pymc\examples\gp
copying pymc/examples/gp\basiscov.py -> build\lib.win-amd64-3.10\pymc/examples/gp
copying pymc/examples/gp\cov.py -> build\lib.win-amd64-3.10\pymc/examples/gp
copying pymc/examples/gp\covparams.py -> build\lib.win-amd64-3.10\pymc/examples/gp
copying pymc/examples/gp\MCMC.py -> build\lib.win-amd64-3.10\pymc/examples/gp
copying pymc/examples/gp\mean.py -> build\lib.win-amd64-3.10\pymc/examples/gp
copying pymc/examples/gp\mesh_choice.py -> build\lib.win-amd64-3.10\pymc/examples/gp
copying pymc/examples/gp\observation.py -> build\lib.win-amd64-3.10\pymc/examples/gp
copying pymc/examples/gp\PyMCmodel.py -> build\lib.win-amd64-3.10\pymc/examples/gp
copying pymc/examples/gp\realizations.py -> build\lib.win-amd64-3.10\pymc/examples/gp
copying pymc/examples/gp\__init__.py -> build\lib.win-amd64-3.10\pymc/examples/gp
creating build\lib.win-amd64-3.10\pymc\tests
copying pymc/tests\objectmodel.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_adaptive.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_AM.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_basiscov.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_binary_step.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_container.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_convergence.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_cov.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_database.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_distributions.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_GP_MCMC.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_gradients.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_graph.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_instantiation.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_interactive.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_MCMCSampler.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_mean.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_missing.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_norm_approx.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_observation.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_realization.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_slice.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_special_methods.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\test_utils.py -> build\lib.win-amd64-3.10\pymc/tests
copying pymc/tests\__init__.py -> build\lib.win-amd64-3.10\pymc/tests
creating build\lib.win-amd64-3.10\pymc\gp
copying pymc/gp\BasisCovariance.py -> build\lib.win-amd64-3.10\pymc/gp
copying pymc/gp\Covariance.py -> build\lib.win-amd64-3.10\pymc/gp
copying pymc/gp\FullRankCovariance.py -> build\lib.win-amd64-3.10\pymc/gp
copying pymc/gp\gpplots.py -> build\lib.win-amd64-3.10\pymc/gp
copying pymc/gp\GPutils.py -> build\lib.win-amd64-3.10\pymc/gp
copying pymc/gp\gp_submodel.py -> build\lib.win-amd64-3.10\pymc/gp
copying pymc/gp\Mean.py -> build\lib.win-amd64-3.10\pymc/gp
copying pymc/gp\NearlyFullRankCovariance.py -> build\lib.win-amd64-3.10\pymc/gp
copying pymc/gp\Realization.py -> build\lib.win-amd64-3.10\pymc/gp
copying pymc/gp\step_methods.py -> build\lib.win-amd64-3.10\pymc/gp
copying pymc/gp\__init__.py -> build\lib.win-amd64-3.10\pymc/gp
creating build\lib.win-amd64-3.10\pymc\gp\cov_funs
copying pymc/gp/cov_funs\bases.py -> build\lib.win-amd64-3.10\pymc/gp/cov_funs
copying pymc/gp/cov_funs\brownian.py -> build\lib.win-amd64-3.10\pymc/gp/cov_funs
copying pymc/gp/cov_funs\cov_utils.py -> build\lib.win-amd64-3.10\pymc/gp/cov_funs
copying pymc/gp/cov_funs\nsmatern.py -> build\lib.win-amd64-3.10\pymc/gp/cov_funs
copying pymc/gp/cov_funs\wrapped_distances.py -> build\lib.win-amd64-3.10\pymc/gp/cov_funs
copying pymc/gp/cov_funs\__init__.py -> build\lib.win-amd64-3.10\pymc/gp/cov_funs
running build_ext
INFO: No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
INFO: customize MSVCCompiler
INFO: customize MSVCCompiler using build_ext
INFO: CCompilerOpt.cc_test_flags[1021] : testing flags (/O2)
error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/
INFO: CCompilerOpt.cache_flush[817] : write cache to path -> C:\Users\amcka\AppData\Local\Temp\pip-wheel-woc7_qlu\pymc_57401977b71e415f944e4810a04b93e6\build\temp.win-amd64-3.10\Release\ccompiler_opt_cache_ext.py
----------------------------------------
ERROR: Failed building wheel for PyMC
ERROR: Failed to build one or more wheels
Traceback (most recent call last):
File "C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\setuptools\installer.py", line 82, in fetch_build_egg
subprocess.check_call(cmd)
File "C:\Users\amcka\miniconda3\envs\hddm\lib\subprocess.py", line 369, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['C:\\Users\\amcka\\miniconda3\\envs\\hddm\\python.exe', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', 'C:\\Users\\amcka\\AppData\\Local\\Temp\\tmp9o4i4de9', '--quiet', 'PyMC<3.0.0,>=2.3.3']' returned non-zero exit status 1.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "C:\Users\amcka\AppData\Local\Temp\pip-req-build-hlnl3t9p\setup.py", line 19, in <module>
setup(
File "C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\setuptools\__init__.py", line 86, in setup
_install_setup_requires(attrs)
File "C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\setuptools\__init__.py", line 80, in _install_setup_requires
dist.fetch_build_eggs(dist.setup_requires)
File "C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\setuptools\dist.py", line 861, in fetch_build_eggs
resolved_dists = pkg_resources.working_set.resolve(
File "C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\pkg_resources\__init__.py", line 777, in resolve
dist = best[req.key] = env.best_match(
File "C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\pkg_resources\__init__.py", line 1062, in best_match
return self.obtain(req, installer)
File "C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\pkg_resources\__init__.py", line 1074, in obtain
return installer(requirement)
File "C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\setuptools\dist.py", line 941, in fetch_build_egg
return fetch_build_egg(self, req)
File "C:\Users\amcka\miniconda3\envs\hddm\lib\site-packages\setuptools\installer.py", line 84, in fetch_build_egg
raise DistutilsError(str(e)) from e
distutils.errors.DistutilsError: Command '['C:\\Users\\amcka\\miniconda3\\envs\\hddm\\python.exe', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', 'C:\\Users\\amcka\\AppData\\Local\\Temp\\tmp9o4i4de9', '--quiet', 'PyMC<3.0.0,>=2.3.3']' returned non-zero exit status 1.
----------------------------------------
WARNING: Discarding git+https://github.com/hddm-devs/hddm. Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
For 0.8, using the conda install -c pymc hddm command. I simply get the non-matching python version errors no matter what python version I have. Ideally, I would like to use 0.9 for my project and would be hesitant to switch to another OS (namely Linux, which many have seem to have done) as I have many other projects/code for the project running on my windows 10 system.
I haven't come up with much luck attempting to diagnose the .9 issue myself, as it looks like an issue similar to that of the Fortran compiler that mac users are reported to have an issue with but i cannot find any resources for what a Windows solution might be. Moreover, different versions of pymc still create this 'failed to build pymc wheel' error.
Any advice would be much appreciated,
Andrew
Andrew
Jun 7, 2022, 4:56:42 AM6/7/22
to hddm-users
Update,
was able to fix this by installing pymc3 from this environment file here : https://github.com/pymc-devs/pymc/issues/4937 . Then using the pip installs reccomended for the hddm github.
However, I noticed that when trying to import hddm; the Zen of Python kept printing. It turns out that in the basic_simulator.py, this file actually imports the 'this' module in line 1 "from this import d". I am unsure if this is intended but as the change was made 3 days ago according to the git repo it seems it might have been a mistake, but deleting that import has kept the package working fine so far.
I would probably consider the issue of installation solved for me here; hopefully this helps others? But also correct this if its misguiding
Any advice appreciated,
Andrew
Krishn Bera
Jun 7, 2022, 3:58:36 PM6/7/22
to hddm-users
Thanks, Andrew, for pointing this out. We have now fixed the issue (in basic_simulator.py).
Best,
Krishn
Best,
Krishn
Reply all
Reply to author
Forward
0 new messages