same install error on both Mac and Linux

iancb...@gmail.com

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Mar 22, 2022, 6:59:03 PM3/22/22

to hddm-users

Hello,

I am running into what seems to be a common problem in which pymc install fails to install because there is no fortran compiler. I tried both on a Mac (silicon chip running Rosetta 2 emulation) and a Linux machine (which has successfully installed older versions of hddm), using a fresh anaconda environment running python 3.7. I've copied the log from my Mac, but both complained about fortran (Linux says "WARN: arm: no Fortran 77 compiler found"). I also tried with python 3.8, 3.5 and 2.7 environments with no luck. Finally, on my Mac, I used hombrew to run the command "brew install gcc@9", but this didn't appear to change anything. I also tried "brew install gfortran",

which also didn't seem to change anything.

Any advice would be greatly appreciated!

-Ian

(hddm37) MacBook-Pro-4:~ ianballard$ pip install git+https://github.com/hddm-devs/hddm
Collecting git+https://github.com/hddm-devs/hddm
Cloning https://github.com/hddm-devs/hddm to /private/var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/pip-req-build-fbd6111r
Running command git clone -q https://github.com/hddm-devs/hddm /private/var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/pip-req-build-fbd6111r
Resolved https://github.com/hddm-devs/hddm to commit 8f1c0c33a7a02bee3429a13b175e04d8124f0762
Running command git submodule update --init --recursive -q
ERROR: Command errored out with exit status 1:
command: /Users/ianballard/anaconda3/envs/hddm37/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/pip-req-build-fbd6111r/setup.py'"'"'; __file__='"'"'/private/var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/pip-req-build-fbd6111r/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 /private/var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/pip-pip-egg-info-ixj1kg5t
cwd: /private/var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/pip-req-build-fbd6111r/
Complete output (490 lines):
ERROR: Command errored out with exit status 1:
command: /Users/ianballard/anaconda3/envs/hddm37/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/pip-wheel-cjjc68zx/pymc_5f234cf3c3e54fc092ab0461b76ff337/setup.py'"'"'; __file__='"'"'/private/var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/pip-wheel-cjjc68zx/pymc_5f234cf3c3e54fc092ab0461b76ff337/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 /private/var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/pip-wheel-_jkgsx7q
cwd: /private/var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/pip-wheel-cjjc68zx/pymc_5f234cf3c3e54fc092ab0461b76ff337/
Complete output (453 lines):
running bdist_wheel
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "pymc.flib" sources
f2py options: ['skip:ppnd7']
adding 'build/src.macosx-10.9-x86_64-3.7/build/src.macosx-10.9-x86_64-3.7/pymc/fortranobject.c' to sources.
adding 'build/src.macosx-10.9-x86_64-3.7/build/src.macosx-10.9-x86_64-3.7/pymc' to include_dirs.
adding 'build/src.macosx-10.9-x86_64-3.7/pymc/flib-f2pywrappers.f' to sources.
building extension "pymc.LazyFunction" sources
building extension "pymc.Container_values" sources
building extension "pymc.gp.linalg_utils" sources
f2py options: []
adding 'build/src.macosx-10.9-x86_64-3.7/build/src.macosx-10.9-x86_64-3.7/pymc/gp/fortranobject.c' to sources.
adding 'build/src.macosx-10.9-x86_64-3.7/build/src.macosx-10.9-x86_64-3.7/pymc/gp' to include_dirs.
building extension "pymc.gp.incomplete_chol" sources
f2py options: []
adding 'build/src.macosx-10.9-x86_64-3.7/build/src.macosx-10.9-x86_64-3.7/pymc/gp/fortranobject.c' to sources.
adding 'build/src.macosx-10.9-x86_64-3.7/build/src.macosx-10.9-x86_64-3.7/pymc/gp' to include_dirs.
building extension "pymc.gp.cov_funs.isotropic_cov_funs" sources
f2py options: []
adding 'build/src.macosx-10.9-x86_64-3.7/build/src.macosx-10.9-x86_64-3.7/pymc/gp/cov_funs/fortranobject.c' to sources.
adding 'build/src.macosx-10.9-x86_64-3.7/build/src.macosx-10.9-x86_64-3.7/pymc/gp/cov_funs' to include_dirs.
adding 'build/src.macosx-10.9-x86_64-3.7/pymc/gp/cov_funs/isotropic_cov_funs-f2pywrappers.f' to sources.
building extension "pymc.gp.cov_funs.distances" sources
f2py options: []
adding 'build/src.macosx-10.9-x86_64-3.7/build/src.macosx-10.9-x86_64-3.7/pymc/gp/cov_funs/fortranobject.c' to sources.
adding 'build/src.macosx-10.9-x86_64-3.7/build/src.macosx-10.9-x86_64-3.7/pymc/gp/cov_funs' to include_dirs.
build_src: building npy-pkg config files
running build_py
creating build/lib.macosx-10.9-x86_64-3.7
creating build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/StepMethods.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/InstantiationDecorators.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/CircularStochastic.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/diagnostics.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/threadpool.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/graph.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/Matplot.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/Container.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/Model.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/distributions.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/MCMC.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/datatypes.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/NormalApproximation.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/progressbar.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/utils.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/PyMCObjects.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/six.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/Node.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/CommonDeterministics.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/calc_utils.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/NumpyDeterministics.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/ScipyDistributions.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
copying pymc/decorators.py -> build/lib.macosx-10.9-x86_64-3.7/pymc
creating build/lib.macosx-10.9-x86_64-3.7/pymc/database
copying pymc/database/no_trace.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/database
copying pymc/database/txt.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/database
copying pymc/database/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/database
copying pymc/database/hdf5.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/database
copying pymc/database/sqlite.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/database
copying pymc/database/pickle.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/database
copying pymc/database/hdf5ea.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/database
copying pymc/database/ram.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/database
copying pymc/database/base.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/database
creating build/lib.macosx-10.9-x86_64-3.7/pymc/examples
copying pymc/examples/melanoma.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples
copying pymc/examples/disaster_model_linear.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples
copying pymc/examples/disaster_model.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples
copying pymc/examples/disaster_model_gof.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples
copying pymc/examples/gelman_bioassay.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples
copying pymc/examples/weibull_fit_gof.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples
copying pymc/examples/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples
copying pymc/examples/melanoma_data.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples
copying pymc/examples/disaster_model_null.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples
copying pymc/examples/zip.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples
copying pymc/examples/custom_step.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples
copying pymc/examples/disaster_model_missing.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples
copying pymc/examples/weibull_fit.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples
creating build/lib.macosx-10.9-x86_64-3.7/pymc/examples/gp
copying pymc/examples/gp/covparams.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples/gp
copying pymc/examples/gp/observation.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples/gp
copying pymc/examples/gp/PyMCmodel.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples/gp
copying pymc/examples/gp/basiscov.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples/gp
copying pymc/examples/gp/realizations.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples/gp
copying pymc/examples/gp/mesh_choice.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples/gp
copying pymc/examples/gp/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples/gp
copying pymc/examples/gp/cov.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples/gp
copying pymc/examples/gp/mean.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples/gp
copying pymc/examples/gp/MCMC.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/examples/gp
creating build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_utils.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_MCMCSampler.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_database.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_cov.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_container.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_missing.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_observation.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_realization.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_convergence.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_AM.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_basiscov.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_GP_MCMC.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_norm_approx.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_mean.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_distributions.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_slice.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_binary_step.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_adaptive.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_special_methods.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_instantiation.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/objectmodel.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_graph.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_gradients.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
copying pymc/tests/test_interactive.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/tests
creating build/lib.macosx-10.9-x86_64-3.7/pymc/gp
copying pymc/gp/step_methods.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/gp
copying pymc/gp/Realization.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/gp
copying pymc/gp/gp_submodel.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/gp
copying pymc/gp/gpplots.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/gp
copying pymc/gp/GPutils.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/gp
copying pymc/gp/Covariance.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/gp
copying pymc/gp/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/gp
copying pymc/gp/Mean.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/gp
copying pymc/gp/FullRankCovariance.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/gp
copying pymc/gp/NearlyFullRankCovariance.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/gp
copying pymc/gp/BasisCovariance.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/gp
creating build/lib.macosx-10.9-x86_64-3.7/pymc/gp/cov_funs
copying pymc/gp/cov_funs/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/gp/cov_funs
copying pymc/gp/cov_funs/wrapped_distances.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/gp/cov_funs
copying pymc/gp/cov_funs/brownian.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/gp/cov_funs
copying pymc/gp/cov_funs/nsmatern.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/gp/cov_funs
copying pymc/gp/cov_funs/cov_utils.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/gp/cov_funs
copying pymc/gp/cov_funs/bases.py -> build/lib.macosx-10.9-x86_64-3.7/pymc/gp/cov_funs
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
CCompilerOpt.cc_test_flags[1013] : testing flags (-march=native)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

creating /var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/tmplis2vg91/Users
creating /var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/tmplis2vg91/Users/ianballard
creating /var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/tmplis2vg91/Users/ianballard/anaconda3
creating /var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/tmplis2vg91/Users/ianballard/anaconda3/envs
creating /var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/tmplis2vg91/Users/ianballard/anaconda3/envs/hddm37
creating /var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/tmplis2vg91/Users/ianballard/anaconda3/envs/hddm37/lib
creating /var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/tmplis2vg91/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7
creating /var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/tmplis2vg91/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages
creating /var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/tmplis2vg91/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/numpy
creating /var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/tmplis2vg91/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/numpy/distutils
creating /var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/tmplis2vg91/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/numpy/distutils/checks
compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-march=native'
CCompilerOpt.cc_test_flags[1013] : testing flags (-O3)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-O3'
CCompilerOpt.cc_test_flags[1013] : testing flags (-Werror)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-Werror'
CCompilerOpt.__init__[1701] : check requested baseline
CCompilerOpt.cc_test_flags[1013] : testing flags (-msse)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse'
CCompilerOpt.cc_test_flags[1013] : testing flags (-msse2)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse2'
CCompilerOpt.feature_test[1468] : testing feature 'SSE' with flags (-msse -msse2)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse -msse2 -Werror'
CCompilerOpt.feature_test[1468] : testing feature 'SSE2' with flags (-msse -msse2)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse -msse2 -Werror'
CCompilerOpt.cc_test_flags[1013] : testing flags (-msse3)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse3'
CCompilerOpt.feature_test[1468] : testing feature 'SSE3' with flags (-msse -msse2 -msse3)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse -msse2 -msse3 -Werror'
CCompilerOpt.__init__[1710] : check requested dispatch-able features
CCompilerOpt.cc_test_flags[1013] : testing flags (-mssse3)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-mssse3'
CCompilerOpt.feature_test[1468] : testing feature 'SSSE3' with flags (-msse -msse2 -msse3 -mssse3)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse -msse2 -msse3 -mssse3 -Werror'
CCompilerOpt.cc_test_flags[1013] : testing flags (-msse4.1)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse4.1'
CCompilerOpt.cc_test_flags[1013] : testing flags (-mpopcnt)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-mpopcnt'
CCompilerOpt.cc_test_flags[1013] : testing flags (-msse4.2)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse4.2'
CCompilerOpt.feature_test[1468] : testing feature 'SSE42' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -Werror'
CCompilerOpt.cc_test_flags[1013] : testing flags (-mavx)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-mavx'
CCompilerOpt.feature_test[1468] : testing feature 'AVX' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -Werror'
CCompilerOpt.cc_test_flags[1013] : testing flags (-mf16c)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-mf16c'
CCompilerOpt.feature_test[1468] : testing feature 'F16C' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -Werror'
CCompilerOpt.cc_test_flags[1013] : testing flags (-mfma)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-mfma'
CCompilerOpt.cc_test_flags[1013] : testing flags (-mavx2)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-mavx2'
CCompilerOpt.cc_test_flags[1013] : testing flags (-mavx512f)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-mavx512f'
CCompilerOpt.cc_test_flags[1013] : testing flags (-mavx512cd)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-mavx512cd'
CCompilerOpt.feature_test[1468] : testing feature 'AVX512CD' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -Werror'
CCompilerOpt.feature_test[1468] : testing feature 'POPCNT' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -Werror'
CCompilerOpt.feature_test[1468] : testing feature 'AVX2' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mavx2)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mavx2 -Werror'
CCompilerOpt.feature_test[1468] : testing feature 'FMA3' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -Werror'
CCompilerOpt.feature_test[1468] : testing feature 'AVX512F' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -Werror'
CCompilerOpt.cc_test_flags[1013] : testing flags (-mavx512vl -mavx512bw -mavx512dq)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-mavx512vl -mavx512bw -mavx512dq'
CCompilerOpt.feature_test[1468] : testing feature 'AVX512_SKX' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -Werror'
CCompilerOpt.feature_test[1468] : testing feature 'SSE41' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -Werror'
CCompilerOpt.cc_test_flags[1013] : testing flags (-mavx512ifma -mavx512vbmi)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-mavx512ifma -mavx512vbmi'
CCompilerOpt.feature_test[1468] : testing feature 'AVX512_CNL' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -mavx512ifma -mavx512vbmi)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -mavx512ifma -mavx512vbmi -Werror'
CCompilerOpt.cc_test_flags[1013] : testing flags (-mavx512vnni)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-mavx512vnni'
CCompilerOpt.feature_test[1468] : testing feature 'AVX512_CLX' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -mavx512vnni)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -mavx512vnni -Werror'
CCompilerOpt.cc_test_flags[1013] : testing flags (-mavx512vbmi2 -mavx512bitalg -mavx512vpopcntdq)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-mavx512vbmi2 -mavx512bitalg -mavx512vpopcntdq'
CCompilerOpt.feature_test[1468] : testing feature 'AVX512_ICL' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -mavx512vnni -mavx512ifma -mavx512vbmi -mavx512vbmi2 -mavx512bitalg -mavx512vpopcntdq)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -mavx512vnni -mavx512ifma -mavx512vbmi -mavx512vbmi2 -mavx512bitalg -mavx512vpopcntdq -Werror'
CCompilerOpt.cc_test_flags[1013] : testing flags (-mavx512er -mavx512pf)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-mavx512er -mavx512pf'
CCompilerOpt.feature_test[1468] : testing feature 'AVX512_KNL' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512er -mavx512pf)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512er -mavx512pf -Werror'
CCompilerOpt.cc_test_flags[1013] : testing flags (-mavx5124fmaps -mavx5124vnniw -mavx512vpopcntdq)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-mavx5124fmaps -mavx5124vnniw -mavx512vpopcntdq'
CCompilerOpt.dist_test[581] : CCompilerOpt._dist_test_spawn[718] : Command (gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c /Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/numpy/distutils/checks/test_flags.c -o /var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/tmplis2vg91/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/numpy/distutils/checks/test_flags.o -MMD -MF /var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/tmplis2vg91/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/numpy/distutils/checks/test_flags.o.d -mavx5124fmaps -mavx5124vnniw -mavx512vpopcntdq) failed with exit status 1 output ->
clang: error: unknown argument: '-mavx5124fmaps'
clang: error: unknown argument: '-mavx5124vnniw'

CCompilerOpt.cc_test_flags[1017] : testing failed
CCompilerOpt.feature_test[1468] : testing feature 'AVX512_KNM' with flags (-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512er -mavx512pf)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512er -mavx512pf -Werror'
CCompilerOpt.dist_test[581] : CCompilerOpt._dist_test_spawn[718] : Command (gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c /Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/numpy/distutils/checks/cpu_avx512_knm.c -o /var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/tmplis2vg91/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/numpy/distutils/checks/cpu_avx512_knm.o -MMD -MF /var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/tmplis2vg91/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/numpy/distutils/checks/cpu_avx512_knm.o.d -msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512er -mavx512pf -Werror) failed with exit status 1 output ->
/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/numpy/distutils/checks/cpu_avx512_knm.c:22:9: error: implicit declaration of function '_mm512_4fmadd_ps' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
b = _mm512_4fmadd_ps(b, b, b, b, b, NULL);
^
/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/numpy/distutils/checks/cpu_avx512_knm.c:22:9: note: did you mean '_mm512_fmadd_ps'?
/Library/Developer/CommandLineTools/usr/lib/clang/13.0.0/include/avx512fintrin.h:2716:1: note: '_mm512_fmadd_ps' declared here
_mm512_fmadd_ps(__m512 __A, __m512 __B, __m512 __C)
^
/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/numpy/distutils/checks/cpu_avx512_knm.c:22:7: error: assigning to '__m512' (vector of 16 'float' values) from incompatible type 'int'
b = _mm512_4fmadd_ps(b, b, b, b, b, NULL);
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/numpy/distutils/checks/cpu_avx512_knm.c:24:9: error: implicit declaration of function '_mm512_4dpwssd_epi32' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
a = _mm512_4dpwssd_epi32(a, a, a, a, a, NULL);
^
/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/numpy/distutils/checks/cpu_avx512_knm.c:24:9: note: did you mean '_mm512_dpwssd_epi32'?
/Library/Developer/CommandLineTools/usr/lib/clang/13.0.0/include/avx512vnniintrin.h:68:1: note: '_mm512_dpwssd_epi32' declared here
_mm512_dpwssd_epi32(__m512i __S, __m512i __A, __m512i __B)
^
/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/numpy/distutils/checks/cpu_avx512_knm.c:24:7: error: assigning to '__m512i' (vector of 8 'long long' values) from incompatible type 'int'
a = _mm512_4dpwssd_epi32(a, a, a, a, a, NULL);
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
4 errors generated.

CCompilerOpt.feature_test[1482] : testing failed
CCompilerOpt.__init__[1723] : skip features (SSE2 SSE SSE3) since its part of baseline
CCompilerOpt.__init__[1726] : initialize targets groups
CCompilerOpt.__init__[1728] : parse target group simd_test
CCompilerOpt._parse_target_tokens[1941] : skip targets (VSX3 NEON ASIMD XOP FMA4 VSX VSX2) not part of baseline or dispatch-able features
CCompilerOpt._parse_policy_not_keepbase[2051] : skip baseline features (SSE2)
CCompilerOpt.generate_dispatch_header[2272] : generate CPU dispatch header: (build/src.macosx-10.9-x86_64-3.7/numpy/distutils/include/npy_cpu_dispatch_config.h)
CCompilerOpt.generate_dispatch_header[2283] : dispatch header dir build/src.macosx-10.9-x86_64-3.7/numpy/distutils/include does not exist, creating it
CCompilerOpt.feature_extra_checks[1546] : Testing extra checks for feature 'AVX512F' (AVX512F_REDUCE)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -Werror'
CCompilerOpt.feature_extra_checks[1546] : Testing extra checks for feature 'AVX512_SKX' (AVX512BW_MASK AVX512DQ_MASK)
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -Werror'
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64 -I/Users/ianballard/anaconda3/envs/hddm37/include -arch x86_64

compile options: '-I/Users/ianballard/anaconda3/envs/hddm37/include/python3.7m -c'
extra options: '-msse -msse2 -msse3 -mssse3 -msse4.1 -mpopcnt -msse4.2 -mavx -mf16c -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -Werror'
get_default_fcompiler: matching types: '['gnu95', 'nag', 'absoft', 'ibm', 'intel', 'gnu', 'g95', 'pg']'
customize Gnu95FCompiler
Could not locate executable gfortran
Could not locate executable f95
customize NAGFCompiler
customize AbsoftFCompiler
Could not locate executable f90
Could not locate executable f77
customize IBMFCompiler
Could not locate executable xlf90
Could not locate executable xlf
customize IntelFCompiler
Could not locate executable ifort
Could not locate executable ifc
customize GnuFCompiler
Could not locate executable g77
customize G95FCompiler
Could not locate executable g95
customize PGroupFCompiler
Could not locate executable pgfortran
don't know how to compile Fortran code on platform 'posix'
warning: build_ext: f77_compiler=None is not available.

building 'pymc.flib' extension
error: extension 'pymc.flib' has Fortran sources but no Fortran compiler found

########### EXT COMPILER OPTIMIZATION ###########
Platform :
Architecture: x64
Compiler : gcc

CPU baseline :
Requested : 'min'
Enabled : SSE SSE2 SSE3
Flags : -msse -msse2 -msse3
Extra checks: none

CPU dispatch :
Requested : 'max -xop -fma4'
Enabled : SSSE3 SSE41 POPCNT SSE42 AVX F16C FMA3 AVX2 AVX512F AVX512CD AVX512_KNL AVX512_SKX AVX512_CLX AVX512_CNL AVX512_ICL
Generated : none
CCompilerOpt.cache_flush[809] : write cache to path -> /private/var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/pip-wheel-cjjc68zx/pymc_5f234cf3c3e54fc092ab0461b76ff337/build/temp.macosx-10.9-x86_64-3.7/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 "/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/setuptools/installer.py", line 75, in fetch_build_egg
subprocess.check_call(cmd)
File "/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/subprocess.py", line 363, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/Users/ianballard/anaconda3/envs/hddm37/bin/python', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/tmp_b3qxtiw', '--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 "/private/var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/pip-req-build-fbd6111r/setup.py", line 41, in <module>
ext_modules = ext_modules
File "/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/setuptools/__init__.py", line 152, in setup
_install_setup_requires(attrs)
File "/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/setuptools/__init__.py", line 147, in _install_setup_requires
dist.fetch_build_eggs(dist.setup_requires)
File "/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/setuptools/dist.py", line 809, in fetch_build_eggs
replace_conflicting=True,
File "/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/pkg_resources/__init__.py", line 768, in resolve
replace_conflicting=replace_conflicting
File "/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1051, in best_match
return self.obtain(req, installer)
File "/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1063, in obtain
return installer(requirement)
File "/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/setuptools/dist.py", line 877, in fetch_build_egg
return fetch_build_egg(self, req)
File "/Users/ianballard/anaconda3/envs/hddm37/lib/python3.7/site-packages/setuptools/installer.py", line 77, in fetch_build_egg
raise DistutilsError(str(e)) from e
distutils.errors.DistutilsError: Command '['/Users/ianballard/anaconda3/envs/hddm37/bin/python', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/var/folders/bn/dzh1ysw54m9cq4n3dnb30ldw0000gn/T/tmp_b3qxtiw', '--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.

Alexander Fengler

unread,

May 12, 2022, 12:56:42 PM5/12/22

to hddm-users

Hi Ian,

you are right this error is fairly common. The pymc installation tends to be the finicky part.

If you type:

gcc --version

and

gfortran --version

what outputs do you get?

Best,

Alex

Patxi Elosegi

unread,

May 13, 2022, 10:07:11 AM5/13/22

to hddm-users

Hi there,

Same error here. I'm trying to install hddm in a conda environment with python 3.7. My computer is a Mac running MacOS Monterey 12.3

//

ggc --version

Apple clang version 13.1.6 (clang-1316.0.21.2)

Target: x86_64-apple-darwin21.4.0

Thread model: posix

InstalledDir: /Library/Developer/CommandLineTools/usr/bin

//gfortran --version

zsh: command not found: gfortran

I have tried downgrading the version of the gcc compiler with ' brew install gcc@9' as suggested on GitHub but it didn't work.

I would appreciate any help with this issue ;) thanks!

Best,

Patxi

Alexander Fengler

unread,

May 17, 2022, 4:18:07 PM5/17/22

to hddm-users

Hi,

Ok try this (If you don't have homebrew on your mac first install homebrew):

--------

brew install gcc@9

--------

then in your ~/.bash_profile file add:

---------

alias gcc='gcc-9'

alias cc='gcc-9'

alias g++='g++-9'

alias c++='c++-9'

alias gfortran='/usr/local/bin/gfortran-9' # -fallow-argument-mismatch'

----------

restart your terminal and check:

----------

gcc --version

---------

this should now show something like:

---------

gcc-9 (Homebrew GCC 9.4.0) 9.4.0

---------

If this doesn't work, try running (after the additions to the bash_profile file as mentioned above):

---------

source ~/.bash_profile

gcc --version

--------

Now try installing pymc again.

Let me know if this still doesn't work.

Best,

Alex

martin.d...@gmail.com

unread,

Aug 1, 2022, 2:13:27 PM8/1/22

to hddm-users

Hi All,

I've been having the same issue with installation. Successfully installed on a Mac running Big Sur, but on a second Mac running Monterey (not M1 Mac) the installation of pymc==2.3.8 always fails. Can confirm that GCC version 9.5 is installed and aliases have been added to the bash profile. This is the error message in full, any help appreciated!

ERROR: Command errored out with exit status 1:

command: /Users/martin/opt/anaconda3/envs/py36/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/my/fnqjb79j6hn7czm0yf573drw0000gq/T/pip-install-9nh2jp4m/pymc_cbb9691e3f464fb7a53b84bc4b6d8522/setup.py'"'"'; __file__='"'"'/private/var/folders/my/fnqjb79j6hn7czm0yf573drw0000gq/T/pip-install-9nh2jp4m/pymc_cbb9691e3f464fb7a53b84bc4b6d8522/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'"'"'))' install --record /private/var/folders/my/fnqjb79j6hn7czm0yf573drw0000gq/T/pip-record-uizprwo1/install-record.txt --single-version-externally-managed --compile --install-headers /Users/martin/opt/anaconda3/envs/py36/include/python3.6m/pymc
cwd: /private/var/folders/my/fnqjb79j6hn7czm0yf573drw0000gq/T/pip-install-9nh2jp4m/pymc_cbb9691e3f464fb7a53b84bc4b6d8522/
Complete output (716 lines):
running install

running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "pymc.flib" sources
f2py options: ['skip:ppnd7']

adding 'build/src.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc/fortranobject.c' to sources.
adding 'build/src.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc' to include_dirs.
adding 'build/src.macosx-10.9-x86_64-3.6/pymc/flib-f2pywrappers.f' to sources.

building extension "pymc.LazyFunction" sources
building extension "pymc.Container_values" sources
building extension "pymc.gp.linalg_utils" sources
f2py options: []

adding 'build/src.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc/gp/fortranobject.c' to sources.
adding 'build/src.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc/gp' to include_dirs.

building extension "pymc.gp.incomplete_chol" sources
f2py options: []

adding 'build/src.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc/gp/fortranobject.c' to sources.
adding 'build/src.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc/gp' to include_dirs.

building extension "pymc.gp.cov_funs.isotropic_cov_funs" sources
f2py options: []

adding 'build/src.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc/gp/cov_funs/fortranobject.c' to sources.
adding 'build/src.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc/gp/cov_funs' to include_dirs.
adding 'build/src.macosx-10.9-x86_64-3.6/pymc/gp/cov_funs/isotropic_cov_funs-f2pywrappers.f' to sources.

building extension "pymc.gp.cov_funs.distances" sources
f2py options: []

adding 'build/src.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc/gp/cov_funs/fortranobject.c' to sources.
adding 'build/src.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc/gp/cov_funs' to include_dirs.

build_src: building npy-pkg config files
running build_py

creating build/lib.macosx-10.9-x86_64-3.6
creating build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/StepMethods.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/InstantiationDecorators.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/CircularStochastic.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/diagnostics.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/threadpool.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/graph.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/Matplot.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/__init__.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/Container.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/Model.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/distributions.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/MCMC.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/datatypes.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/NormalApproximation.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/progressbar.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/utils.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/PyMCObjects.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/six.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/Node.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/CommonDeterministics.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/calc_utils.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/NumpyDeterministics.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/ScipyDistributions.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
copying pymc/decorators.py -> build/lib.macosx-10.9-x86_64-3.6/pymc
creating build/lib.macosx-10.9-x86_64-3.6/pymc/database
copying pymc/database/no_trace.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/database
copying pymc/database/txt.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/database
copying pymc/database/__init__.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/database
copying pymc/database/hdf5.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/database
copying pymc/database/sqlite.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/database
copying pymc/database/pickle.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/database
copying pymc/database/hdf5ea.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/database
copying pymc/database/ram.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/database
copying pymc/database/base.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/database
creating build/lib.macosx-10.9-x86_64-3.6/pymc/examples
copying pymc/examples/melanoma.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples
copying pymc/examples/disaster_model_linear.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples
copying pymc/examples/disaster_model.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples
copying pymc/examples/disaster_model_gof.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples
copying pymc/examples/gelman_bioassay.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples
copying pymc/examples/weibull_fit_gof.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples
copying pymc/examples/__init__.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples
copying pymc/examples/melanoma_data.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples
copying pymc/examples/disaster_model_null.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples
copying pymc/examples/zip.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples
copying pymc/examples/custom_step.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples
copying pymc/examples/disaster_model_missing.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples
copying pymc/examples/weibull_fit.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples
creating build/lib.macosx-10.9-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/covparams.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/observation.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/PyMCmodel.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/basiscov.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/realizations.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/mesh_choice.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/__init__.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/cov.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/mean.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/MCMC.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/examples/gp
creating build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_utils.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_MCMCSampler.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_database.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_cov.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_container.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_missing.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_observation.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_realization.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_convergence.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_AM.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_basiscov.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_GP_MCMC.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_norm_approx.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_mean.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_distributions.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_slice.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_binary_step.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_adaptive.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_special_methods.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_instantiation.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/objectmodel.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_graph.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_gradients.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
copying pymc/tests/test_interactive.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/tests
creating build/lib.macosx-10.9-x86_64-3.6/pymc/gp
copying pymc/gp/step_methods.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/gp
copying pymc/gp/Realization.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/gp
copying pymc/gp/gp_submodel.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/gp
copying pymc/gp/gpplots.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/gp
copying pymc/gp/GPutils.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/gp
copying pymc/gp/Covariance.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/gp
copying pymc/gp/__init__.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/gp
copying pymc/gp/Mean.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/gp
copying pymc/gp/FullRankCovariance.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/gp
copying pymc/gp/NearlyFullRankCovariance.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/gp
copying pymc/gp/BasisCovariance.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/gp
creating build/lib.macosx-10.9-x86_64-3.6/pymc/gp/cov_funs
copying pymc/gp/cov_funs/__init__.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/gp/cov_funs
copying pymc/gp/cov_funs/wrapped_distances.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/gp/cov_funs
copying pymc/gp/cov_funs/brownian.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/gp/cov_funs
copying pymc/gp/cov_funs/nsmatern.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/gp/cov_funs
copying pymc/gp/cov_funs/cov_utils.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/gp/cov_funs
copying pymc/gp/cov_funs/bases.py -> build/lib.macosx-10.9-x86_64-3.6/pymc/gp/cov_funs

running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext

get_default_fcompiler: matching types: '['gnu95', 'nag', 'absoft', 'ibm', 'intel', 'gnu', 'g95', 'pg']'
customize Gnu95FCompiler

Found executable /usr/local/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'pymc.flib' extension
compiling C sources
C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/martin/opt/anaconda3/envs/py36/include -arch x86_64 -I/Users/martin/opt/anaconda3/envs/py36/include -arch x86_64

creating build/temp.macosx-10.9-x86_64-3.6/cephes
creating build/temp.macosx-10.9-x86_64-3.6/build
creating build/temp.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6
creating build/temp.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc
creating build/temp.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/build
creating build/temp.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6
creating build/temp.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc
compile options: '-DNO_ATLAS_INFO=3 -DHAVE_CBLAS -Ibuild/src.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc -I/Users/martin/opt/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/Users/martin/opt/anaconda3/envs/py36/include/python3.6m -c'
extra options: '-msse3 -I/System/Library/Frameworks/vecLib.framework/Headers'
gcc: cephes/i0.c
gcc: cephes/chbevl.c
gcc: build/src.macosx-10.9-x86_64-3.6/pymc/flibmodule.c
gcc: cephes/c2f.c
gcc: build/src.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc/fortranobject.c
cephes/c2f.c:8:8: warning: function declaration isn't a prototype [-Wstrict-prototypes]
8 | double i0_(x)
| ^~~
cephes/i0.c: In function 'cephes_i0':
cephes/i0.c:372:30: warning: passing argument 2 of 'chbevl' from incompatible pointer type [-Wincompatible-pointer-types]
372 | return( exp(x) * chbevl( y, A, 30 ) );
| ^
| |
| short unsigned int *
In file included from cephes/mconf.h:171,
from cephes/i0.c:77:
cephes/protos.h:22:42: note: expected 'double *' but argument is of type 'short unsigned int *'
22 | extern double chbevl ( double x, double *P, int n );
| ~~~~~~~~^
cephes/i0.c:375:41: warning: passing argument 2 of 'chbevl' from incompatible pointer type [-Wincompatible-pointer-types]
375 | return( exp(x) * chbevl( 32.0/x - 2.0, B, 25 ) / sqrt(x) );
| ^
| |
| short unsigned int *
In file included from cephes/mconf.h:171,
from cephes/i0.c:77:
cephes/protos.h:22:42: note: expected 'double *' but argument is of type 'short unsigned int *'
22 | extern double chbevl ( double x, double *P, int n );
| ~~~~~~~~^
cephes/i0.c: In function 'cephes_i0e':
cephes/i0.c:392:21: warning: passing argument 2 of 'chbevl' from incompatible pointer type [-Wincompatible-pointer-types]
392 | return( chbevl( y, A, 30 ) );
| ^
| |
| short unsigned int *
In file included from cephes/mconf.h:171,
from cephes/i0.c:77:
cephes/protos.h:22:42: note: expected 'double *' but argument is of type 'short unsigned int *'
22 | extern double chbevl ( double x, double *P, int n );
| ~~~~~~~~^
cephes/i0.c:395:32: warning: passing argument 2 of 'chbevl' from incompatible pointer type [-Wincompatible-pointer-types]
395 | return( chbevl( 32.0/x - 2.0, B, 25 ) / sqrt(x) );
| ^
| |
| short unsigned int *
In file included from cephes/mconf.h:171,
from cephes/i0.c:77:
cephes/protos.h:22:42: note: expected 'double *' but argument is of type 'short unsigned int *'
22 | extern double chbevl ( double x, double *P, int n );
| ~~~~~~~~^
In file included from /Users/martin/opt/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
from /Users/martin/opt/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /Users/martin/opt/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from build/src.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc/fortranobject.h:13,
from build/src.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc/fortranobject.c:2:
/Users/martin/opt/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
In file included from /Users/martin/opt/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
from /Users/martin/opt/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /Users/martin/opt/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from build/src.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc/fortranobject.h:13,
from build/src.macosx-10.9-x86_64-3.6/pymc/flibmodule.c:16:
/Users/martin/opt/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
build/src.macosx-10.9-x86_64-3.6/pymc/flibmodule.c:186:12: warning: 'f2py_size' defined but not used [-Wunused-function]
186 | static int f2py_size(PyArrayObject* var, ...)
| ^~~~~~~~~
build/src.macosx-10.9-x86_64-3.6/pymc/flibmodule.c: In function 'f2py_rout_flib_fixed_binsize_nd':
build/src.macosx-10.9-x86_64-3.6/pymc/flibmodule.c:91:36: warning: array subscript 2 is above array bounds of 'npy_intp[2]' {aka 'long int[2]'} [-Warray-bounds]
91 | #define shape(var,dim) var ## _Dims[dim]
| ^
build/src.macosx-10.9-x86_64-3.6/pymc/flibmodule.c:17456:7: note: in expansion of macro 'shape'
17456 | d = shape(x,2);
| ^~~~~
build/src.macosx-10.9-x86_64-3.6/pymc/flibmodule.c:17397:12: note: while referencing 'x_Dims'
17397 | npy_intp x_Dims[2] = {-1, -1};
| ^~~~~~
compiling Fortran sources
Fortran f77 compiler: /usr/local/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -arch x86_64 -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/local/bin/gfortran -Wall -g -fno-second-underscore -arch x86_64 -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/local/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -arch x86_64 -fPIC -O3 -funroll-loops
creating build/temp.macosx-10.9-x86_64-3.6/pymc
compile options: '-DNO_ATLAS_INFO=3 -DHAVE_CBLAS -Ibuild/src.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc -I/Users/martin/opt/anaconda3/envs/py36/lib/python3.6/site-packages/numpy/core/include -I/Users/martin/opt/anaconda3/envs/py36/include/python3.6m -c'
gfortran:f77: pymc/histogram.f
gfortran:f77: pymc/flib.f
gfortran:f77: pymc/flib_blas.f
gfortran:f77: build/src.macosx-10.9-x86_64-3.6/pymc/flib-f2pywrappers.f
gfortran:f77: pymc/gibbsit.f
gfortran:f77: pymc/math.f
gfortran:f77: pymc/blas_wrap.f
pymc/flib_blas.f:202.25:

DOUBLE PRECISION PI
1
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pymc/math.f:396.6:

DOUBLE PRECISION FUNCTION DERF(X)
1
Warning: 'derf' declared at (1) is also the name of an intrinsic. It can only be called via an explicit interface or if declared EXTERNAL.
pymc/math.f:417.6:

DOUBLE PRECISION FUNCTION DERFC(X)
1
Warning: 'derfc' declared at (1) is also the name of an intrinsic. It can only be called via an explicit interface or if declared EXTERNAL.
pymc/gibbsit.f:2160.5:

215 IF (R .GT. .5898437) GO TO 220
1
Warning: Label 215 at (1) defined but not used
pymc/gibbsit.f:2077.5:

115 IF (R .GT. .5898437) GO TO 120
1
Warning: Label 115 at (1) defined but not used
pymc/gibbsit.f:2064.5:

15 IF (KFLAG.GE.1) GO TO 30
1
Warning: Label 15 at (1) defined but not used
pymc/gibbsit.f:1204.48:

cutpt = empquant(original,iteracnt,qhat,work)
1
Warning: Type mismatch in argument 'work' at (1); passed INTEGER(4) to REAL(8)
pymc/flib.f:316.55:

DOUBLE PRECISION mu_now, tau_now, alph_now, d_now, like
1
Warning: Unused variable 'd_now' declared at (1)
pymc/flib.f:314.42:

INTEGER i, nx, nalph, nmu, ntau, tnx
1
Warning: Unused variable 'tnx' declared at (1)
pymc/flib.f:442.71:

subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
1
Warning: Unused dummy argument 'gradxlike' at (1)
pymc/flib.f:461.40:

DOUBLE PRECISION like, low, high
1
Warning: Unused variable 'high' declared at (1)
pymc/flib.f:458.36:

INTEGER n, nlower, nupper, i
1
Warning: Unused variable 'i' declared at (1)
pymc/flib.f:461.29:

DOUBLE PRECISION like, low, high
1
Warning: Unused variable 'like' declared at (1)
pymc/flib.f:461.34:

DOUBLE PRECISION like, low, high
1
Warning: Unused variable 'low' declared at (1)
pymc/flib.f:442.39:

subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
1
Warning: Unused dummy argument 'lower' at (1)
pymc/flib.f:442.45:

subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
1
Warning: Unused dummy argument 'upper' at (1)
pymc/flib.f:442.33:

subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
1
Warning: Unused dummy argument 'x' at (1)
pymc/flib.f:692.41:

DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1)
pymc/flib.f:760.41:

DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1)
pymc/flib.f:834.41:

DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1)
pymc/flib.f:906.41:

DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1)
pymc/flib.f:976.41:

DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1)
pymc/flib.f:1186.29:

DOUBLE PRECISION factln
1
Warning: Unused variable 'factln' declared at (1)
pymc/flib.f:1185.51:

DOUBLE PRECISION sumx, mut, infinity, sumfact
1
Warning: Unused variable 'sumfact' declared at (1)
pymc/flib.f:1185.27:

DOUBLE PRECISION sumx, mut, infinity, sumfact
1
Warning: Unused variable 'sumx' declared at (1)
pymc/flib.f:1300.55:

DOUBLE PRECISION mu(nmu), gradlike(nmu),grad, cdf
1
Warning: Unused variable 'cdf' declared at (1)
pymc/flib.f:1302.29:

DOUBLE PRECISION factln, gammq
1
Warning: Unused variable 'factln' declared at (1)
pymc/flib.f:1302.36:

DOUBLE PRECISION factln, gammq
1
Warning: Unused variable 'gammq' declared at (1)
pymc/flib.f:1301.59:

DOUBLE PRECISION sumx, mut, infinity, sumfact, sumcdf
1
Warning: Unused variable 'sumcdf' declared at (1)
pymc/flib.f:1301.51:

DOUBLE PRECISION sumx, mut, infinity, sumfact, sumcdf
1
Warning: Unused variable 'sumfact' declared at (1)
pymc/flib.f:1301.27:

DOUBLE PRECISION sumx, mut, infinity, sumfact, sumcdf
1
Warning: Unused variable 'sumx' declared at (1)
pymc/flib.f:1402.29:

DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:2154.40:

DOUBLE PRECISION gradlike(n), grad
1
Warning: Unused variable 'grad' declared at (1)
pymc/flib.f:2665.29:

DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:2728.29:

DOUBLE PRECISION gammln, psi
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:2793.29:

DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:2903.29:

DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:2959.29:

DOUBLE PRECISION gammln, psi
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:3021.29:

DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:3396.58:

DOUBLE PRECISION gradlike(nx), atmp, btmp, PI, glike
1
Warning: Unused variable 'glike' declared at (1)
pymc/flib.f:3646.37:

DOUBLE PRECISION gammln, factln
1
Warning: Unused variable 'factln' declared at (1)
pymc/flib.f:3646.29:

DOUBLE PRECISION gammln, factln
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:3706.37:

DOUBLE PRECISION gammln, factln, psi
1
Warning: Unused variable 'factln' declared at (1)
pymc/flib.f:3706.29:

DOUBLE PRECISION gammln, factln, psi
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:3836.29:

DOUBLE PRECISION factln
1
Warning: Unused variable 'factln' declared at (1)
pymc/flib.f:4039.26:

DOUBLE PRECISION psi
1
Warning: Unused variable 'psi' declared at (1)
pymc/flib.f:4276.29:

DOUBLE PRECISION gammln, psi
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:4342.29:

DOUBLE PRECISION gammln, psi
1
Warning: Unused variable 'gammln' declared at (1)
pymc/flib.f:5194.35:

DOUBLE PRECISION like, factln, infinity, sump
1
Warning: Unused variable 'factln' declared at (1)
pymc/flib.f:5196.23:

INTEGER i,j,n_tmp
1
Warning: Unused variable 'n_tmp' declared at (1)
pymc/flib.f:5444.26:

DOUBLE PRECISION tmp
1
Warning: Unused variable 'tmp' declared at (1)
pymc/flib.f:5498.25:

DOUBLE PRECISION i0
1
Warning: Unused variable 'i0' declared at (1)
pymc/flib.f:5491.26:

DOUBLE PRECISION tmp
1
Warning: Unused variable 'tmp' declared at (1)
pymc/flib.f:5545.25:

DOUBLE PRECISION i0
1
Warning: Unused variable 'i0' declared at (1)
pymc/flib.f:5538.26:

DOUBLE PRECISION tmp
1
Warning: Unused variable 'tmp' declared at (1)
pymc/flib.f: In function ‘elgs’:
pymc/flib.f:4892:0: warning: ‘k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
K = I
^
pymc/flib.f: In function ‘exponweib_gl’:
pymc/flib.f:778:0: warning: ‘nc’ may be used uninitialized in this function [-Wmaybe-uninitialized]
do i = 1,nc
^
pymc/flib.f: In function ‘exponweib_gs’:
pymc/flib.f:994:0: warning: ‘nc’ may be used uninitialized in this function [-Wmaybe-uninitialized]
do i = 1,nc
^
/usr/local/bin/gfortran -Wall -g -arch x86_64 -Wall -g -undefined dynamic_lookup -bundle build/temp.macosx-10.9-x86_64-3.6/cephes/i0.o build/temp.macosx-10.9-x86_64-3.6/cephes/c2f.o build/temp.macosx-10.9-x86_64-3.6/cephes/chbevl.o build/temp.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc/flibmodule.o build/temp.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc/fortranobject.o build/temp.macosx-10.9-x86_64-3.6/pymc/flib.o build/temp.macosx-10.9-x86_64-3.6/pymc/histogram.o build/temp.macosx-10.9-x86_64-3.6/pymc/flib_blas.o build/temp.macosx-10.9-x86_64-3.6/pymc/blas_wrap.o build/temp.macosx-10.9-x86_64-3.6/pymc/math.o build/temp.macosx-10.9-x86_64-3.6/pymc/gibbsit.o build/temp.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc/flib-f2pywrappers.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin12/4.8.2 -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin12/4.8.2/../../.. -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin12/4.8.2/../../.. -lgfortran -o build/lib.macosx-10.9-x86_64-3.6/pymc/flib.cpython-36m-darwin.so -Wl,-framework -Wl,Accelerate
ld: framework not found Accelerate
collect2: error: ld returned 1 exit status
error: Command "/usr/local/bin/gfortran -Wall -g -arch x86_64 -Wall -g -undefined dynamic_lookup -bundle build/temp.macosx-10.9-x86_64-3.6/cephes/i0.o build/temp.macosx-10.9-x86_64-3.6/cephes/c2f.o build/temp.macosx-10.9-x86_64-3.6/cephes/chbevl.o build/temp.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc/flibmodule.o build/temp.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc/fortranobject.o build/temp.macosx-10.9-x86_64-3.6/pymc/flib.o build/temp.macosx-10.9-x86_64-3.6/pymc/histogram.o build/temp.macosx-10.9-x86_64-3.6/pymc/flib_blas.o build/temp.macosx-10.9-x86_64-3.6/pymc/blas_wrap.o build/temp.macosx-10.9-x86_64-3.6/pymc/math.o build/temp.macosx-10.9-x86_64-3.6/pymc/gibbsit.o build/temp.macosx-10.9-x86_64-3.6/build/src.macosx-10.9-x86_64-3.6/pymc/flib-f2pywrappers.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin12/4.8.2 -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin12/4.8.2/../../.. -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin12/4.8.2/../../.. -lgfortran -o build/lib.macosx-10.9-x86_64-3.6/pymc/flib.cpython-36m-darwin.so -Wl,-framework -Wl,Accelerate" failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /Users/martin/opt/anaconda3/envs/py36/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/my/fnqjb79j6hn7czm0yf573drw0000gq/T/pip-install-9nh2jp4m/pymc_cbb9691e3f464fb7a53b84bc4b6d8522/setup.py'"'"'; __file__='"'"'/private/var/folders/my/fnqjb79j6hn7czm0yf573drw0000gq/T/pip-install-9nh2jp4m/pymc_cbb9691e3f464fb7a53b84bc4b6d8522/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'"'"'))' install --record /private/var/folders/my/fnqjb79j6hn7czm0yf573drw0000gq/T/pip-record-uizprwo1/install-record.txt --single-version-externally-managed --compile --install-headers /Users/martin/opt/anaconda3/envs/py36/include/python3.6m/pymc Check the logs for full command output.

martin.d...@gmail.com

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Aug 5, 2022, 10:54:57 AM8/5/22

to hddm-users

Just a quick note on this. I was able to successfully install by using conda (pip install pymc==2.3.8 still fails, but this works).

conda install -c condaforge pymc==2.3.8

Camilla Eva Andersen

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Aug 8, 2022, 6:13:57 AM8/8/22

to hddm-users

I was able to install HDDM and PyMC in a python 3.6 env. In case that helps, here are my steps:

Create an env via the terminal:

conda create -vv -n HDDM36 python=3.6 jupyter

Install Ipykernal (If not already done:

conda install -c anaconda ipykernel

Activate the env:
conda activate HDDM36

Install the env so that you can open it in Juliter notebook:

python -m ipykernel install --user --name=HDDM36

Install HDDM inside the env:

conda activate HDDM36
conda install conda-build
conda install pymc=2.3.8 -c conda-forge
conda install pandas patsy
export MACOSX_DEPLOYMENT_TARGET=10.11
pip install cython
pip install hddm
conda install jupyter

Michael J Frank

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Aug 8, 2022, 1:56:43 PM8/8/22

to hddm-...@googlegroups.com

Thanks Camilla!

Michael

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Stephanie Smith

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Aug 11, 2022, 2:28:53 PM8/11/22

to hddm-users

This sequence (unfortunately) does not seem to work for Python 3.9 - it still gets stuck installing pymc. Since Python 3.6 is no longer supported... any chance anyone has had luck with this in Python 3.7 or later? (Or a different sequence of commands/steps?)

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