Closed rachel-rodrigues closed 2 years ago
fonnesbeck
commented
2 years ago Hey, @rachel-rodrigues. Is there a good reason for you to be using PyMC 2.x rather than PyMC3? We strongly recommend using PyMC3, as it is significantly better for Bayesian inference due to its use of gradient-based samplers (among other things). PyMC2 really only exists for legacy models and such.
If you do want 2.3.8, you should just use pip rather than conda.
rachel-rodrigues
commented
2 years ago Hi @fonnesbeck, I'm using a package called hddm that needs pymc (I installed pymc3 and tried running the code with this too, but sadly didn't work)
Thank you for your pip suggestion, I did pip install pymc but keep getting the following error (I also tried in a new environment and got the same error) and was wondering whether you had any advice to get around this?
Collecting pymc Using cached pymc-2.3.8.tar.gz (385 kB) Building wheels for collected packages: pymc Building wheel for pymc (setup.py) ... error ERROR: Command errored out with exit status 1: command: /opt/anaconda3/envs/hddm/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/x_/h717mvks0q77vfkyldhwrqmm0000gn/T/pip-install-hh166rgy/pymc8b5ca74843354c65aeb17b59fe85fa3c/setup.py'"'"'; file='"'"'/private/var/folders/x/h717mvks0q77vfkyldhwrqmm0000gn/T/pip-install-hh166rgy/pymc_8b5ca74843354c65aeb17b59fe85fa3c/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'"'"'))' bdistwheel -d /private/var/folders/x/h717mvks0q77vfkyldhwrqmm0000gn/T/pip-wheel-jr7zzx4 cwd: /private/var/folders/x/h717mvks0q77vfkyldhwrqmm0000gn/T/pip-install-hh166rgy/pymc_8b5ca74843354c65aeb17b59fe85fa3c/ Complete output (168 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_64-3.6/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 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.
ERROR: Failed building wheel for pymc Running setup.py clean for pymc Failed to build pymc Installing collected packages: pymc Running setup.py install for pymc ... error ERROR: Command errored out with exit status 1: command: /opt/anaconda3/envs/hddm/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/x_/h717mvks0q77vfkyldhwrqmm0000gn/T/pip-install-hh166rgy/pymc8b5ca74843354c65aeb17b59fe85fa3c/setup.py'"'"'; file='"'"'/private/var/folders/x/h717mvks0q77vfkyldhwrqmm0000gn/T/pip-install-hh166rgy/pymc8b5ca74843354c65aeb17b59fe85fa3c/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/x/h717mvks0q77vfkyldhwrqmm0000gn/T/pip-record-sb9shnvj/install-record.txt --single-version-externally-managed --compile --install-headers /opt/anaconda3/envs/hddm/include/python3.6m/pymc cwd: /private/var/folders/x_/h717mvks0q77vfkyldhwrqmm0000gn/T/pip-install-hh166rgy/pymc_8b5ca74843354c65aeb17b59fe85fa3c/ Complete output (168 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 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
----------------------------------------ERROR: Command errored out with exit status 1: /opt/anaconda3/envs/hddm/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/x_/h717mvks0q77vfkyldhwrqmm0000gn/T/pip-install-hh166rgy/pymc8b5ca74843354c65aeb17b59fe85fa3c/setup.py'"'"'; file='"'"'/private/var/folders/x/h717mvks0q77vfkyldhwrqmm0000gn/T/pip-install-hh166rgy/pymc8b5ca74843354c65aeb17b59fe85fa3c/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/x/h717mvks0q77vfkyldhwrqmm0000gn/T/pip-record-sb9shnvj/install-record.txt --single-version-externally-managed --compile --install-headers /opt/anaconda3/envs/hddm/include/python3.6m/pymc Check the logs for full command output.
rachel-rodrigues
commented
2 years ago Hi @fonnesbeck, just wanted to say 2.3.8 installed successfully using pip after I downloaded Xcode, many thanks for your help
Best wishes Rachel
Dear all, I specifically need pymc 2.3.8 for some analysis. I've tried installing through conda-forge using
conda install -c conda-forge pymcbut it keeps wanting to install 2.3.7. Does anyone know any other way of getting version 2.3.8?I'm using Mac OSX-64 and python 3.6 (3.6 is needed for some other packages to run)
Many thanks Rachel