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pymc-devs / pymc

Bayesian Modeling and Probabilistic Programming in Python
https://docs.pymc.io/
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Installation Issue on MacOs #1370

Closed MartinLiebig closed 7 years ago

MartinLiebig commented 8 years ago

Dear All,

i just tried to install pyMC3 on my macbook. It's not working and i cannot figure out how to fix it. Here is the shell output:

`Martins-MacBook-Pro:CODING mschmitz$ pip install git+https://github.com/pymc-devs/pymc3
Collecting git+https://github.com/pymc-devs/pymc3
  Cloning https://github.com/pymc-devs/pymc3 to /var/folders/mb/6lxs_l_x19zgdbxrs231hl5m0000gn/T/pip-gj9s_t7q-build
Requirement already satisfied (use --upgrade to upgrade): numpy>=1.11.0 in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): scipy>=0.12.0 in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): matplotlib>=1.5.0 in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): theano>=0.8.2 in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): pandas>=0.18.0 in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): patsy>=0.4.0 in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): joblib>=0.9 in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): CommonMark==0.5.4 in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): recommonmark in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): sphinx in /Users/mschmitz/anaconda/lib/python3.5/site-packages/Sphinx-1.3.1-py3.5.egg (from pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): nbsphinx in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): numpydoc in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): pyparsing!=2.0.0,!=2.0.4,!=2.1.2,>=1.5.6 in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from matplotlib>=1.5.0->pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): python-dateutil in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from matplotlib>=1.5.0->pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): pytz in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from matplotlib>=1.5.0->pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): cycler in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from matplotlib>=1.5.0->pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): six>=1.9.0 in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from theano>=0.8.2->pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): docutils>=0.11 in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from recommonmark->pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): Jinja2>=2.3 in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from sphinx->pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): Pygments>=2.0 in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from sphinx->pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): snowballstemmer>=1.1 in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from sphinx->pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): babel>=1.3 in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from sphinx->pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): alabaster<0.8,>=0.7 in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from sphinx->pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): sphinx_rtd_theme<0.2,>=0.1 in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from sphinx->pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): nbconvert in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from nbsphinx->pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): nbformat in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from nbsphinx->pymc3==3.0rc1)
Requirement already satisfied (use --upgrade to upgrade): MarkupSafe in /Users/mschmitz/anaconda/lib/python3.5/site-packages (from Jinja2>=2.3->sphinx->pymc3==3.0rc1)
Installing collected packages: pymc3
  Running setup.py install for pymc3 ... error
    Complete output from command /Users/mschmitz/anaconda/bin/python -u -c "import setuptools, tokenize;__file__='/var/folders/mb/6lxs_l_x19zgdbxrs231hl5m0000gn/T/pip-gj9s_t7q-build/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/mb/6lxs_l_x19zgdbxrs231hl5m0000gn/T/pip-lb3vnc44-record/install-record.txt --single-version-externally-managed --compile:
    WARNING: '.' not a valid package name; please use only .-separated package names in setup.py
    /Users/mschmitz/anaconda/lib/python3.5/site-packages/setuptools-20.7.0-py3.5.egg/setuptools/dist.py:285: UserWarning: Normalizing '3.0.rc1' to '3.0rc1'
    running install
    running build
    running build_py
    creating build
    creating build/lib
    creating build/lib/pymc3
    copying pymc3/__init__.py -> build/lib/pymc3
    copying pymc3/blocking.py -> build/lib/pymc3
    copying pymc3/data.py -> build/lib/pymc3
    copying pymc3/debug.py -> build/lib/pymc3
    copying pymc3/diagnostics.py -> build/lib/pymc3
    copying pymc3/interactive_sampling.py -> build/lib/pymc3
    copying pymc3/math.py -> build/lib/pymc3
    copying pymc3/memoize.py -> build/lib/pymc3
    copying pymc3/model.py -> build/lib/pymc3
    copying pymc3/plots.py -> build/lib/pymc3
    copying pymc3/progressbar.py -> build/lib/pymc3
    copying pymc3/sampling.py -> build/lib/pymc3
    copying pymc3/stats.py -> build/lib/pymc3
    copying pymc3/theanof.py -> build/lib/pymc3
    copying pymc3/vartypes.py -> build/lib/pymc3
    creating build/lib/pymc3/distributions
    copying pymc3/distributions/__init__.py -> build/lib/pymc3/distributions
    copying pymc3/distributions/continuous.py -> build/lib/pymc3/distributions
    copying pymc3/distributions/discrete.py -> build/lib/pymc3/distributions
    copying pymc3/distributions/dist_math.py -> build/lib/pymc3/distributions
    copying pymc3/distributions/distribution.py -> build/lib/pymc3/distributions
    copying pymc3/distributions/multivariate.py -> build/lib/pymc3/distributions
    copying pymc3/distributions/special.py -> build/lib/pymc3/distributions
    copying pymc3/distributions/timeseries.py -> build/lib/pymc3/distributions
    copying pymc3/distributions/transforms.py -> build/lib/pymc3/distributions
    creating build/lib/pymc3/step_methods
    copying pymc3/step_methods/__init__.py -> build/lib/pymc3/step_methods
    copying pymc3/step_methods/arraystep.py -> build/lib/pymc3/step_methods
    copying pymc3/step_methods/ATMCMC.py -> build/lib/pymc3/step_methods
    copying pymc3/step_methods/compound.py -> build/lib/pymc3/step_methods
    copying pymc3/step_methods/gibbs.py -> build/lib/pymc3/step_methods
    copying pymc3/step_methods/hmc.py -> build/lib/pymc3/step_methods
    copying pymc3/step_methods/metropolis.py -> build/lib/pymc3/step_methods
    copying pymc3/step_methods/nuts.py -> build/lib/pymc3/step_methods
    copying pymc3/step_methods/quadpotential.py -> build/lib/pymc3/step_methods
    copying pymc3/step_methods/slicer.py -> build/lib/pymc3/step_methods
    creating build/lib/pymc3/tuning
    copying pymc3/tuning/__init__.py -> build/lib/pymc3/tuning
    copying pymc3/tuning/scaling.py -> build/lib/pymc3/tuning
    copying pymc3/tuning/starting.py -> build/lib/pymc3/tuning
    creating build/lib/pymc3/tests
    copying pymc3/tests/__init__.py -> build/lib/pymc3/tests
    copying pymc3/tests/backend_fixtures.py -> build/lib/pymc3/tests
    copying pymc3/tests/checks.py -> build/lib/pymc3/tests
    copying pymc3/tests/helpers.py -> build/lib/pymc3/tests
    copying pymc3/tests/knownfailure.py -> build/lib/pymc3/tests
    copying pymc3/tests/models.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_advi.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_diagnostics.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_distribution_defaults.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_distributions.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_distributions_random.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_examples.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_glm.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_hmc.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_memo.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_missing.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_model_func.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_ndarray_backend.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_plots.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_posdef_sym.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_profile.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_sampling.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_shared.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_special_functions.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_sqlite_backend.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_starting.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_stats.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_step.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_text_backend.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_tracetab.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_transforms.py -> build/lib/pymc3/tests
    copying pymc3/tests/test_tuning.py -> build/lib/pymc3/tests
    creating build/lib/pymc3/glm
    copying pymc3/glm/__init__.py -> build/lib/pymc3/glm
    copying pymc3/glm/families.py -> build/lib/pymc3/glm
    copying pymc3/glm/glm.py -> build/lib/pymc3/glm
    creating build/lib/pymc3/examples
    copying pymc3/examples/__init__.py -> build/lib/pymc3/examples
    copying pymc3/examples/arbitrary_stochastic.py -> build/lib/pymc3/examples
    copying pymc3/examples/ARM12_6.py -> build/lib/pymc3/examples
    copying pymc3/examples/ARM12_6uranium.py -> build/lib/pymc3/examples
    copying pymc3/examples/ARM5_4.py -> build/lib/pymc3/examples
    copying pymc3/examples/arma_example.py -> build/lib/pymc3/examples
    copying pymc3/examples/ATMIP_2gaussians.py -> build/lib/pymc3/examples
    copying pymc3/examples/banana.py -> build/lib/pymc3/examples
    copying pymc3/examples/best.py -> build/lib/pymc3/examples
    copying pymc3/examples/custom_dists.py -> build/lib/pymc3/examples
    copying pymc3/examples/dirichlet.py -> build/lib/pymc3/examples
    copying pymc3/examples/disaster_model.py -> build/lib/pymc3/examples
    copying pymc3/examples/disaster_model_arbitrary_deterministic.py -> build/lib/pymc3/examples
    copying pymc3/examples/disaster_model_missing.py -> build/lib/pymc3/examples
    copying pymc3/examples/discrete_find_MAP.py -> build/lib/pymc3/examples
    copying pymc3/examples/factor_potential.py -> build/lib/pymc3/examples
    copying pymc3/examples/garch_example.py -> build/lib/pymc3/examples
    copying pymc3/examples/gelman_bioassay.py -> build/lib/pymc3/examples
    copying pymc3/examples/gelman_schools.py -> build/lib/pymc3/examples
    copying pymc3/examples/GHME_2013.py -> build/lib/pymc3/examples
    copying pymc3/examples/glm_linear.py -> build/lib/pymc3/examples
    copying pymc3/examples/glm_robust.py -> build/lib/pymc3/examples
    copying pymc3/examples/hierarchical.py -> build/lib/pymc3/examples
    copying pymc3/examples/hierarchical_sqlite.py -> build/lib/pymc3/examples
    copying pymc3/examples/lasso_block_update.py -> build/lib/pymc3/examples
    copying pymc3/examples/lasso_missing.py -> build/lib/pymc3/examples
    copying pymc3/examples/latent_occupancy.py -> build/lib/pymc3/examples
    copying pymc3/examples/lightspeed_example.py -> build/lib/pymc3/examples
    copying pymc3/examples/LKJ_correlation.py -> build/lib/pymc3/examples
    copying pymc3/examples/logistic.py -> build/lib/pymc3/examples
    copying pymc3/examples/normal.py -> build/lib/pymc3/examples
    copying pymc3/examples/nutstest.py -> build/lib/pymc3/examples
    copying pymc3/examples/python_vs_c.py -> build/lib/pymc3/examples
    copying pymc3/examples/rsv.py -> build/lib/pymc3/examples
    copying pymc3/examples/simpletest.py -> build/lib/pymc3/examples
    copying pymc3/examples/speedtest_pymc3.py -> build/lib/pymc3/examples
    copying pymc3/examples/stochastic_volatility.py -> build/lib/pymc3/examples
    copying pymc3/examples/tutorial.py -> build/lib/pymc3/examples
    copying pymc3/examples/wishart.py -> build/lib/pymc3/examples
    creating build/lib/pymc3/backends
    copying pymc3/backends/__init__.py -> build/lib/pymc3/backends
    copying pymc3/backends/base.py -> build/lib/pymc3/backends
    copying pymc3/backends/ndarray.py -> build/lib/pymc3/backends
    copying pymc3/backends/sqlite.py -> build/lib/pymc3/backends
    copying pymc3/backends/text.py -> build/lib/pymc3/backends
    copying pymc3/backends/tracetab.py -> build/lib/pymc3/backends
    creating build/lib/pymc3/variational
    copying pymc3/variational/__init__.py -> build/lib/pymc3/variational
    copying pymc3/variational/advi.py -> build/lib/pymc3/variational
    copying pymc3/variational/advi_minibatch.py -> build/lib/pymc3/variational
    package init file 'docs/__init__.py' not found (or not a regular file)
    package init file '__init__.py' not found (or not a regular file)
    copying setup.py -> build/lib
    copying setupegg.py -> build/lib
    creating build/lib/pymc3/examples/data
    copying pymc3/examples/data/__init__.py -> build/lib/pymc3/examples/data
    copying pymc3/examples/data/cty.dat -> build/lib/pymc3/examples/data
    copying pymc3/examples/data/Guber1999data.txt -> build/lib/pymc3/examples/data
    copying pymc3/examples/data/HtWt.csv -> build/lib/pymc3/examples/data
    copying pymc3/examples/data/jester-dataset-v1-dense-first-1000.csv -> build/lib/pymc3/examples/data
    copying pymc3/examples/data/pancreatitis.csv -> build/lib/pymc3/examples/data
    copying pymc3/examples/data/radon.csv -> build/lib/pymc3/examples/data
    copying pymc3/examples/data/SP500.csv -> build/lib/pymc3/examples/data
    copying pymc3/examples/data/srrs2.dat -> build/lib/pymc3/examples/data
    copying pymc3/examples/data/test_scores.csv -> build/lib/pymc3/examples/data
    copying pymc3/examples/data/wells.dat -> build/lib/pymc3/examples/data
    creating build/lib/docs
    creating build/lib/docs/source
    creating build/lib/docs/source/data
    error: can't copy 'docs/source/data/6bb8d06c69c0666e6da14c094d4320d115f1ffc8': doesn't exist or not a regular file

    ----------------------------------------
Command "/Users/mschmitz/anaconda/bin/python -u -c "import setuptools, tokenize;__file__='/var/folders/mb/6lxs_l_x19zgdbxrs231hl5m0000gn/T/pip-gj9s_t7q-build/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/mb/6lxs_l_x19zgdbxrs231hl5m0000gn/T/pip-lb3vnc44-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /var/folders/mb/6lxs_l_x19zgdbxrs231hl5m0000gn/T/pip-gj9s_t7q-build/`

I am running most recent macOs with a kind of standard anaconda stack

fonnesbeck commented 8 years ago

Sorry, editing this, as I see that is the command you had issued. We will look into this.

fonnesbeck commented 8 years ago

This is odd, because this was an issue I believe we had fixed from the release candidate. Can you try adding .git to the end of the install command, so:

pip install -U git+https://github.com/pymc-devs/pymc3.git

I wonder if leaving it off installs the release?

twiecki commented 7 years ago

@MartinSchmitzDo Can you retry from current master?

MartinLiebig commented 7 years ago

i've tried pip install git+https://github.com/pymc-devs/pymc3.git again. Still the same error.

fonnesbeck commented 7 years ago

This is bizarre, as this was fixed in master. You might try adding -U --force-reinstall to the pip command. Are you using Anaconda? If so, you can also try creating a clean virtualenv and trying to install it there.

MartinLiebig commented 7 years ago

since this is my private laptop which I only use for fun/science projects i went for the most extreme way and reinstalled anaconda. After installing sphinx via conda and not pip it works now.

Thanks for the help.

~Martin