akelleh / causality Goto Github PK
View Code? Open in Web Editor NEWTools for causal analysis
License: MIT License
causality's People
Contributors
Stargazers
Watchers
Forkers
samsach ee08b397 mtlc ingrid88 throughaglass stewartsiu chen0031 ruchowdh light44 msihl benjamesbabala sjstreicher alenzhao chirayukong hehuanshu96 wavelets arunce awesome-python guhjy codeaudit kira8565 ecore2018 frmsaul jattenberg kapiya wangtz1994 ryanmetz anhaner dc33 tedzzx anirband 80286 akellehe soknif mengyuan404 tianxi1118 tonydeep mozzielol ghostintheshellarise dreinstein10 ericmjl sotomsa vishalbelsare hungnk25 tinglo wangqianwen0418 feitianyiren abdaladiasse hiepbt pricingpapi 2torus akju jamco88 yanlirock jbdatascience scottishfold007 jabogithub hannahwang1110 booblu joeyqiang949 seekshreyas sahanduiuc dlnan drotich arita37 n8sty diogoribeiro7 qpanscience xuezhizhang xrosliang nikolaospapachristou srhruc918 shalevy1 ahoyosid arithmometer dotrado evelynqian andy-wagner hxwen9784 cognoscentai crlsmcl jaryaman ajeytiwary dfwlab smily1984 computableai yangxhcaf muchway2019 samrat-halder octeufer tvjoseph dscausality imohitmayank drahnreb damon03 agno3xzy q-leo vitlib inetkenya zjcanjuxcausality's Issues
Doesn't install for Python3
I tried to install it for Python 3, but wasn't able to as the package depends on pymc, and even though I have pymc3 installed, doesn't connect to that one instead
Causality installation error (cephes?)
Hi,
First of all, I'm still learning python so this might be an obvious question, but I wanted to try this library out and I tried to install causality using pip but I got an error that I think is related to a dependency called chephes, please see the image attached.
How do I install chephes? Am I missing something?
Thanks in advance
Difference between analysis and estimation
I am a bit confused, what is the difference between Causal Analysis of the dataframe ("This method lets you control for a set of variables, z, when you're trying to estimate the effect"), and the causality.estimation module which "contains tools for estimating causal effects"?
One uses Robin-G, and the other Propensity Score Matching? (or these methods serve different purposes?)
TypeError: can only concatenate list (not "dict_keys") to list
From:
https://medium.com/@akelleh/causal-inference-with-pandas-dataframes-fc3e64fce5d
I believe I did this:
pip install git+https://github.com/akelleh/causality.git@c52425a2db16d27780746295ec68752b7986890c --upgrade
X.zplot(x='x', y='y', z={'z1': 'c', 'z2': 'c'}, kind='line', model_type='kernel')
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-5-c084bc38fd7e> in <module>()
----> 1 X.zplot(x='x', y='y', z={'z1': 'c', 'z2': 'c'}, kind='line', model_type='kernel')
~\Anaconda3\envs\inference\lib\site-packages\causality\analysis\dataframe.py in zplot(self, *args, **kwargs)
9 if kwargs.get('z', {}):
10 if kwargs.get('kind') == 'line':
---> 11 return self._line_zplot(*args, **kwargs)
12 if kwargs.get('kind') == 'bar':
13 return self._bar_zplot(*args, **kwargs)
~\Anaconda3\envs\inference\lib\site-packages\causality\analysis\dataframe.py in _line_zplot(self, *args, **kwargs)
23
24 def _line_zplot(self, *args, **kwargs):
---> 25 model, arg_key = self._get_model(*args, **kwargs)
26 if arg_key:
27 del kwargs[arg_key]
~\Anaconda3\envs\inference\lib\site-packages\causality\analysis\dataframe.py in _get_model(self, *args, **kwargs)
123 model = KernelModelWrapper()
124 arg_key = 'model_type'
--> 125 model.fit(self[[treatment] + confounders], self[outcome], variable_types=variable_types)
126 else:
127 model = RandomForestRegressor()
TypeError: can only concatenate list (not "dict_keys") to list(awesome blog post btw!)
issue installing on osx (no conda)
When I first tried to install it complained that numpy was not available. After I installed it I get the following error
pipenv install causality
Installing causality…
Looking in indexes: https://pypi.python.org/simple
Collecting causality
Collecting statsmodels (from causality)
Using cached https://files.pythonhosted.org/packages/29/df/1f8233500d8bb90f16fd066560f3805197e568af611ca97eddd5fb81b012/statsmodels-0.9.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting pytz (from causality)
Using cached https://files.pythonhosted.org/packages/30/4e/27c34b62430286c6d59177a0842ed90dc789ce5d1ed740887653b898779a/pytz-2018.5-py2.py3-none-any.whl
Collecting decorator (from causality)
Using cached https://files.pythonhosted.org/packages/bc/bb/a24838832ba35baf52f32ab1a49b906b5f82fb7c76b2f6a7e35e140bac30/decorator-4.3.0-py2.py3-none-any.whl
Collecting networkx (from causality)
Using cached https://files.pythonhosted.org/packages/11/42/f951cc6838a4dff6ce57211c4d7f8444809ccbe2134179950301e5c4c83c/networkx-2.1.zip
Requirement already satisfied: numpy in /Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/lib/python3.6/site-packages (from causality) (1.14.5)
Collecting patsy (from causality)
Using cached https://files.pythonhosted.org/packages/5d/eb/92c4b45ca47a2dd1339c958636e083b50ffadb5162a599a1cbbe92f89832/patsy-0.5.0-py2.py3-none-any.whl
Collecting six (from causality)
Using cached https://files.pythonhosted.org/packages/67/4b/141a581104b1f6397bfa78ac9d43d8ad29a7ca43ea90a2d863fe3056e86a/six-1.11.0-py2.py3-none-any.whl
Collecting pandas (from causality)
Downloading https://files.pythonhosted.org/packages/d8/ba/d2c6578afca709e211ac1cd836a66a6a042f1a773a970be345d9d08be426/pandas-0.23.3-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (14.0MB)
Collecting pymc (from causality)
Using cached https://files.pythonhosted.org/packages/0c/1c/2eb7016284e04ccf401fdcf11b817b160629cf8cf230240ceb348311ac2e/pymc-2.3.6.tar.gz
Collecting python-dateutil (from causality)
Using cached https://files.pythonhosted.org/packages/cf/f5/af2b09c957ace60dcfac112b669c45c8c97e32f94aa8b56da4c6d1682825/python_dateutil-2.7.3-py2.py3-none-any.whl
Collecting scipy (from causality)
Using cached https://files.pythonhosted.org/packages/a0/b6/70bf61c1badb5fea82d4c558e05e76c2dee5e77bb072fe465d7c7a87287d/scipy-1.1.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Building wheels for collected packages: networkx, pymc
Running setup.py bdist_wheel for networkx: started
Running setup.py bdist_wheel for networkx: finished with status 'done'
Stored in directory: /Users/harrymoreno/Library/Caches/pip/wheels/44/c0/34/6f98693a554301bdb405f8d65d95bbcd3e50180cbfdd98a94e
Running setup.py bdist_wheel for pymc: started
Running setup.py bdist_wheel for pymc: finished with status 'error'
Complete output from command /Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/private/var/folders/6y/kf699bqj2sgcgjshb20fr5zh0000gn/T/pip-install-ooarg4tj/pymc/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /private/var/folders/6y/kf699bqj2sgcgjshb20fr5zh0000gn/T/pip-wheel-8ejm2src --python-tag cp36:
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-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/fortranobject.c' to sources.
adding 'build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc' to include_dirs.
adding 'build/src.macosx-10.13-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-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/gp/fortranobject.c' to sources.
adding 'build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/gp' to include_dirs.
building extension "pymc.gp.incomplete_chol" sources
f2py options: []
adding 'build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/gp/fortranobject.c' to sources.
adding 'build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-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-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/gp/cov_funs/fortranobject.c' to sources.
adding 'build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/gp/cov_funs' to include_dirs.
adding 'build/src.macosx-10.13-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-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/gp/cov_funs/fortranobject.c' to sources.
adding 'build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-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-10.13-x86_64-3.6
creating build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/StepMethods.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/InstantiationDecorators.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/CircularStochastic.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/diagnostics.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/threadpool.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/graph.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/Matplot.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/__init__.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/Container.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/Model.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/distributions.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/MCMC.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/datatypes.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/NormalApproximation.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/progressbar.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/utils.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/PyMCObjects.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/six.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/Node.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/CommonDeterministics.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/calc_utils.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/NumpyDeterministics.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/ScipyDistributions.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/decorators.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
creating build/lib.macosx-10.13-x86_64-3.6/pymc/database
copying pymc/database/no_trace.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/database
copying pymc/database/txt.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/database
copying pymc/database/__init__.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/database
copying pymc/database/hdf5.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/database
copying pymc/database/sqlite.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/database
copying pymc/database/pickle.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/database
copying pymc/database/hdf5ea.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/database
copying pymc/database/ram.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/database
copying pymc/database/base.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/database
creating build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/melanoma.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/disaster_model_linear.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/disaster_model.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/disaster_model_gof.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/gelman_bioassay.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/weibull_fit_gof.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/__init__.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/melanoma_data.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/disaster_model_null.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/zip.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/custom_step.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/disaster_model_missing.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/weibull_fit.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
creating build/lib.macosx-10.13-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/covparams.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/observation.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/PyMCmodel.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/basiscov.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/realizations.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/mesh_choice.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/__init__.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/cov.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/mean.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/MCMC.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples/gp
creating build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_utils.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_MCMCSampler.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_database.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_cov.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_container.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_missing.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_observation.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_realization.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_convergence.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/__init__.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_AM.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_basiscov.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_GP_MCMC.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_norm_approx.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_mean.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_distributions.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_slice.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_binary_step.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_adaptive.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_special_methods.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_instantiation.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/objectmodel.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_graph.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_gradients.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_interactive.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
creating build/lib.macosx-10.13-x86_64-3.6/pymc/gp
copying pymc/gp/step_methods.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp
copying pymc/gp/Realization.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp
copying pymc/gp/gp_submodel.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp
copying pymc/gp/gpplots.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp
copying pymc/gp/GPutils.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp
copying pymc/gp/Covariance.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp
copying pymc/gp/__init__.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp
copying pymc/gp/Mean.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp
copying pymc/gp/FullRankCovariance.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp
copying pymc/gp/NearlyFullRankCovariance.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp
copying pymc/gp/BasisCovariance.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp
creating build/lib.macosx-10.13-x86_64-3.6/pymc/gp/cov_funs
copying pymc/gp/cov_funs/__init__.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp/cov_funs
copying pymc/gp/cov_funs/wrapped_distances.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp/cov_funs
copying pymc/gp/cov_funs/brownian.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp/cov_funs
copying pymc/gp/cov_funs/nsmatern.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp/cov_funs
copying pymc/gp/cov_funs/cov_utils.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp/cov_funs
copying pymc/gp/cov_funs/bases.py -> build/lib.macosx-10.13-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: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers
creating build/temp.macosx-10.13-x86_64-3.6/cephes
creating build/temp.macosx-10.13-x86_64-3.6/build
creating build/temp.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6
creating build/temp.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc
creating build/temp.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/build
creating build/temp.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6
creating build/temp.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc
compile options: '-DNO_ATLAS_INFO=3 -DHAVE_CBLAS -Ibuild/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc -I/Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/lib/python3.6/site-packages/numpy/core/include -I/usr/local/Cellar/python/3.6.5/Frameworks/Python.framework/Versions/3.6/include/python3.6m -c'
extra options: '-msse3'
clang: cephes/i0.c
cephes/i0.c:372:30: warning: incompatible pointer types passing 'unsigned short [120]' to parameter of type 'double *' [-Wincompatible-pointer-types]
return( exp(x) * chbevl( y, A, 30 ) );
^
cephes/i0.c:355:40: note: passing argument to parameter here
extern double chbevl ( double, double *, int );
^
cephes/i0.c:375:41: warning: incompatible pointer types passing 'unsigned short [100]' to parameter of type 'double *' [-Wincompatible-pointer-types]
return( exp(x) * chbevl( 32.0/x - 2.0, B, 25 ) / sqrt(x) );
^
cephes/i0.c:355:40: note: passing argument to parameter here
extern double chbevl ( double, double *, int );
^
cephes/i0.c:392:21: warning: incompatible pointer types passing 'unsigned short [120]' to parameter of type 'double *' [-Wincompatible-pointer-types]
return( chbevl( y, A, 30 ) );
^
cephes/i0.c:355:40: note: passing argument to parameter here
extern double chbevl ( double, double *, int );
^
cephes/i0.c:395:32: warning: incompatible pointer types passing 'unsigned short [100]' to parameter of type 'double *' [-Wincompatible-pointer-types]
return( chbevl( 32.0/x - 2.0, B, 25 ) / sqrt(x) );
^
cephes/i0.c:355:40: note: passing argument to parameter here
extern double chbevl ( double, double *, int );
^
4 warnings generated.
clang: cephes/c2f.c
cephes/c2f.c:8:11: warning: this old-style function definition is not preceded by a prototype [-Wstrict-prototypes]
double i0_(x)
^
1 warning generated.
clang: cephes/chbevl.c
clang: build/src.macosx-10.13-x86_64-3.6/pymc/flibmodule.c
In file included from build/src.macosx-10.13-x86_64-3.6/pymc/flibmodule.c:16:
In file included from build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/fortranobject.h:13:
In file included from /Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:
/Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
^
build/src.macosx-10.13-x86_64-3.6/pymc/flibmodule.c:16773:7: warning: array index 2 is past the end of the array (which contains 2 elements) [-Warray-bounds]
d = shape(x,2);
^ ~
build/src.macosx-10.13-x86_64-3.6/pymc/flibmodule.c:84:24: note: expanded from macro 'shape'
#define shape(var,dim) var ## _Dims[dim]
^ ~~~
<scratch space>:231:1: note: expanded from here
x_Dims
^
build/src.macosx-10.13-x86_64-3.6/pymc/flibmodule.c:16716:3: note: array 'x_Dims' declared here
npy_intp x_Dims[2] = {-1, -1};
^
build/src.macosx-10.13-x86_64-3.6/pymc/flibmodule.c:179:12: warning: unused function 'f2py_size' [-Wunused-function]
static int f2py_size(PyArrayObject* var, ...)
^
3 warnings generated.
clang: build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/fortranobject.c
In file included from build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/fortranobject.c:2:
In file included from build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/fortranobject.h:13:
In file included from /Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:
/Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
^
build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/fortranobject.c:138:18: warning: comparison of integers of different signs: 'Py_ssize_t' (aka 'long') and 'unsigned long' [-Wsign-compare]
if (size < sizeof(notalloc)) {
~~~~ ^ ~~~~~~~~~~~~~~~~
2 warnings generated.
compiling Fortran sources
Fortran f77 compiler: /usr/local/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/local/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/local/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
creating build/temp.macosx-10.13-x86_64-3.6/pymc
compile options: '-DNO_ATLAS_INFO=3 -DHAVE_CBLAS -Ibuild/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc -I/Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/lib/python3.6/site-packages/numpy/core/include -I/usr/local/Cellar/python/3.6.5/Frameworks/Python.framework/Versions/3.6/include/python3.6m -c'
gfortran:f77: pymc/flib.f
f951: Warning: Nonconforming tab character in column 1 of line 509 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 510 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 511 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 512 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 513 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 557 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 558 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 559 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 560 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 561 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 707 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 711 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 715 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 723 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 775 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 779 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 783 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 791 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 849 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 853 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 857 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 865 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 921 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 925 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 929 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 937 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 991 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 995 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 999 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1007 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1195 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1196 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1197 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1200 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1201 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1408 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1409 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1412 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1420 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1421 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1422 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1423 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1424 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1425 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1452 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1454 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1457 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1465 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1466 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1467 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1469 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1470 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1471 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1472 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1473 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1478 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1499 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1501 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1504 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1512 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1513 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1514 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1515 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1516 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1517 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1740 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1743 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1746 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1755 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1783 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1786 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1789 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1798 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1800 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1832 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1835 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1838 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1847 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1849 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1977 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1978 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2030 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2031 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2079 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2080 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2168 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2174 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2218 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2224 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2339 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2395 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2692 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2693 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2694 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2696 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2697 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2756 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2820 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2881 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3191 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3192 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3656 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3657 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3658 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3660 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3661 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3662 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3664 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3665 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3666 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3716 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3717 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3718 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3720 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3721 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3722 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3724 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3725 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3726 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3732 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3846 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3847 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3849 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3851 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3875 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3876 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3877 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3878 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4276 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4277 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4278 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4280 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4281 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4282 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4284 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4285 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4286 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4288 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4289 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4290 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4342 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4343 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4344 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4346 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4347 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4348 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4350 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4351 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4352 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4354 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4355 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4356 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4620 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4622 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4623 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4624 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4626 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4628 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4630 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4632 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4633 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4634 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4635 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4637 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4638 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4639 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4640 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4642 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4643 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4644 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4645 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4646 [-Wtabs]
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) [-Wunused-variable]
pymc/flib.f:314:42:
INTEGER i, nx, nalph, nmu, ntau, tnx
1
Warning: Unused variable 'tnx' declared at (1) [-Wunused-variable]
pymc/flib.f:442:71:
subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
1
Warning: Unused dummy argument 'gradxlike' at (1) [-Wunused-dummy-argument]
pymc/flib.f:461:40:
DOUBLE PRECISION like, low, high
1
Warning: Unused variable 'high' declared at (1) [-Wunused-variable]
pymc/flib.f:458:36:
INTEGER n, nlower, nupper, i
1
Warning: Unused variable 'i' declared at (1) [-Wunused-variable]
pymc/flib.f:461:29:
DOUBLE PRECISION like, low, high
1
Warning: Unused variable 'like' declared at (1) [-Wunused-variable]
pymc/flib.f:461:34:
DOUBLE PRECISION like, low, high
1
Warning: Unused variable 'low' declared at (1) [-Wunused-variable]
pymc/flib.f:442:39:
subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
1
Warning: Unused dummy argument 'lower' at (1) [-Wunused-dummy-argument]
pymc/flib.f:442:45:
subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
1
Warning: Unused dummy argument 'upper' at (1) [-Wunused-dummy-argument]
pymc/flib.f:442:33:
subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
1
Warning: Unused dummy argument 'x' at (1) [-Wunused-dummy-argument]
pymc/flib.f:692:41:
DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1) [-Wunused-variable]
pymc/flib.f:760:41:
DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1) [-Wunused-variable]
pymc/flib.f:834:41:
DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1) [-Wunused-variable]
pymc/flib.f:906:41:
DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1) [-Wunused-variable]
pymc/flib.f:976:41:
DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1) [-Wunused-variable]
pymc/flib.f:1186:29:
DOUBLE PRECISION factln
1
Warning: Unused variable 'factln' declared at (1) [-Wunused-variable]
pymc/flib.f:1185:51:
DOUBLE PRECISION sumx, mut, infinity, sumfact
1
Warning: Unused variable 'sumfact' declared at (1) [-Wunused-variable]
pymc/flib.f:1185:27:
DOUBLE PRECISION sumx, mut, infinity, sumfact
1
Warning: Unused variable 'sumx' declared at (1) [-Wunused-variable]
pymc/flib.f:1300:55:
DOUBLE PRECISION mu(nmu), gradlike(nmu),grad, cdf
1
Warning: Unused variable 'cdf' declared at (1) [-Wunused-variable]
pymc/flib.f:1302:29:
DOUBLE PRECISION factln, gammq
1
Warning: Unused variable 'factln' declared at (1) [-Wunused-variable]
pymc/flib.f:1302:36:
DOUBLE PRECISION factln, gammq
1
Warning: Unused variable 'gammq' declared at (1) [-Wunused-variable]
pymc/flib.f:1301:59:
DOUBLE PRECISION sumx, mut, infinity, sumfact, sumcdf
1
Warning: Unused variable 'sumcdf' declared at (1) [-Wunused-variable]
pymc/flib.f:1301:51:
DOUBLE PRECISION sumx, mut, infinity, sumfact, sumcdf
1
Warning: Unused variable 'sumfact' declared at (1) [-Wunused-variable]
pymc/flib.f:1301:27:
DOUBLE PRECISION sumx, mut, infinity, sumfact, sumcdf
1
Warning: Unused variable 'sumx' declared at (1) [-Wunused-variable]
pymc/flib.f:1402:29:
DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]
pymc/flib.f:2154:40:
DOUBLE PRECISION gradlike(n), grad
1
Warning: Unused variable 'grad' declared at (1) [-Wunused-variable]
pymc/flib.f:2665:29:
DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]
pymc/flib.f:2728:29:
DOUBLE PRECISION gammln, psi
1
Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]
pymc/flib.f:2793:29:
DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]
pymc/flib.f:2903:29:
DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]
pymc/flib.f:2959:29:
DOUBLE PRECISION gammln, psi
1
Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]
pymc/flib.f:3021:29:
DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]
pymc/flib.f:3396:58:
DOUBLE PRECISION gradlike(nx), atmp, btmp, PI, glike
1
Warning: Unused variable 'glike' declared at (1) [-Wunused-variable]
pymc/flib.f:3646:37:
DOUBLE PRECISION gammln, factln
1
Warning: Unused variable 'factln' declared at (1) [-Wunused-variable]
pymc/flib.f:3646:29:
DOUBLE PRECISION gammln, factln
1
Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]
pymc/flib.f:3706:37:
DOUBLE PRECISION gammln, factln, psi
1
Warning: Unused variable 'factln' declared at (1) [-Wunused-variable]
pymc/flib.f:3706:29:
DOUBLE PRECISION gammln, factln, psi
1
Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]
pymc/flib.f:3836:29:
DOUBLE PRECISION factln
1
Warning: Unused variable 'factln' declared at (1) [-Wunused-variable]
pymc/flib.f:4039:26:
DOUBLE PRECISION psi
1
Warning: Unused variable 'psi' declared at (1) [-Wunused-variable]
pymc/flib.f:4266:29:
DOUBLE PRECISION gammln, psi
1
Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]
pymc/flib.f:4332:29:
DOUBLE PRECISION gammln, psi
1
Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]
pymc/flib.f:5184:35:
DOUBLE PRECISION like, factln, infinity, sump
1
Warning: Unused variable 'factln' declared at (1) [-Wunused-variable]
pymc/flib.f:5186:23:
INTEGER i,j,n_tmp
1
Warning: Unused variable 'n_tmp' declared at (1) [-Wunused-variable]
pymc/flib.f:5434:26:
DOUBLE PRECISION tmp
1
Warning: Unused variable 'tmp' declared at (1) [-Wunused-variable]
pymc/flib.f:5488:25:
DOUBLE PRECISION i0
1
Warning: Unused variable 'i0' declared at (1) [-Wunused-variable]
pymc/flib.f:5481:26:
DOUBLE PRECISION tmp
1
Warning: Unused variable 'tmp' declared at (1) [-Wunused-variable]
pymc/flib.f:5535:25:
DOUBLE PRECISION i0
1
Warning: Unused variable 'i0' declared at (1) [-Wunused-variable]
pymc/flib.f:5528:26:
DOUBLE PRECISION tmp
1
Warning: Unused variable 'tmp' declared at (1) [-Wunused-variable]
pymc/flib.f:4882:0:
K = I
Warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
pymc/flib.f:4882:0: Warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran:f77: pymc/histogram.f
gfortran:f77: pymc/flib_blas.f
pymc/flib_blas.f:202:25:
DOUBLE PRECISION PI
1
Warning: Unused variable 'pi' declared at (1) [-Wunused-variable]
gfortran:f77: pymc/blas_wrap.f
gfortran:f77: pymc/math.f
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. [-Wintrinsic-shadow]
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. [-Wintrinsic-shadow]
gfortran:f77: pymc/gibbsit.f
pymc/gibbsit.f:2160:5:
215 IF (R .GT. .5898437) GO TO 220
1
Warning: Label 215 at (1) defined but not used [-Wunused-label]
pymc/gibbsit.f:2077:5:
115 IF (R .GT. .5898437) GO TO 120
1
Warning: Label 115 at (1) defined but not used [-Wunused-label]
pymc/gibbsit.f:2064:5:
15 IF (KFLAG.GE.1) GO TO 30
1
Warning: Label 15 at (1) defined but not used [-Wunused-label]
pymc/gibbsit.f:1204:16:
cutpt = empquant(original,iteracnt,qhat,work)
1
Warning: Type mismatch in argument 'work' at (1); passed INTEGER(4) to REAL(8) [-Wargument-mismatch]
gfortran:f77: build/src.macosx-10.13-x86_64-3.6/pymc/flib-f2pywrappers.f
/usr/local/bin/gfortran -Wall -g -Wall -g -undefined dynamic_lookup -bundle build/temp.macosx-10.13-x86_64-3.6/cephes/i0.o build/temp.macosx-10.13-x86_64-3.6/cephes/c2f.o build/temp.macosx-10.13-x86_64-3.6/cephes/chbevl.o build/temp.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/flibmodule.o build/temp.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/fortranobject.o build/temp.macosx-10.13-x86_64-3.6/pymc/flib.o build/temp.macosx-10.13-x86_64-3.6/pymc/histogram.o build/temp.macosx-10.13-x86_64-3.6/pymc/flib_blas.o build/temp.macosx-10.13-x86_64-3.6/pymc/blas_wrap.o build/temp.macosx-10.13-x86_64-3.6/pymc/math.o build/temp.macosx-10.13-x86_64-3.6/pymc/gibbsit.o build/temp.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/flib-f2pywrappers.o -L/usr/local/Cellar/gcc/7.1.0/lib/gcc/7/gcc/x86_64-apple-darwin16.7.0/7.1.0 -L/usr/local/Cellar/gcc/7.1.0/lib/gcc/7/gcc/x86_64-apple-darwin16.7.0/7.1.0/../../.. -L/usr/local/Cellar/gcc/7.1.0/lib/gcc/7/gcc/x86_64-apple-darwin16.7.0/7.1.0/../../.. -lgfortran -o build/lib.macosx-10.13-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
ld: framework not found Accelerate
collect2: error: ld returned 1 exit status
error: Command "/usr/local/bin/gfortran -Wall -g -Wall -g -undefined dynamic_lookup -bundle build/temp.macosx-10.13-x86_64-3.6/cephes/i0.o build/temp.macosx-10.13-x86_64-3.6/cephes/c2f.o build/temp.macosx-10.13-x86_64-3.6/cephes/chbevl.o build/temp.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/flibmodule.o build/temp.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/fortranobject.o build/temp.macosx-10.13-x86_64-3.6/pymc/flib.o build/temp.macosx-10.13-x86_64-3.6/pymc/histogram.o build/temp.macosx-10.13-x86_64-3.6/pymc/flib_blas.o build/temp.macosx-10.13-x86_64-3.6/pymc/blas_wrap.o build/temp.macosx-10.13-x86_64-3.6/pymc/math.o build/temp.macosx-10.13-x86_64-3.6/pymc/gibbsit.o build/temp.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/flib-f2pywrappers.o -L/usr/local/Cellar/gcc/7.1.0/lib/gcc/7/gcc/x86_64-apple-darwin16.7.0/7.1.0 -L/usr/local/Cellar/gcc/7.1.0/lib/gcc/7/gcc/x86_64-apple-darwin16.7.0/7.1.0/../../.. -L/usr/local/Cellar/gcc/7.1.0/lib/gcc/7/gcc/x86_64-apple-darwin16.7.0/7.1.0/../../.. -lgfortran -o build/lib.macosx-10.13-x86_64-3.6/pymc/flib.cpython-36m-darwin.so -Wl,-framework -Wl,Accelerate" failed with exit status 1
----------------------------------------
Running setup.py clean for pymc
Successfully built networkx
Failed to build pymc
Installing collected packages: pytz, six, python-dateutil, pandas, patsy, statsmodels, decorator, networkx, pymc, scipy, causality
Running setup.py install for pymc: started
Running setup.py install for pymc: finished with status 'error'
Complete output from command /Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/private/var/folders/6y/kf699bqj2sgcgjshb20fr5zh0000gn/T/pip-install-ooarg4tj/pymc/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/6y/kf699bqj2sgcgjshb20fr5zh0000gn/T/pip-record-gqvxbuoq/install-record.txt --single-version-externally-managed --compile --install-headers /Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/bin/../include/site/python3.6/pymc:
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-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/fortranobject.c' to sources.
adding 'build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc' to include_dirs.
adding 'build/src.macosx-10.13-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-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/gp/fortranobject.c' to sources.
adding 'build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/gp' to include_dirs.
building extension "pymc.gp.incomplete_chol" sources
f2py options: []
adding 'build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/gp/fortranobject.c' to sources.
adding 'build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-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-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/gp/cov_funs/fortranobject.c' to sources.
adding 'build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/gp/cov_funs' to include_dirs.
adding 'build/src.macosx-10.13-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-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/gp/cov_funs/fortranobject.c' to sources.
adding 'build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-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-10.13-x86_64-3.6
creating build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/StepMethods.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/InstantiationDecorators.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/CircularStochastic.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/diagnostics.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/threadpool.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/graph.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/Matplot.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/__init__.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/Container.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/Model.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/distributions.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/MCMC.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/datatypes.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/NormalApproximation.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/progressbar.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/utils.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/PyMCObjects.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/six.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/Node.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/CommonDeterministics.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/calc_utils.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/NumpyDeterministics.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/ScipyDistributions.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
copying pymc/decorators.py -> build/lib.macosx-10.13-x86_64-3.6/pymc
creating build/lib.macosx-10.13-x86_64-3.6/pymc/database
copying pymc/database/no_trace.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/database
copying pymc/database/txt.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/database
copying pymc/database/__init__.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/database
copying pymc/database/hdf5.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/database
copying pymc/database/sqlite.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/database
copying pymc/database/pickle.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/database
copying pymc/database/hdf5ea.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/database
copying pymc/database/ram.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/database
copying pymc/database/base.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/database
creating build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/melanoma.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/disaster_model_linear.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/disaster_model.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/disaster_model_gof.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/gelman_bioassay.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/weibull_fit_gof.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/__init__.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/melanoma_data.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/disaster_model_null.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/zip.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/custom_step.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/disaster_model_missing.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
copying pymc/examples/weibull_fit.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples
creating build/lib.macosx-10.13-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/covparams.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/observation.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/PyMCmodel.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/basiscov.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/realizations.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/mesh_choice.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/__init__.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/cov.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/mean.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples/gp
copying pymc/examples/gp/MCMC.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/examples/gp
creating build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_utils.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_MCMCSampler.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_database.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_cov.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_container.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_missing.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_observation.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_realization.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_convergence.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/__init__.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_AM.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_basiscov.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_GP_MCMC.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_norm_approx.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_mean.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_distributions.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_slice.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_binary_step.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_adaptive.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_special_methods.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_instantiation.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/objectmodel.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_graph.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_gradients.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
copying pymc/tests/test_interactive.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/tests
creating build/lib.macosx-10.13-x86_64-3.6/pymc/gp
copying pymc/gp/step_methods.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp
copying pymc/gp/Realization.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp
copying pymc/gp/gp_submodel.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp
copying pymc/gp/gpplots.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp
copying pymc/gp/GPutils.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp
copying pymc/gp/Covariance.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp
copying pymc/gp/__init__.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp
copying pymc/gp/Mean.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp
copying pymc/gp/FullRankCovariance.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp
copying pymc/gp/NearlyFullRankCovariance.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp
copying pymc/gp/BasisCovariance.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp
creating build/lib.macosx-10.13-x86_64-3.6/pymc/gp/cov_funs
copying pymc/gp/cov_funs/__init__.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp/cov_funs
copying pymc/gp/cov_funs/wrapped_distances.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp/cov_funs
copying pymc/gp/cov_funs/brownian.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp/cov_funs
copying pymc/gp/cov_funs/nsmatern.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp/cov_funs
copying pymc/gp/cov_funs/cov_utils.py -> build/lib.macosx-10.13-x86_64-3.6/pymc/gp/cov_funs
copying pymc/gp/cov_funs/bases.py -> build/lib.macosx-10.13-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: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers
creating build/temp.macosx-10.13-x86_64-3.6/cephes
creating build/temp.macosx-10.13-x86_64-3.6/build
creating build/temp.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6
creating build/temp.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc
creating build/temp.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/build
creating build/temp.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6
creating build/temp.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc
compile options: '-DNO_ATLAS_INFO=3 -DHAVE_CBLAS -Ibuild/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc -I/Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/lib/python3.6/site-packages/numpy/core/include -I/usr/local/Cellar/python/3.6.5/Frameworks/Python.framework/Versions/3.6/include/python3.6m -c'
extra options: '-msse3'
clang: cephes/i0.c
cephes/i0.c:372:30: warning: incompatible pointer types passing 'unsigned short [120]' to parameter of type 'double *' [-Wincompatible-pointer-types]
return( exp(x) * chbevl( y, A, 30 ) );
^
cephes/i0.c:355:40: note: passing argument to parameter here
extern double chbevl ( double, double *, int );
^
cephes/i0.c:375:41: warning: incompatible pointer types passing 'unsigned short [100]' to parameter of type 'double *' [-Wincompatible-pointer-types]
return( exp(x) * chbevl( 32.0/x - 2.0, B, 25 ) / sqrt(x) );
^
cephes/i0.c:355:40: note: passing argument to parameter here
extern double chbevl ( double, double *, int );
^
cephes/i0.c:392:21: warning: incompatible pointer types passing 'unsigned short [120]' to parameter of type 'double *' [-Wincompatible-pointer-types]
return( chbevl( y, A, 30 ) );
^
cephes/i0.c:355:40: note: passing argument to parameter here
extern double chbevl ( double, double *, int );
^
cephes/i0.c:395:32: warning: incompatible pointer types passing 'unsigned short [100]' to parameter of type 'double *' [-Wincompatible-pointer-types]
return( chbevl( 32.0/x - 2.0, B, 25 ) / sqrt(x) );
^
cephes/i0.c:355:40: note: passing argument to parameter here
extern double chbevl ( double, double *, int );
^
4 warnings generated.
clang: cephes/c2f.c
cephes/c2f.c:8:11: warning: this old-style function definition is not preceded by a prototype [-Wstrict-prototypes]
double i0_(x)
^
1 warning generated.
clang: cephes/chbevl.c
clang: build/src.macosx-10.13-x86_64-3.6/pymc/flibmodule.c
In file included from build/src.macosx-10.13-x86_64-3.6/pymc/flibmodule.c:16:
In file included from build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/fortranobject.h:13:
In file included from /Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:
/Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
^
build/src.macosx-10.13-x86_64-3.6/pymc/flibmodule.c:16773:7: warning: array index 2 is past the end of the array (which contains 2 elements) [-Warray-bounds]
d = shape(x,2);
^ ~
build/src.macosx-10.13-x86_64-3.6/pymc/flibmodule.c:84:24: note: expanded from macro 'shape'
#define shape(var,dim) var ## _Dims[dim]
^ ~~~
<scratch space>:231:1: note: expanded from here
x_Dims
^
build/src.macosx-10.13-x86_64-3.6/pymc/flibmodule.c:16716:3: note: array 'x_Dims' declared here
npy_intp x_Dims[2] = {-1, -1};
^
build/src.macosx-10.13-x86_64-3.6/pymc/flibmodule.c:179:12: warning: unused function 'f2py_size' [-Wunused-function]
static int f2py_size(PyArrayObject* var, ...)
^
3 warnings generated.
clang: build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/fortranobject.c
In file included from build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/fortranobject.c:2:
In file included from build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/fortranobject.h:13:
In file included from /Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:
/Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
^
build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/fortranobject.c:138:18: warning: comparison of integers of different signs: 'Py_ssize_t' (aka 'long') and 'unsigned long' [-Wsign-compare]
if (size < sizeof(notalloc)) {
~~~~ ^ ~~~~~~~~~~~~~~~~
2 warnings generated.
compiling Fortran sources
Fortran f77 compiler: /usr/local/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/local/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/local/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
creating build/temp.macosx-10.13-x86_64-3.6/pymc
compile options: '-DNO_ATLAS_INFO=3 -DHAVE_CBLAS -Ibuild/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc -I/Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/lib/python3.6/site-packages/numpy/core/include -I/usr/local/Cellar/python/3.6.5/Frameworks/Python.framework/Versions/3.6/include/python3.6m -c'
gfortran:f77: pymc/flib.f
f951: Warning: Nonconforming tab character in column 1 of line 509 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 510 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 511 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 512 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 513 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 557 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 558 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 559 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 560 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 561 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 707 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 711 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 715 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 723 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 775 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 779 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 783 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 791 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 849 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 853 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 857 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 865 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 921 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 925 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 929 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 937 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 991 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 995 [-Wtabs]
f951: Warning: Nonconforming tab character in column 6 of line 999 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1007 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1195 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1196 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1197 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1200 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1201 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1408 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1409 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1412 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1420 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1421 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1422 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1423 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1424 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1425 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1452 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1454 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1457 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1465 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1466 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1467 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1469 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1470 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1471 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1472 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1473 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1478 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1499 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1501 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1504 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1512 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1513 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1514 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1515 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1516 [-Wtabs]
f951: Warning: Nonconforming tab character in column 5 of line 1517 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1740 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1743 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1746 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1755 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1783 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1786 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1789 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1798 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1800 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1832 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1835 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1838 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1847 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1849 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1977 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 1978 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2030 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2031 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2079 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2080 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2168 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2174 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2218 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2224 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2339 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2395 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2692 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2693 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2694 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2696 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2697 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2756 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2820 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 2881 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3191 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3192 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3656 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3657 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3658 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3660 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3661 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3662 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3664 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3665 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3666 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3716 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3717 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3718 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3720 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3721 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3722 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3724 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3725 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3726 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3732 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3846 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3847 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3849 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3851 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3875 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3876 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3877 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 3878 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4276 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4277 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4278 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4280 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4281 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4282 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4284 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4285 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4286 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4288 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4289 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4290 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4342 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4343 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4344 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4346 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4347 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4348 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4350 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4351 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4352 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4354 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4355 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4356 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4620 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4622 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4623 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4624 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4626 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4628 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4630 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4632 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4633 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4634 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4635 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4637 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4638 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4639 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4640 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4642 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4643 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4644 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4645 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 4646 [-Wtabs]
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) [-Wunused-variable]
pymc/flib.f:314:42:
INTEGER i, nx, nalph, nmu, ntau, tnx
1
Warning: Unused variable 'tnx' declared at (1) [-Wunused-variable]
pymc/flib.f:442:71:
subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
1
Warning: Unused dummy argument 'gradxlike' at (1) [-Wunused-dummy-argument]
pymc/flib.f:461:40:
DOUBLE PRECISION like, low, high
1
Warning: Unused variable 'high' declared at (1) [-Wunused-variable]
pymc/flib.f:458:36:
INTEGER n, nlower, nupper, i
1
Warning: Unused variable 'i' declared at (1) [-Wunused-variable]
pymc/flib.f:461:29:
DOUBLE PRECISION like, low, high
1
Warning: Unused variable 'like' declared at (1) [-Wunused-variable]
pymc/flib.f:461:34:
DOUBLE PRECISION like, low, high
1
Warning: Unused variable 'low' declared at (1) [-Wunused-variable]
pymc/flib.f:442:39:
subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
1
Warning: Unused dummy argument 'lower' at (1) [-Wunused-dummy-argument]
pymc/flib.f:442:45:
subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
1
Warning: Unused dummy argument 'upper' at (1) [-Wunused-dummy-argument]
pymc/flib.f:442:33:
subroutine uniform_grad_x(x,lower,upper,n,nlower,nupper,gradxlike)
1
Warning: Unused dummy argument 'x' at (1) [-Wunused-dummy-argument]
pymc/flib.f:692:41:
DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1) [-Wunused-variable]
pymc/flib.f:760:41:
DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1) [-Wunused-variable]
pymc/flib.f:834:41:
DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1) [-Wunused-variable]
pymc/flib.f:906:41:
DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1) [-Wunused-variable]
pymc/flib.f:976:41:
DOUBLE PRECISION aa, cc, sigma, pdf
1
Warning: Unused variable 'pdf' declared at (1) [-Wunused-variable]
pymc/flib.f:1186:29:
DOUBLE PRECISION factln
1
Warning: Unused variable 'factln' declared at (1) [-Wunused-variable]
pymc/flib.f:1185:51:
DOUBLE PRECISION sumx, mut, infinity, sumfact
1
Warning: Unused variable 'sumfact' declared at (1) [-Wunused-variable]
pymc/flib.f:1185:27:
DOUBLE PRECISION sumx, mut, infinity, sumfact
1
Warning: Unused variable 'sumx' declared at (1) [-Wunused-variable]
pymc/flib.f:1300:55:
DOUBLE PRECISION mu(nmu), gradlike(nmu),grad, cdf
1
Warning: Unused variable 'cdf' declared at (1) [-Wunused-variable]
pymc/flib.f:1302:29:
DOUBLE PRECISION factln, gammq
1
Warning: Unused variable 'factln' declared at (1) [-Wunused-variable]
pymc/flib.f:1302:36:
DOUBLE PRECISION factln, gammq
1
Warning: Unused variable 'gammq' declared at (1) [-Wunused-variable]
pymc/flib.f:1301:59:
DOUBLE PRECISION sumx, mut, infinity, sumfact, sumcdf
1
Warning: Unused variable 'sumcdf' declared at (1) [-Wunused-variable]
pymc/flib.f:1301:51:
DOUBLE PRECISION sumx, mut, infinity, sumfact, sumcdf
1
Warning: Unused variable 'sumfact' declared at (1) [-Wunused-variable]
pymc/flib.f:1301:27:
DOUBLE PRECISION sumx, mut, infinity, sumfact, sumcdf
1
Warning: Unused variable 'sumx' declared at (1) [-Wunused-variable]
pymc/flib.f:1402:29:
DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]
pymc/flib.f:2154:40:
DOUBLE PRECISION gradlike(n), grad
1
Warning: Unused variable 'grad' declared at (1) [-Wunused-variable]
pymc/flib.f:2665:29:
DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]
pymc/flib.f:2728:29:
DOUBLE PRECISION gammln, psi
1
Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]
pymc/flib.f:2793:29:
DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]
pymc/flib.f:2903:29:
DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]
pymc/flib.f:2959:29:
DOUBLE PRECISION gammln, psi
1
Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]
pymc/flib.f:3021:29:
DOUBLE PRECISION gammln
1
Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]
pymc/flib.f:3396:58:
DOUBLE PRECISION gradlike(nx), atmp, btmp, PI, glike
1
Warning: Unused variable 'glike' declared at (1) [-Wunused-variable]
pymc/flib.f:3646:37:
DOUBLE PRECISION gammln, factln
1
Warning: Unused variable 'factln' declared at (1) [-Wunused-variable]
pymc/flib.f:3646:29:
DOUBLE PRECISION gammln, factln
1
Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]
pymc/flib.f:3706:37:
DOUBLE PRECISION gammln, factln, psi
1
Warning: Unused variable 'factln' declared at (1) [-Wunused-variable]
pymc/flib.f:3706:29:
DOUBLE PRECISION gammln, factln, psi
1
Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]
pymc/flib.f:3836:29:
DOUBLE PRECISION factln
1
Warning: Unused variable 'factln' declared at (1) [-Wunused-variable]
pymc/flib.f:4039:26:
DOUBLE PRECISION psi
1
Warning: Unused variable 'psi' declared at (1) [-Wunused-variable]
pymc/flib.f:4266:29:
DOUBLE PRECISION gammln, psi
1
Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]
pymc/flib.f:4332:29:
DOUBLE PRECISION gammln, psi
1
Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]
pymc/flib.f:5184:35:
DOUBLE PRECISION like, factln, infinity, sump
1
Warning: Unused variable 'factln' declared at (1) [-Wunused-variable]
pymc/flib.f:5186:23:
INTEGER i,j,n_tmp
1
Warning: Unused variable 'n_tmp' declared at (1) [-Wunused-variable]
pymc/flib.f:5434:26:
DOUBLE PRECISION tmp
1
Warning: Unused variable 'tmp' declared at (1) [-Wunused-variable]
pymc/flib.f:5488:25:
DOUBLE PRECISION i0
1
Warning: Unused variable 'i0' declared at (1) [-Wunused-variable]
pymc/flib.f:5481:26:
DOUBLE PRECISION tmp
1
Warning: Unused variable 'tmp' declared at (1) [-Wunused-variable]
pymc/flib.f:5535:25:
DOUBLE PRECISION i0
1
Warning: Unused variable 'i0' declared at (1) [-Wunused-variable]
pymc/flib.f:5528:26:
DOUBLE PRECISION tmp
1
Warning: Unused variable 'tmp' declared at (1) [-Wunused-variable]
pymc/flib.f:4882:0:
K = I
Warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
pymc/flib.f:4882:0: Warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran:f77: pymc/histogram.f
gfortran:f77: pymc/flib_blas.f
pymc/flib_blas.f:202:25:
DOUBLE PRECISION PI
1
Warning: Unused variable 'pi' declared at (1) [-Wunused-variable]
gfortran:f77: pymc/blas_wrap.f
gfortran:f77: pymc/math.f
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. [-Wintrinsic-shadow]
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. [-Wintrinsic-shadow]
gfortran:f77: pymc/gibbsit.f
pymc/gibbsit.f:2160:5:
215 IF (R .GT. .5898437) GO TO 220
1
Warning: Label 215 at (1) defined but not used [-Wunused-label]
pymc/gibbsit.f:2077:5:
115 IF (R .GT. .5898437) GO TO 120
1
Warning: Label 115 at (1) defined but not used [-Wunused-label]
pymc/gibbsit.f:2064:5:
15 IF (KFLAG.GE.1) GO TO 30
1
Warning: Label 15 at (1) defined but not used [-Wunused-label]
pymc/gibbsit.f:1204:16:
cutpt = empquant(original,iteracnt,qhat,work)
1
Warning: Type mismatch in argument 'work' at (1); passed INTEGER(4) to REAL(8) [-Wargument-mismatch]
gfortran:f77: build/src.macosx-10.13-x86_64-3.6/pymc/flib-f2pywrappers.f
/usr/local/bin/gfortran -Wall -g -Wall -g -undefined dynamic_lookup -bundle build/temp.macosx-10.13-x86_64-3.6/cephes/i0.o build/temp.macosx-10.13-x86_64-3.6/cephes/c2f.o build/temp.macosx-10.13-x86_64-3.6/cephes/chbevl.o build/temp.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/flibmodule.o build/temp.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/fortranobject.o build/temp.macosx-10.13-x86_64-3.6/pymc/flib.o build/temp.macosx-10.13-x86_64-3.6/pymc/histogram.o build/temp.macosx-10.13-x86_64-3.6/pymc/flib_blas.o build/temp.macosx-10.13-x86_64-3.6/pymc/blas_wrap.o build/temp.macosx-10.13-x86_64-3.6/pymc/math.o build/temp.macosx-10.13-x86_64-3.6/pymc/gibbsit.o build/temp.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/flib-f2pywrappers.o -L/usr/local/Cellar/gcc/7.1.0/lib/gcc/7/gcc/x86_64-apple-darwin16.7.0/7.1.0 -L/usr/local/Cellar/gcc/7.1.0/lib/gcc/7/gcc/x86_64-apple-darwin16.7.0/7.1.0/../../.. -L/usr/local/Cellar/gcc/7.1.0/lib/gcc/7/gcc/x86_64-apple-darwin16.7.0/7.1.0/../../.. -lgfortran -o build/lib.macosx-10.13-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
ld: framework not found Accelerate
collect2: error: ld returned 1 exit status
error: Command "/usr/local/bin/gfortran -Wall -g -Wall -g -undefined dynamic_lookup -bundle build/temp.macosx-10.13-x86_64-3.6/cephes/i0.o build/temp.macosx-10.13-x86_64-3.6/cephes/c2f.o build/temp.macosx-10.13-x86_64-3.6/cephes/chbevl.o build/temp.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/flibmodule.o build/temp.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/fortranobject.o build/temp.macosx-10.13-x86_64-3.6/pymc/flib.o build/temp.macosx-10.13-x86_64-3.6/pymc/histogram.o build/temp.macosx-10.13-x86_64-3.6/pymc/flib_blas.o build/temp.macosx-10.13-x86_64-3.6/pymc/blas_wrap.o build/temp.macosx-10.13-x86_64-3.6/pymc/math.o build/temp.macosx-10.13-x86_64-3.6/pymc/gibbsit.o build/temp.macosx-10.13-x86_64-3.6/build/src.macosx-10.13-x86_64-3.6/pymc/flib-f2pywrappers.o -L/usr/local/Cellar/gcc/7.1.0/lib/gcc/7/gcc/x86_64-apple-darwin16.7.0/7.1.0 -L/usr/local/Cellar/gcc/7.1.0/lib/gcc/7/gcc/x86_64-apple-darwin16.7.0/7.1.0/../../.. -L/usr/local/Cellar/gcc/7.1.0/lib/gcc/7/gcc/x86_64-apple-darwin16.7.0/7.1.0/../../.. -lgfortran -o build/lib.macosx-10.13-x86_64-3.6/pymc/flib.cpython-36m-darwin.so -Wl,-framework -Wl,Accelerate" failed with exit status 1
----------------------------------------
Error: An error occurred while installing causality!
Cache entry deserialization failed, entry ignored
Cache entry deserialization failed, entry ignored
Failed building wheel for pymc
Command "/Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/private/var/folders/6y/kf699bqj2sgcgjshb20fr5zh0000gn/T/pip-install-ooarg4tj/pymc/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/6y/kf699bqj2sgcgjshb20fr5zh0000gn/T/pip-record-gqvxbuoq/install-record.txt --single-version-externally-managed --compile --install-headers /Users/harrymoreno/.local/share/virtualenvs/causality-yR51rIwE/bin/../include/site/python3.6/pymc" failed with error code 1 in /private/var/folders/6y/kf699bqj2sgcgjshb20fr5zh0000gn/T/pip-install-ooarg4tj/pymc/'Graph' object has no attribute 'node'
In NetworkX 2.4, G.node has been depreciated.
Issues, issues, who's got the issues.
RIP Gene Wilder.
networkx version problem?
I am trying to run the example given at the causality main github page but I run into the following problem:
Traceback (most recent call last):
File "", line 25, in
graph = ic_algorithm.search(X, variable_types)
File "...../causality/inference/search/init.py", line 26, in search
self._find_skeleton(data, variable_types)
File "......./causality/inference/search/init.py", line 126, in _find_skeleton
z_candidates = list(set(x_neighbors + y_neighbors) - set([x,y]))
TypeError: unsupported operand type(s) for +: 'dict_keyiterator' and 'dict_keyiterator'
The x_neighbor and y_neighbors are variables returned by the networkx.Graph.neighbors function which returns an iterator over all neighbors of node n. At least for version 2.0 as is specified by the requirements.txt. For earlier versions (e.g. 1.10) this function returns a list of nodes that are adjacent to n. Can it be that the causality package only runs with version 1.10 of networkx and not the 2.0 verson?
thanks for the help,
Jeroen
I wonder if this package can achieve the functions shown in the picture? thanks!
license
What license is this released under please?
Change `node` to `nodes` in `inference/search/__init__.py`
This should fix #82 for the IC algorithm.
Interpretation of edges in causal graph inference
I have some results like edge ('x2', 'x4', {'arrows': ['x2', 'x2', 'x4' ], 'marked': False}) when I test with the causal graph inference. How do I interpret the issue? Does this mean its a undirected edge like ('x2', 'x4', {'arrows': [], 'marked': False}).
Transition to PyMC3
Hi,
Are there any plans to transition to pymc3?
I'v noticed that pymc is somewhat old and doesn't have a lot of development going for it, yet pymc3 provides new features and serious performance boost. How difficult would it be to transition from pymc to pymc3?
Saul
trouble pip installing, Python 3.4.3
$ sudo pip install causality
The directory '/Users/me/Library/Caches/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
The directory '/Users/me/Library/Caches/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
Collecting causality
Downloading causality-0.0.1.tar.gz
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/private/tmp/pip-build-zarx22qb/causality/setup.py", line 6, in <module>
with open(path.join(here, 'README.md'), encoding='utf-8') as f:
File "/Users/me/.virtualenvs/shopkeep/lib/python3.4/codecs.py", line 891, in open
file = builtins.open(filename, mode, buffering)
FileNotFoundError: [Errno 2] No such file or directory: '/private/tmp/pip-build-zarx22qb/causality/README.md'
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /private/tmp/pip-build-zarx22qb/causality
Should this line be "del matched_treated['treated_index']"?
https://github.com/akelleh/causality/blob/aa458538224ec162b751c1e225b1ff02cb474191/causality/estimation/parametric.py#L201C34-L201C34
In the get_treated_matches function of the PropensityScoringModel class, after join, did you mean to delete the treated_index instead of control_index? Because I think what we need in the matched_treated is the control_index which has been deleted in this version.
categorical attributes
In the given example, all the attributes are continuous numbers.
What should I do if I have categorical attributes that are expressed as string?
check statsmodels pandas.core.datetools dependency
pandas.core.datetools is deprecated, being replaced by pandas.tseries. Statsmodels has a datetools dependency in the RobustRegressionTest. Check into the dependency, and whether statsmodels will upgrade.
is there any reason you don't add (non-propensity) matching?
Just wondering - do you think this is a wrong package to add feature distance matching / standardized mean diff/propensity scores? I will be happy to PR.
I know there is another package (just one?!), causal_inference, but can't say I like their dict-based approach
Non-fully parallel jobs for causal estimation with large data sets.
Yo. I realized that for large data sets your code sets the n_jobs field to 4 instead of -1. I'm guessing this is a typo since it should ideally run with as many cores as possible (i'm running 96 cores simultaneously).
It's in the 'nonparametric.py' script herehttps://github.com/akelleh/causality/blob/79cb779069b67f0d336745fc0d1aad343a3385fa/causality/estimation/nonparametric.py, line 34.
'self.defaults=EstimatorSettings(n_jobs=4, efficient=True)' should be 'self.defaults=EstimatorSettings(n_jobs=-1, efficient=True)'
readme out of date
These lines in the readme are out of date
ic_algorithm = IC(RobustRegressionTest, X, variable_types)
graph = ic_algorithm.search()
it should be
ic_algorithm = IC(RobustRegressionTest)
graph = ic_algorithm.search(X, variable_types)
Parallelize skeleton
issues with concat of dictionaries
Tried your examples (this and your blog) in python 3.6. [treatment] + confounders gives issues. replacing confounders with list(confounders.keys()) seems to fix most of it (needs to be done in a couple of places). Separating z_types from z is also an avenue to fix it. Hope this projects continues to improve.
list of improvements to be made
I see that there is a list of notes for improvements at the bottom of the readme, is there any file in the repo that shows what is left to do? I can take a look at some of the remaining methods to be implemented.
ValueError: zero-size array to reduction operation maximum which has no identity
Hi there. First of all, great library to compliment Judea Pearl's book. I am causality on a df that has about 120 rows by 500 columns, and I am getting the following error:
51 # run the search
52 ic_algorithm = IC(RobustRegressionTest, data_frame, variable_types)
---> 53 graph = ic_algorithm.search()
54 solution = graph.edges(data=True)
55
/Users/luissanchez/anaconda/lib/python2.7/site-packages/causality/inference/search/__init__.pyc in search(self)
23 def search(self):
24 self._build_g()
---> 25 self._find_skeleton()
26 self._orient_colliders()
27
/Users/luissanchez/anaconda/lib/python2.7/site-packages/causality/inference/search/__init__.pyc in _find_skeleton(self)
124 for z in itertools.combinations(z_candidates, N):
125 test = self.independence_test([y], [x], list(z),
--> 126 self.data, self.alpha)
127 if test.independent():
128 self._g.remove_edge(x,y)
/Users/luissanchez/anaconda/lib/python2.7/site-packages/causality/inference/independence_tests/__init__.pyc in __init__(self, y, x, z, data, alpha)
4 class RobustRegressionTest():
5 def __init__(self, y, x, z, data, alpha):
----> 6 self.regression = sm.RLM(data[y], data[x+z])
7 self.result = self.regression.fit()
8 self.coefficient = self.result.params[x][0]
/Users/luissanchez/anaconda/lib/python2.7/site-packages/statsmodels/robust/robust_linear_model.pyc in __init__(self, endog, exog, M, missing, **kwargs)
115 self.M = M
116 super(base.LikelihoodModel, self).__init__(endog, exog,
--> 117 missing=missing, **kwargs)
118 self._initialize()
119 #things to remove_data
/Users/luissanchez/anaconda/lib/python2.7/site-packages/statsmodels/base/model.pyc in __init__(self, endog, exog, **kwargs)
58 hasconst = kwargs.pop('hasconst', None)
59 self.data = self._handle_data(endog, exog, missing, hasconst,
---> 60 **kwargs)
61 self.k_constant = self.data.k_constant
62 self.exog = self.data.exog
/Users/luissanchez/anaconda/lib/python2.7/site-packages/statsmodels/base/model.pyc in _handle_data(self, endog, exog, missing, hasconst, **kwargs)
82
83 def _handle_data(self, endog, exog, missing, hasconst, **kwargs):
---> 84 data = handle_data(endog, exog, missing, hasconst, **kwargs)
85 # kwargs arrays could have changed, easier to just attach here
86 for key in kwargs:
/Users/luissanchez/anaconda/lib/python2.7/site-packages/statsmodels/base/data.pyc in handle_data(endog, exog, missing, hasconst, **kwargs)
564 klass = handle_data_class_factory(endog, exog)
565 return klass(endog, exog=exog, missing=missing, hasconst=hasconst,
--> 566 **kwargs)
/Users/luissanchez/anaconda/lib/python2.7/site-packages/statsmodels/base/data.pyc in __init__(self, endog, exog, missing, hasconst, **kwargs)
73
74 # this has side-effects, attaches k_constant and const_idx
---> 75 self._handle_constant(hasconst)
76 self._check_integrity()
77 self._cache = resettable_cache()
/Users/luissanchez/anaconda/lib/python2.7/site-packages/statsmodels/base/data.pyc in _handle_constant(self, hasconst)
91 # detect where the constant is
92 check_implicit = False
---> 93 const_idx = np.where(self.exog.ptp(axis=0) == 0)[0].squeeze()
94 self.k_constant = const_idx.size
95
ValueError: zero-size array to reduction operation maximum which has no identity
other less dense dfs are running fine. Any idea about what could be wrong?
Thanks
Symmetry in _apply_recursion_rule_2
The function loops over edges (a,b) and checks whether it should add an arrow from a to b, but it does not check whether it should add an arrow from b to a. Note that self._g.edges() has only one entry for each unordered pair.
I tried to submit a pull request, but I apparently I can't push a new branch to the repository.
Fail to import the package
This is the first time I try this package. When trying to import RobustRegressionTest I got the following error.
ImportError Traceback (most recent call last)
<ipython-input-97-30a81870761e> in <module>
1 from causality.inference.search import IC
----> 2 from causality.inference.independence_tests import RobustRegressionTest
~/bin/anaconda3/lib/python3.7/site-packages/causality/inference/independence_tests/__init__.py in <module>
1 import pandas as pd
2 import numpy as np
----> 3 import statsmodels.api as sm
4 import scipy.stats
5 import itertools
~/bin/anaconda3/lib/python3.7/site-packages/statsmodels/api.py in <module>
14 from . import robust
15 from .robust.robust_linear_model import RLM
---> 16 from .discrete.discrete_model import (Poisson, Logit, Probit,
17 MNLogit, NegativeBinomial,
18 GeneralizedPoisson,
~/bin/anaconda3/lib/python3.7/site-packages/statsmodels/discrete/discrete_model.py in <module>
43
44 from statsmodels.base.l1_slsqp import fit_l1_slsqp
---> 45 from statsmodels.distributions import genpoisson_p
46
47 try:
~/bin/anaconda3/lib/python3.7/site-packages/statsmodels/distributions/__init__.py in <module>
1 from .empirical_distribution import ECDF, monotone_fn_inverter, StepFunction
----> 2 from .edgeworth import ExpandedNormal
3 from .discrete import genpoisson_p, zipoisson, zigenpoisson, zinegbin
~/bin/anaconda3/lib/python3.7/site-packages/statsmodels/distributions/edgeworth.py in <module>
5 import numpy as np
6 from numpy.polynomial.hermite_e import HermiteE
----> 7 from scipy.misc import factorial
8 from scipy.stats import rv_continuous
9 import scipy.special as special
ImportError: cannot import name 'factorial' from 'scipy.misc' (~/bin/anaconda3/lib/python3.7/site-packages/scipy/misc/__init__.py)This is the installation output stating the installed packages versions:
Collecting causality
Downloading causality-0.0.9-py3-none-any.whl (24 kB)
Requirement already satisfied: patsy in ~/bin/anaconda3/lib/python3.7/site-packages (from causality) (0.5.1)
Requirement already satisfied: pandas in ~bin/anaconda3/lib/python3.7/site-packages (from causality) (1.1.2)
Requirement already satisfied: networkx in ~/bin/anaconda3/lib/python3.7/site-packages (from causality) (2.1)
Requirement already satisfied: python-dateutil in ~/bin/anaconda3/lib/python3.7/site-packages (from causality) (2.8.1)
Requirement already satisfied: scipy in ~/bin/anaconda3/lib/python3.7/site-packages (from causality) (1.5.2)
Requirement already satisfied: numpy in ~/bin/anaconda3/lib/python3.7/site-packages (from causality) (1.19.2)
Requirement already satisfied: pytz in ~bin/anaconda3/lib/python3.7/site-packages (from causality) (2020.1)
Requirement already satisfied: statsmodels in ~/bin/anaconda3/lib/python3.7/site-packages (from causality) (0.9.0)
Requirement already satisfied: decorator in ~/bin/anaconda3/lib/python3.7/site-packages (from causality) (4.3.0)
Requirement already satisfied: six in ~/bin/anaconda3/lib/python3.7/site-packages (from causality) (1.15.0)
Installing collected packages: causality
Successfully installed causality-0.0.9Python Package: Problems with Codeline “effect.pdf(x)”
I recently installed the causality package. And, I am working through the example on the package's PyPi page: https://pypi.org/project/causality/
Everything seems to work well until I get to the last line with the code: effect.pdf(x)
I get the KeyError "KeyError: 'b'"
The offending block of code:
> from causality.estimation.nonparametric import CausalEffect
> admissable_set = adjustment.admissable_set(g,['x2'], ['x3'])
> effect = CausalEffect(X, ['x2'], ['x3'], variable_types=variable_types,
> admissable_set=list(admissable_set))
> x = pd.DataFrame({'x2' : [0.], 'x3' : [0.]})
> effect.pdf(x)
I think it's just a problem with the syntax of the code. I am new to Python and am not able to figure out what it is. Please help
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.