Installation instructions for OSX

Thomas Wiecki

unread,

Dec 28, 2019, 5:03:36 AM12/28/19

to hddm-...@googlegroups.com

Hi all,

Just got HDDM to compile under most recent OSX and Python 3.5.

First I created a new environment after installing miniconda or anaconda:

conda create --name hddmpy35 python=3.5 anaconda

conda activate hddmpy35

conda install pymc pandas patsy conda-build

pip install kabuki

Then you'll want to download the HDDM source from github. I needed to set the following env variable: export MACOSX_DEPLOYMENT_TARGET=10.11

And change setup.py as follows:

setup.py:

from setuptools import setup
from setuptools import Extension

try:
from Cython.Build import cythonize
ext_modules = cythonize([Extension('wfpt', ['src/wfpt.pyx'], language='c++', extra_compile_args=['-stdlib=libc++'], extra_link_args=['-stdlib=libc++', "-mmacosx-version-min=10.9"]),
Extension('cdfdif_wrapper', ['src/cdfdif_wrapper.pyx', 'src/cdfdif.c'])
])

except ImportError:
ext_modules = [Extension('wfpt', ['src/wfpt.cpp'], language='c++'),
Extension('cdfdif_wrapper', ['src/cdfdif_wrapper.c', 'src/cdfdif.cpp'])
]

import numpy as np

setup(
name='HDDM',
version='0.7.1',
author='Thomas V. Wiecki, Imri Sofer, Michael J. Frank',
author_email='thomas...@gmail.com',
url='http://github.com/hddm-devs/hddm',
packages=['hddm', 'hddm.tests', 'hddm.models', 'hddm.examples'],
package_data={'hddm':['examples/*.csv', 'examples/*.conf']},
scripts=['scripts/hddm_demo.py'],
description='HDDM is a python module that implements Hierarchical Bayesian estimation of Drift Diffusion Models.',
install_requires=['NumPy >=1.6.0', 'SciPy >= 0.6.0', 'kabuki >= 0.6.0', 'PyMC>=2.3.3', 'pandas >= 0.12.0', 'patsy'],
setup_requires=['NumPy >=1.6.0', 'SciPy >= 0.6.0', 'kabuki >= 0.6.0', 'PyMC>=2.3.3', 'pandas >= 0.12.0', 'patsy'],
include_dirs = [np.get_include()],
classifiers=[
'Development Status :: 5 - Production/Stable',
'Environment :: Console',
'Operating System :: OS Independent',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: BSD License',
'Programming Language :: Python',
'Topic :: Scientific/Engineering',
],
ext_modules = ext_modules
)

inside the dir you can call: bash clean_build.sh to compile everything

Then you can run conda develop . to add the HDDM directory to your path.

Good luck!

Thomas

Hitchcock, Peter

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Dec 28, 2019, 9:25:57 AM12/28/19

to hddm-...@googlegroups.com

Hi Thomas,

I just tried this and got stuck on the pip install kabuki step. This seemed to be because of lack of a Fortran compiler, so I used homebrew to install gcc as in this post helpfully linked to the other day https://gist.github.com/birkin/3b17a11ccbfa512a59565296ce4c7ff4. But I'm still running into issues with the compilation with the below error.

One step up I had also changed conda install pymc pandas patsy conda-build to conda install pymc3* pandas patsy conda-build

because the former was returning a dependency error.

Best,

Pete

Running setup.py clean for pymc

Failed to build pymc

Installing collected packages: pymc, kabuki

Running setup.py install for pymc ... error

ERROR: Command errored out with exit status 1:

command: /Users/pete/opt/anaconda3/envs/hddm35/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/7n/ps6r1d1x5hg7_jydw54yww1h0000gn/T/pip-install-fpqbihwn/pymc/setup.py'"'"'; __file__='"'"'/private/var/folders/7n/ps6r1d1x5hg7_jydw54yww1h0000gn/T/pip-install-fpqbihwn/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/7n/ps6r1d1x5hg7_jydw54yww1h0000gn/T/pip-record-qcdvoy3o/install-record.txt --single-version-externally-managed --compile

cwd: /private/var/folders/7n/ps6r1d1x5hg7_jydw54yww1h0000gn/T/pip-install-fpqbihwn/pymc/

Complete output (1104 lines):

running install

running build

running config_cc

unifing config_cc, config, build_clib, build_ext, build commands --compiler options

running config_fc

unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options

running build_src

build_src

building extension "pymc.flib" sources

f2py options: ['skip:ppnd7']

adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc/fortranobject.c' to sources.

adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc' to include_dirs.

adding 'build/src.macosx-10.6-x86_64-3.5/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-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc/gp/fortranobject.c' to sources.

adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc/gp' to include_dirs.

building extension "pymc.gp.incomplete_chol" sources

f2py options: []

adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc/gp/fortranobject.c' to sources.

adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc/gp' to include_dirs.

building extension "pymc.gp.cov_funs.isotropic_cov_funs" sources

f2py options: []

adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc/gp/cov_funs/fortranobject.c' to sources.

adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc/gp/cov_funs' to include_dirs.

adding 'build/src.macosx-10.6-x86_64-3.5/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-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc/gp/cov_funs/fortranobject.c' to sources.

adding 'build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc/gp/cov_funs' to include_dirs.

build_src: building npy-pkg config files

running build_py

creating build/lib.macosx-10.6-x86_64-3.5

creating build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/StepMethods.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/InstantiationDecorators.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/CircularStochastic.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/diagnostics.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/threadpool.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/graph.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/Matplot.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/__init__.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/Container.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/Model.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/distributions.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/MCMC.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/datatypes.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/NormalApproximation.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/progressbar.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/utils.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/PyMCObjects.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/six.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/Node.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/CommonDeterministics.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/calc_utils.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/NumpyDeterministics.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/ScipyDistributions.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

copying pymc/decorators.py -> build/lib.macosx-10.6-x86_64-3.5/pymc

creating build/lib.macosx-10.6-x86_64-3.5/pymc/database

copying pymc/database/no_trace.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/database

copying pymc/database/txt.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/database

copying pymc/database/__init__.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/database

copying pymc/database/hdf5.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/database

copying pymc/database/sqlite.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/database

copying pymc/database/pickle.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/database

copying pymc/database/hdf5ea.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/database

copying pymc/database/ram.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/database

copying pymc/database/base.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/database

creating build/lib.macosx-10.6-x86_64-3.5/pymc/examples

copying pymc/examples/melanoma.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples

copying pymc/examples/disaster_model_linear.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples

copying pymc/examples/disaster_model.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples

copying pymc/examples/disaster_model_gof.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples

copying pymc/examples/gelman_bioassay.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples

copying pymc/examples/weibull_fit_gof.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples

copying pymc/examples/__init__.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples

copying pymc/examples/melanoma_data.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples

copying pymc/examples/disaster_model_null.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples

copying pymc/examples/zip.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples

copying pymc/examples/custom_step.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples

copying pymc/examples/disaster_model_missing.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples

copying pymc/examples/weibull_fit.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples

creating build/lib.macosx-10.6-x86_64-3.5/pymc/examples/gp

copying pymc/examples/gp/covparams.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples/gp

copying pymc/examples/gp/observation.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples/gp

copying pymc/examples/gp/PyMCmodel.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples/gp

copying pymc/examples/gp/basiscov.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples/gp

copying pymc/examples/gp/realizations.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples/gp

copying pymc/examples/gp/mesh_choice.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples/gp

copying pymc/examples/gp/__init__.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples/gp

copying pymc/examples/gp/cov.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples/gp

copying pymc/examples/gp/mean.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples/gp

copying pymc/examples/gp/MCMC.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/examples/gp

creating build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_utils.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_MCMCSampler.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_database.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_cov.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_container.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_missing.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_observation.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_realization.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_convergence.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/__init__.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_AM.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_basiscov.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_GP_MCMC.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_norm_approx.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_mean.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_distributions.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_slice.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_binary_step.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_adaptive.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_special_methods.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_instantiation.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/objectmodel.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_graph.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_gradients.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

copying pymc/tests/test_interactive.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/tests

creating build/lib.macosx-10.6-x86_64-3.5/pymc/gp

copying pymc/gp/step_methods.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/gp

copying pymc/gp/Realization.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/gp

copying pymc/gp/gp_submodel.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/gp

copying pymc/gp/gpplots.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/gp

copying pymc/gp/GPutils.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/gp

copying pymc/gp/Covariance.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/gp

copying pymc/gp/__init__.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/gp

copying pymc/gp/Mean.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/gp

copying pymc/gp/FullRankCovariance.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/gp

copying pymc/gp/NearlyFullRankCovariance.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/gp

copying pymc/gp/BasisCovariance.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/gp

creating build/lib.macosx-10.6-x86_64-3.5/pymc/gp/cov_funs

copying pymc/gp/cov_funs/__init__.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/gp/cov_funs

copying pymc/gp/cov_funs/wrapped_distances.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/gp/cov_funs

copying pymc/gp/cov_funs/brownian.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/gp/cov_funs

copying pymc/gp/cov_funs/nsmatern.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/gp/cov_funs

copying pymc/gp/cov_funs/cov_utils.py -> build/lib.macosx-10.6-x86_64-3.5/pymc/gp/cov_funs

copying pymc/gp/cov_funs/bases.py -> build/lib.macosx-10.6-x86_64-3.5/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

Found executable /Users/pete/opt/anaconda3/envs/hddm35/bin/x86_64-apple-darwin13.4.0-ld

Found executable /Users/pete/opt/anaconda3/envs/hddm35/bin/x86_64-apple-darwin13.4.0-ar

Found executable /Users/pete/opt/anaconda3/envs/hddm35/bin/x86_64-apple-darwin13.4.0-ranlib

customize Gnu95FCompiler

customize Gnu95FCompiler using build_ext

building 'pymc.flib' extension

compiling C sources

C compiler: x86_64-apple-darwin13.4.0-clang -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9

creating build/temp.macosx-10.6-x86_64-3.5/cephes

creating build/temp.macosx-10.6-x86_64-3.5/build

creating build/temp.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5

creating build/temp.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc

creating build/temp.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/build

creating build/temp.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5

creating build/temp.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc

compile options: '-DSCIPY_MKL_H -DHAVE_CBLAS -I/Users/pete/opt/anaconda3/envs/hddm35/include -Ibuild/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc -I/Users/pete/opt/anaconda3/envs/hddm35/lib/python3.5/site-packages/numpy/core/include -I/Users/pete/opt/anaconda3/envs/hddm35/include/python3.5m -c'

x86_64-apple-darwin13.4.0-clang: build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc/fortranobject.c

In file included from build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc/fortranobject.c:2:

In file included from build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc/fortranobject.h:13:

In file included from /Users/pete/opt/anaconda3/envs/hddm35/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4:

In file included from /Users/pete/opt/anaconda3/envs/hddm35/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:

In file included from /Users/pete/opt/anaconda3/envs/hddm35/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:

/Users/pete/opt/anaconda3/envs/hddm35/lib/python3.5/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 " \

^

1 warning generated.

x86_64-apple-darwin13.4.0-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.

x86_64-apple-darwin13.4.0-clang: cephes/chbevl.c

x86_64-apple-darwin13.4.0-clang: build/src.macosx-10.6-x86_64-3.5/pymc/flibmodule.c

In file included from build/src.macosx-10.6-x86_64-3.5/pymc/flibmodule.c:16:

In file included from build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc/fortranobject.h:13:

In file included from /Users/pete/opt/anaconda3/envs/hddm35/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4:

In file included from /Users/pete/opt/anaconda3/envs/hddm35/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:

In file included from /Users/pete/opt/anaconda3/envs/hddm35/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:

/Users/pete/opt/anaconda3/envs/hddm35/lib/python3.5/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-10.6-x86_64-3.5/pymc/flibmodule.c:16805:7: warning: array index 2 is past the end of the array (which contains 2 elements) [-Warray-bounds]

d = shape(x,2);

^ ~

build/src.macosx-10.6-x86_64-3.5/pymc/flibmodule.c:84:24: note: expanded from macro 'shape'

#define shape(var,dim) var ## _Dims[dim]

^ ~~~

<scratch space>:289:1: note: expanded from here

x_Dims

^

build/src.macosx-10.6-x86_64-3.5/pymc/flibmodule.c:16716:3: note: array 'x_Dims' declared here

npy_intp x_Dims[2] = {-1, -1};

^

build/src.macosx-10.6-x86_64-3.5/pymc/flibmodule.c:179:12: warning: unused function 'f2py_size' [-Wunused-function]

static int f2py_size(PyArrayObject* var, ...)

^

3 warnings generated.

x86_64-apple-darwin13.4.0-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.

compiling Fortran sources

Fortran f77 compiler: /usr/local/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -m64 -fPIC -O3 -funroll-loops

Fortran f90 compiler: /usr/local/bin/gfortran -Wall -g -fno-second-underscore -m64 -fPIC -O3 -funroll-loops

Fortran fix compiler: /usr/local/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -m64 -fPIC -O3 -funroll-loops

creating build/temp.macosx-10.6-x86_64-3.5/pymc

compile options: '-DSCIPY_MKL_H -DHAVE_CBLAS -I/Users/pete/opt/anaconda3/envs/hddm35/include -Ibuild/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc -I/Users/pete/opt/anaconda3/envs/hddm35/lib/python3.5/site-packages/numpy/core/include -I/Users/pete/opt/anaconda3/envs/hddm35/include/python3.5m -c'

gfortran:f77: pymc/flib.f

f951: Warning: Nonconforming tab character in column 1 of line 509 [-Wtabs]

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f951: Warning: Nonconforming tab character in column 1 of line 4646 [-Wtabs]

pymc/flib.f:316:55:

316 | 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:

314 | INTEGER i, nx, nalph, nmu, ntau, tnx

| 1

Warning: Unused variable 'tnx' declared at (1) [-Wunused-variable]

pymc/flib.f:442:71:

442 | 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:

461 | DOUBLE PRECISION like, low, high

| 1

Warning: Unused variable 'high' declared at (1) [-Wunused-variable]

pymc/flib.f:458:36:

458 | INTEGER n, nlower, nupper, i

| 1

Warning: Unused variable 'i' declared at (1) [-Wunused-variable]

pymc/flib.f:461:29:

461 | DOUBLE PRECISION like, low, high

| 1

Warning: Unused variable 'like' declared at (1) [-Wunused-variable]

pymc/flib.f:461:34:

461 | DOUBLE PRECISION like, low, high

| 1

Warning: Unused variable 'low' declared at (1) [-Wunused-variable]

pymc/flib.f:442:39:

442 | 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:

442 | 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:

442 | 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:

692 | DOUBLE PRECISION aa, cc, sigma, pdf

| 1

Warning: Unused variable 'pdf' declared at (1) [-Wunused-variable]

pymc/flib.f:760:41:

760 | DOUBLE PRECISION aa, cc, sigma, pdf

| 1

Warning: Unused variable 'pdf' declared at (1) [-Wunused-variable]

pymc/flib.f:834:41:

834 | DOUBLE PRECISION aa, cc, sigma, pdf

| 1

Warning: Unused variable 'pdf' declared at (1) [-Wunused-variable]

pymc/flib.f:906:41:

906 | DOUBLE PRECISION aa, cc, sigma, pdf

| 1

Warning: Unused variable 'pdf' declared at (1) [-Wunused-variable]

pymc/flib.f:976:41:

976 | DOUBLE PRECISION aa, cc, sigma, pdf

| 1

Warning: Unused variable 'pdf' declared at (1) [-Wunused-variable]

pymc/flib.f:1186:29:

1186 | DOUBLE PRECISION factln

| 1

Warning: Unused variable 'factln' declared at (1) [-Wunused-variable]

pymc/flib.f:1185:51:

1185 | DOUBLE PRECISION sumx, mut, infinity, sumfact

| 1

Warning: Unused variable 'sumfact' declared at (1) [-Wunused-variable]

pymc/flib.f:1185:27:

1185 | DOUBLE PRECISION sumx, mut, infinity, sumfact

| 1

Warning: Unused variable 'sumx' declared at (1) [-Wunused-variable]

pymc/flib.f:1300:55:

1300 | DOUBLE PRECISION mu(nmu), gradlike(nmu),grad, cdf

| 1

Warning: Unused variable 'cdf' declared at (1) [-Wunused-variable]

pymc/flib.f:1302:29:

1302 | DOUBLE PRECISION factln, gammq

| 1

Warning: Unused variable 'factln' declared at (1) [-Wunused-variable]

pymc/flib.f:1302:36:

1302 | DOUBLE PRECISION factln, gammq

| 1

Warning: Unused variable 'gammq' declared at (1) [-Wunused-variable]

pymc/flib.f:1301:59:

1301 | DOUBLE PRECISION sumx, mut, infinity, sumfact, sumcdf

| 1

Warning: Unused variable 'sumcdf' declared at (1) [-Wunused-variable]

pymc/flib.f:1301:51:

1301 | DOUBLE PRECISION sumx, mut, infinity, sumfact, sumcdf

| 1

Warning: Unused variable 'sumfact' declared at (1) [-Wunused-variable]

pymc/flib.f:1301:27:

1301 | DOUBLE PRECISION sumx, mut, infinity, sumfact, sumcdf

| 1

Warning: Unused variable 'sumx' declared at (1) [-Wunused-variable]

pymc/flib.f:1402:29:

1402 | DOUBLE PRECISION gammln

| 1

Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]

pymc/flib.f:2154:40:

2154 | DOUBLE PRECISION gradlike(n), grad

| 1

Warning: Unused variable 'grad' declared at (1) [-Wunused-variable]

pymc/flib.f:2665:29:

2665 | DOUBLE PRECISION gammln

| 1

Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]

pymc/flib.f:2728:29:

2728 | DOUBLE PRECISION gammln, psi

| 1

Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]

pymc/flib.f:2793:29:

2793 | DOUBLE PRECISION gammln

| 1

Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]

pymc/flib.f:2903:29:

2903 | DOUBLE PRECISION gammln

| 1

Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]

pymc/flib.f:2959:29:

2959 | DOUBLE PRECISION gammln, psi

| 1

Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]

pymc/flib.f:3021:29:

3021 | DOUBLE PRECISION gammln

| 1

Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]

pymc/flib.f:3396:58:

3396 | DOUBLE PRECISION gradlike(nx), atmp, btmp, PI, glike

| 1

Warning: Unused variable 'glike' declared at (1) [-Wunused-variable]

pymc/flib.f:3646:37:

3646 | DOUBLE PRECISION gammln, factln

| 1

Warning: Unused variable 'factln' declared at (1) [-Wunused-variable]

pymc/flib.f:3646:29:

3646 | DOUBLE PRECISION gammln, factln

| 1

Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]

pymc/flib.f:3706:37:

3706 | DOUBLE PRECISION gammln, factln, psi

| 1

Warning: Unused variable 'factln' declared at (1) [-Wunused-variable]

pymc/flib.f:3706:29:

3706 | DOUBLE PRECISION gammln, factln, psi

| 1

Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]

pymc/flib.f:3836:29:

3836 | DOUBLE PRECISION factln

| 1

Warning: Unused variable 'factln' declared at (1) [-Wunused-variable]

pymc/flib.f:4039:26:

4039 | DOUBLE PRECISION psi

| 1

Warning: Unused variable 'psi' declared at (1) [-Wunused-variable]

pymc/flib.f:4266:29:

4266 | DOUBLE PRECISION gammln, psi

| 1

Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]

pymc/flib.f:4332:29:

4332 | DOUBLE PRECISION gammln, psi

| 1

Warning: Unused variable 'gammln' declared at (1) [-Wunused-variable]

pymc/flib.f:5184:35:

5184 | DOUBLE PRECISION like, factln, infinity, sump

| 1

Warning: Unused variable 'factln' declared at (1) [-Wunused-variable]

pymc/flib.f:5186:23:

5186 | INTEGER i,j,n_tmp

| 1

Warning: Unused variable 'n_tmp' declared at (1) [-Wunused-variable]

pymc/flib.f:5434:26:

5434 | DOUBLE PRECISION tmp

| 1

Warning: Unused variable 'tmp' declared at (1) [-Wunused-variable]

pymc/flib.f:5488:25:

5488 | DOUBLE PRECISION i0

| 1

Warning: Unused variable 'i0' declared at (1) [-Wunused-variable]

pymc/flib.f:5481:26:

5481 | DOUBLE PRECISION tmp

| 1

Warning: Unused variable 'tmp' declared at (1) [-Wunused-variable]

pymc/flib.f:5535:25:

5535 | DOUBLE PRECISION i0

| 1

Warning: Unused variable 'i0' declared at (1) [-Wunused-variable]

pymc/flib.f:5528:26:

5528 | DOUBLE PRECISION tmp

| 1

Warning: Unused variable 'tmp' declared at (1) [-Wunused-variable]

pymc/flib.f:4882:0:

4882 | K = I

|

Warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]

gfortran:f77: pymc/histogram.f

pymc/histogram.f:235:72:

235 | 1 ORD(I)=I

| 1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 1 at (1)

gfortran:f77: pymc/flib_blas.f

pymc/flib_blas.f:202:25:

202 | 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:

396 | 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:

417 | 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:2066:72:

2066 | 20 X(I) = -X(I)

| 1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 20 at (1)

pymc/gibbsit.f:2255:72:

2255 | 310 X(I) = -X(I)

| 1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 310 at (1)

pymc/gibbsit.f:2160:5:

2160 | 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:

2077 | 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:

2064 | 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:

1204 | 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-10.6-x86_64-3.5/pymc/flib-f2pywrappers.f

/usr/local/bin/gfortran -Wall -g -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs build/temp.macosx-10.6-x86_64-3.5/cephes/i0.o build/temp.macosx-10.6-x86_64-3.5/cephes/c2f.o build/temp.macosx-10.6-x86_64-3.5/cephes/chbevl.o build/temp.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc/flibmodule.o build/temp.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc/fortranobject.o build/temp.macosx-10.6-x86_64-3.5/pymc/flib.o build/temp.macosx-10.6-x86_64-3.5/pymc/histogram.o build/temp.macosx-10.6-x86_64-3.5/pymc/flib_blas.o build/temp.macosx-10.6-x86_64-3.5/pymc/blas_wrap.o build/temp.macosx-10.6-x86_64-3.5/pymc/math.o build/temp.macosx-10.6-x86_64-3.5/pymc/gibbsit.o build/temp.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc/flib-f2pywrappers.o -L/Users/pete/opt/anaconda3/envs/hddm35/lib -L/usr/local/Cellar/gcc/9.2.0_2/lib/gcc/9/gcc/x86_64-apple-darwin19/9.2.0 -L/usr/local/Cellar/gcc/9.2.0_2/lib/gcc/9/gcc/x86_64-apple-darwin19/9.2.0/../../.. -L/usr/local/Cellar/gcc/9.2.0_2/lib/gcc/9/gcc/x86_64-apple-darwin19/9.2.0/../../.. -lmkl_rt -lpthread -lgfortran -o build/lib.macosx-10.6-x86_64-3.5/pymc/flib.cpython-35m-darwin.so

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_fortran_setattr in fortranobject.o

"_PyDict_SetItemString", referenced from:

_PyInit_flib in flibmodule.o

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_fortran_getattr in fortranobject.o

_fortran_setattr in fortranobject.o

"_PyErr_Clear", referenced from:

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_double_from_pyobj in flibmodule.o

_F2PyDict_SetItemString in fortranobject.o

_fortran_getattr in fortranobject.o

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_F2PyCapsule_FromVoidPtr in fortranobject.o

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"_PyErr_Print", referenced from:

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"_PyEval_SaveThread", referenced from:

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_f2py_rout_flib_standardize in flibmodule.o

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"_PyExc_AttributeError", referenced from:

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...

ld: symbol(s) not found for architecture x86_64

collect2: error: ld returned 1 exit status

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"_PyBytes_FromString", referenced from:

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"_PyCapsule_New", referenced from:

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"_PyCapsule_Type", referenced from:

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"_PyErr_Format", referenced from:

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"_PyErr_Print", referenced from:

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_F2PyDict_SetItemString in fortranobject.o

"_PyErr_SetString", referenced from:

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"_PyUnicode_Concat", referenced from:

_fortran_getattr in fortranobject.o

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"_PyUnicode_FromString", referenced from:

_PyInit_flib in flibmodule.o

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"_Py_BuildValue", referenced from:

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...

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...

ld: symbol(s) not found for architecture x86_64

collect2: error: ld returned 1 exit status

error: Command "/usr/local/bin/gfortran -Wall -g -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs build/temp.macosx-10.6-x86_64-3.5/cephes/i0.o build/temp.macosx-10.6-x86_64-3.5/cephes/c2f.o build/temp.macosx-10.6-x86_64-3.5/cephes/chbevl.o build/temp.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc/flibmodule.o build/temp.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc/fortranobject.o build/temp.macosx-10.6-x86_64-3.5/pymc/flib.o build/temp.macosx-10.6-x86_64-3.5/pymc/histogram.o build/temp.macosx-10.6-x86_64-3.5/pymc/flib_blas.o build/temp.macosx-10.6-x86_64-3.5/pymc/blas_wrap.o build/temp.macosx-10.6-x86_64-3.5/pymc/math.o build/temp.macosx-10.6-x86_64-3.5/pymc/gibbsit.o build/temp.macosx-10.6-x86_64-3.5/build/src.macosx-10.6-x86_64-3.5/pymc/flib-f2pywrappers.o -L/Users/pete/opt/anaconda3/envs/hddm35/lib -L/usr/local/Cellar/gcc/9.2.0_2/lib/gcc/9/gcc/x86_64-apple-darwin19/9.2.0 -L/usr/local/Cellar/gcc/9.2.0_2/lib/gcc/9/gcc/x86_64-apple-darwin19/9.2.0/../../.. -L/usr/local/Cellar/gcc/9.2.0_2/lib/gcc/9/gcc/x86_64-apple-darwin19/9.2.0/../../.. -lmkl_rt -lpthread -lgfortran -o build/lib.macosx-10.6-x86_64-3.5/pymc/flib.cpython-35m-darwin.so" failed with exit status 1

----------------------------------------

ERROR: Command errored out with exit status 1: /Users/pete/opt/anaconda3/envs/hddm35/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/7n/ps6r1d1x5hg7_jydw54yww1h0000gn/T/pip-install-fpqbihwn/pymc/setup.py'"'"'; __file__='"'"'/private/var/folders/7n/ps6r1d1x5hg7_jydw54yww1h0000gn/T/pip-install-fpqbihwn/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/7n/ps6r1d1x5hg7_jydw54yww1h0000gn/T/pip-record-qcdvoy3o/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.

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Thomas Wiecki

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Dec 28, 2019, 9:28:41 AM12/28/19

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The kabuki error is because pymc could not be installed. Installing pymc3 is not the right solution as hddm depends on pymc, not pymc3. Can you send which error conda install pymc returned?

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Hitchcock, Peter

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Dec 28, 2019, 10:38:39 AM12/28/19

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Ahh okay, thanks for the info. Here's the error.

Specifications:

- conda-build -> python[version='<=3.3']

- pymc -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0']

Your python: python=3.5

If python is on the left-most side of the chain, that's the version you've asked for.

When python appears to the right, that indicates that the thing on the left is somehow

not available for the python version you are constrained to. Note that conda will not

change your python version to a different minor version unless you explicitly specify

that.

I did try conda install pymc python=2.7 and was then able to follow the rest of the steps without issue, however then python 2.7 is in the conda environment rather than 3.5.

On Sat, Dec 28, 2019 at 9:28 AM Thomas Wiecki <thomas...@gmail.com> wrote:

The kabuki error is because pymc could not be installed. Installing pymc3 is not the right solution as hddm depends on pymc, not pymc3. Can you send which error conda install pymc returned?

On Sat, Dec 28, 2019 at 3:25 PM Hitchcock, Peter <peter_h...@brown.edu> wrote:

Hi Thomas,

I just tried this and got stuck on the pip install kabuki step. This seemed to be because of lack of a Fortran compiler, so I used homebrew to install gcc as in this post helpfully linked to the other day https://gist.github.com/birkin/3b17a11ccbfa512a59565296ce4c7ff4. But I'm still running into issues with the compilation with the below error.

One step up I had also changed conda install pymc pandas patsy conda-build to conda install pymc3* pandas patsy conda-build
because the former was returning a dependency error.

Best,
Pete

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Thomas Wiecki

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Dec 29, 2019, 5:40:51 AM12/29/19

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Well if it works with python 2.7 I suppose that's sufficient, although I'm surprised that it worked for me on 3.5.

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Esin Turkakin

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Dec 29, 2019, 7:12:10 AM12/29/19

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Won't sticking with 2.7 be a problem with support for Python 2 ending in a few days?

Anyway, I finally managed to install hddm (0.7.2) with python 3.6 on MacOS 10.14, following a combination of steps described here and in this thread.

The steps that worked for me (with Anaconda-Navigator 1.9.7 installed, in case that matters, but all commands executed in the regular Terminal):

conda create --name py36 python=3.6

conda activate py36

conda install conda-build

conda install pymc

conda install pandas patsy

export MACOSX_DEPLOYMENT_TARGET=10.11

pip install cython

pip install hddm

conda install spyder

Some notes:

- Installing conda-build separately (not in combination with the other three packages) worked to avoid the python <=3.3 requirement it was complaining about otherwise

- I failed to install pymc on 3.5 or 3.7 as it seems to specifically require version 3.6 (thus the switch to 3.6)

- The manual compile for the downloaded source (with the edited setup.py) didn't work for me, which may be due to me missing something obvious, but the eventual error I got (after some other warnings) was: "clang: error: no such file or directory: 'src/cdfdif.cpp'"

- All steps after the environment variable setting were executed in the directory of the downloaded source, with the edited setup.py (I don't think this matters, but I can't be sure anymore)

- The previous thread (linked above) used to fail for me at the pip install hddm step (see this issue) before I added the conda-build (and patsy and pandas) install and the environment variable (the export command) as described in this thread. Not sure which one was the actual fix, and not willing to try different combinations as this was the first time it worked after several tries in the course of the past 2? years.

Best of luck to everyone who tries this, and hope it works for you as well :)

Cheers,

Esin

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Laboratory of Neural Computation and Cognition

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James Wei Chen

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Dec 29, 2019, 7:48:50 AM12/29/19

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Dear Esin,

Thanks a lot.

Your instruction also works on macOS 10.15.2.

I got a warning that I need some kinda developmental tool after the "pip install hddm" step,

but after following the system's instruction, and rerun the above command, I succeed.

Also, since I use jupyter notebook more often than Spyder.

I installed jupyter instead and it works as well.

Best Regards,

Dr. James Wei Chen

Assistant Research Fellow

Behavioral and Data Science Research Center

National Taiwan University

Esin Turkakin <esin.t...@gmail.com> 於 2019年12月29日週日下午8:12寫道：

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Thomas Wiecki

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Dec 30, 2019, 6:55:46 AM12/30/19

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As Esin found out I introduced a filename bug in 0.7.2 which I now fixed and released 0.7.3.

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Esin Turkakin

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Feb 17, 2020, 11:42:30 AM2/17/20

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Just a post-upgrade update to this thread:

In case you followed the steps listed above for installing hddm with python 3.6 and want to upgrade to the newer versions, setting the environment variable again (this turns out to be a necessary step) and updating via pip as follows seems to work (once you're in the relevant environment with python 3.6 and hddm):

export MACOSX_DEPLOYMENT_TARGET=10.11

pip install --upgrade hddm

Also, following the issue pointed out in this thread, if you use the geweke statistic as a convergence diagnostic, adding the following line gets the check_geweke function working again:

conda install statsmodels

Hope that helps someone.

Cheers,

Esin

On Monday, December 30, 2019 at 12:55:46 PM UTC+1, Thomas wrote:

As Esin found out I introduced a filename bug in 0.7.2 which I now fixed and released 0.7.3.

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Thomas Wiecki

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Feb 17, 2020, 12:16:22 PM2/17/20

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Thanks for following up!

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Jamie Hoefakker

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May 15, 2020, 8:43:49 AM5/15/20

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Thank you so much! I spent hours trying to figure this out (being a total newbie) and I finally installed HDDM this way. Now on to getting it to work haha. thanks again!

Op zondag 29 december 2019 13:12:10 UTC+1 schreef Esin Turkakin:

Michael Spezio

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May 29, 2020, 9:11:35 PM5/29/20

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Thomas, would it be possible to provide a link to this HDDM Group discussion or, even better, list these steps under the current HDDM 0.7.7 Installation Instructions. I've had success with these steps, and it seems that others have as well, and it might help users to have Esin's protocol listed on the main page?

Best, Michael

Thanks for following up!

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Thomas Wiecki

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May 31, 2020, 4:16:57 PM5/31/20

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Can someone do a pull request on GitHub?

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Konstantina Sokratous

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Oct 2, 2020, 5:20:10 PM10/2/20

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Hi ! Did someone manage to install HDDM with Python 3.8 and macOS 10.15 ? I have tried following every possible solution I have found online, but I just can't get HDDM installed.

Mark Hu

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Mar 2, 2021, 9:01:42 AM3/2/21

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Dear Esin

Thank you very much for providing this instruction. I have successfully installed the HDDM on my macOS 10.15.7 by following your post.

In addition, I am thinking about upgrading my system to the newly released Big Sur (macOS 11), and I wonder if there will be any compatibility issues with installing and upgrading the HDDM? I notice that one line of the code in your instruction is "export MACOSX_DEPLOYMENT_TARGET=10.11", which seems to require the system to be macOS 10 series (sorry if I were wrong), so I wonder if this would still work with the Big Sur system? Many thanks!

Best wishes

Tianqi

Ying

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Aug 27, 2021, 9:48:09 AM8/27/21

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Hello,

(I think my post didn't sent if it did sorry for the duplicate)

I updated my mac to BigSur and am trying to install HDDM.

I've done this:

conda create --name hddmpy35 python=3.5 anaconda

conda activate hddmpy35

but for the next step it's stuck with these messages:

Collecting package metadata (current_repodata.json): done

Solving environment: failed with initial frozen solve. Retrying with flexible solve.

Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.

Collecting package metadata (repodata.json): done

Solving environment: failed with initial frozen solve. Retrying with flexible solve.

Solving environment: /

Found conflicts! Looking for incompatible packages.

This can take several minutes. Press CTRL-C to abort.

Examining conflict for xlrd ipykernel testpath scikit-learn fastcache itsdangerous nbconvert no/

I'm not sure if I'm missing something?

Thank you,

Ying

Thomas Wiecki

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Aug 27, 2021, 12:56:23 PM8/27/21

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I would try with a more recent python like 3.8.

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Ying

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Aug 30, 2021, 9:49:55 AM8/30/21

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I don't think it works with 3.8

error message:

Specifications:

- hddm -> python[version='2.7.*|3.4.*|3.5.*']

Your python: python=3.8

Alexander Fengler

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Aug 30, 2021, 2:40:00 PM8/30/21

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Are you using the newest version of HDDM here?

This should not be an issue.

You can try this command to install:

pip install git+https://github.com/hddm-devs/hddm

Best,

Alex

Ying

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Aug 30, 2021, 9:39:20 PM8/30/21

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I got these types of errors. I did some googling, seems like a Mac OS BigSur issue?

Screen Shot 2021-08-30 at 9.37.35 PM.png

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Ziliang Xiong

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Jan 24, 2023, 4:34:44 AM1/24/23

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Hi Esin,

Your solution worked out great for me! until I tried to install Spyder. I didn't see this being mentioned elsewhere in this thread so is Spyder necessary for using hddm? Because otherwise I think I have successfully installed hddm without configuring Spyder. Looking forward to your response.

Many thanks,

Ziliang

Hitchcock, Peter

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Jan 24, 2023, 10:13:31 AM1/24/23

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Hi Ziliang,

Spyder is not necessary to use HDDM — you can also edit with and run code from VS Code or terminal, as examples. If the installation looked like it was working until the point of installing Sypder, you may want to try again and skip the Spyder step. You'll just need to make sure the conda environment (py36 in Esin's example) is activated when you want to run your code.

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Irene Dolfini

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May 21, 2024, 9:55:31 AM5/21/24

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Hello! I'm trying to install hddm on a mac M1, macOS 13.0.1. Since I'm quite new in this field, I'm running into many errors and I was wondering if any of you could help me.

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