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hddm-devs / hddm

HDDM is a python module that implements Hierarchical Bayesian parameter estimation of Drift Diffusion Models (via PyMC).
http://ski.clps.brown.edu/hddm_docs/
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Installation problem #41

Open DominiqueMakowski opened 7 years ago

DominiqueMakowski commented 7 years ago

Hey, I can't install hddm using pip on python 3.5.2.2, windows 10 64x (I'm using WinPyhon).

Do you have any idea on why is this erroring?

Thanks a lot!

Here's the full error log:

Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,>=1.5.6 in c:\users\dom\desktop\winpython-64bit-3.5.2.2\python-3.5.2.amd64\lib\site-packages (from matplotlib>=1.0.0->kabuki>=0.6.0->HDDM==0.6.1)
Requirement already satisfied: cycler in c:\users\dom\desktop\winpython-64bit-3.5.2.2\python-3.5.2.amd64\lib\site-packages (from matplotlib>=1.0.0->kabuki>=0.6.0->HDDM==0.6.1)
Installing collected packages: HDDM
  Running setup.py install for HDDM ... error
    Complete output from command C:\Users\Dom\Desktop\WinPython-64bit-3.5.2.2\python-
3.5.2.amd64\python.exe -u -c "import setuptools, 
tokenize;__file__='C:\\Users\\Dom\\AppData\\Local\\Temp\\pip-eaetvo7a-
build\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', 
'\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\Dom\AppData\Local\Temp\pip-
uc4akrza-record\install-record.txt --single-version-externally-managed --compile:
    running install
    running build
    running build_py
    creating build
    creating build\lib.win-amd64-3.5
    creating build\lib.win-amd64-3.5\hddm
    copying hddm\diag.py -> build\lib.win-amd64-3.5\hddm
    copying hddm\generate.py -> build\lib.win-amd64-3.5\hddm
    copying hddm\likelihoods.py -> build\lib.win-amd64-3.5\hddm
    copying hddm\MPLTraits.py -> build\lib.win-amd64-3.5\hddm
    copying hddm\MPLTraits_qt.py -> build\lib.win-amd64-3.5\hddm
    copying hddm\utils.py -> build\lib.win-amd64-3.5\hddm
    copying hddm\__init__.py -> build\lib.win-amd64-3.5\hddm
    creating build\lib.win-amd64-3.5\hddm\tests
    copying hddm\tests\benchmark.py -> build\lib.win-amd64-3.5\hddm\tests
    copying hddm\tests\matlab_values.py -> build\lib.win-amd64-3.5\hddm\tests
    copying hddm\tests\test_generate.py -> build\lib.win-amd64-3.5\hddm\tests
    copying hddm\tests\test_likelihoods.py -> build\lib.win-amd64-3.5\hddm\tests
    copying hddm\tests\test_models.py -> build\lib.win-amd64-3.5\hddm\tests
    copying hddm\tests\test_optimization.py -> build\lib.win-amd64-3.5\hddm\tests
    copying hddm\tests\__init__.py -> build\lib.win-amd64-3.5\hddm\tests
    creating build\lib.win-amd64-3.5\hddm\models
    copying hddm\models\base.py -> build\lib.win-amd64-3.5\hddm\models
    copying hddm\models\hddm_info.py -> build\lib.win-amd64-3.5\hddm\models
    copying hddm\models\hddm_regression.py -> build\lib.win-amd64-3.5\hddm\models
    copying hddm\models\hddm_stimcoding.py -> build\lib.win-amd64-3.5\hddm\models
    copying hddm\models\hddm_transformed.py -> build\lib.win-amd64-3.5\hddm\models
    copying hddm\models\hddm_truncated.py -> build\lib.win-amd64-3.5\hddm\models
    copying hddm\models\__init__.py -> build\lib.win-amd64-3.5\hddm\models
    creating build\lib.win-amd64-3.5\hddm\examples
    copying hddm\examples\plot_posterior_quantiles.py -> build\lib.win-amd64-3.5\hddm\examples
    copying hddm\examples\simple_model.py -> build\lib.win-amd64-3.5\hddm\examples
    copying hddm\examples\__init__.py -> build\lib.win-amd64-3.5\hddm\examples
    copying hddm\examples\cavanagh_theta_nn.csv -> build\lib.win-amd64-3.5\hddm\examples
    copying hddm\examples\simple_difficulty.csv -> build\lib.win-amd64-3.5\hddm\examples
    copying hddm\examples\simple_subjs_difficulty.csv -> build\lib.win-amd64-3.5\hddm\examples
    copying hddm\examples\simple_subjs_difficulty_single.csv -> build\lib.win-amd64-3.5\hddm\examples
    copying hddm\examples\simple_difficulty.conf -> build\lib.win-amd64-3.5\hddm\examples
    running build_ext
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "C:\Users\Dom\AppData\Local\Temp\pip-eaetvo7a-build\setup.py", line 39, in <module>
        ext_modules = ext_modules
      File "C:\Users\Dom\Desktop\WinPython-64bit-3.5.2.2\python-3.5.2.amd64\lib\distutils\core.py", line 148, in setup
        dist.run_commands()
      File "C:\Users\Dom\Desktop\WinPython-64bit-3.5.2.2\python-3.5.2.amd64\lib\distutils\dist.py", line 955, in run_commands
        self.run_command(cmd)
      File "C:\Users\Dom\Desktop\WinPython-64bit-3.5.2.2\python-3.5.2.amd64\lib\distutils\dist.py", line 974, in run_command
        cmd_obj.run()
      File "C:\Users\Dom\Desktop\WinPython-64bit-3.5.2.2\python-3.5.2.amd64\lib\site-packages\setuptools\command\install.py", line 61, in run
        return orig.install.run(self)
      File "C:\Users\Dom\Desktop\WinPython-64bit-3.5.2.2\python-3.5.2.amd64\lib\distutils\command\install.py", line 539, in run
        self.run_command('build')
      File "C:\Users\Dom\Desktop\WinPython-64bit-3.5.2.2\python-3.5.2.amd64\lib\distutils\cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "C:\Users\Dom\Desktop\WinPython-64bit-3.5.2.2\python-3.5.2.amd64\lib\distutils\dist.py", line 974, in run_command
        cmd_obj.run()
      File "C:\Users\Dom\Desktop\WinPython-64bit-3.5.2.2\python-3.5.2.amd64\lib\distutils\command\build.py", line 135, in run
        self.run_command(cmd_name)
      File "C:\Users\Dom\Desktop\WinPython-64bit-3.5.2.2\python-3.5.2.amd64\lib\distutils\cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "C:\Users\Dom\Desktop\WinPython-64bit-3.5.2.2\python-3.5.2.amd64\lib\distutils\dist.py", line 974, in run_command
        cmd_obj.run()
      File "C:\Users\Dom\Desktop\WinPython-64bit-3.5.2.2\python-3.5.2.amd64\lib\site-packages\setuptools\command\build_ext.py", line 68, in run
        _build_ext.run(self)
      File "C:\Users\Dom\Desktop\WinPython-64bit-3.5.2.2\python-3.5.2.amd64\lib\site-packages\Cython\Distutils\build_ext.py", line 164, in run
        _build_ext.build_ext.run(self)
      File "C:\Users\Dom\Desktop\WinPython-64bit-3.5.2.2\python-3.5.2.amd64\lib\distutils\command\build_ext.py", line 307, in run
        force=self.force)
      File "C:\Users\Dom\Desktop\WinPython-64bit-3.5.2.2\python-3.5.2.amd64\lib\distutils\ccompiler.py", line 1031, in new_compiler
        return klass(None, dry_run, force)
      File "C:\Users\Dom\Desktop\WinPython-64bit-3.5.2.2\python-3.5.2.amd64\lib\distutils\cygwinccompiler.py", line 282, in __init__
        CygwinCCompiler.__init__ (self, verbose, dry_run, force)
      File "C:\Users\Dom\Desktop\WinPython-64bit-3.5.2.2\python-3.5.2.amd64\lib\distutils\cygwinccompiler.py", line 126, in __init__
        if self.ld_version >= "2.10.90":
    TypeError: unorderable types: NoneType() >= str()

    ----------------------------------------
Command "C:\Users\Dom\Desktop\WinPython-64bit-3.5.2.2\python-3.5.2.amd64\python.exe -u -c 
"import setuptools, tokenize;__file__='C:\\Users\\Dom\\AppData\\Local\\Temp\\pip-eaetvo7a-
build\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', 
'\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\Dom\AppData\Local\Temp\pip-
uc4akrza-record\install-record.txt --single-version-externally-managed --compile" failed with error code 
1 in C:\Users\Dom\AppData\Local\Temp\pip-eaetvo7a-build\
josemceb commented 7 years ago

I'm having the same issue on my Mac:

Command "//anaconda/envs/Py3.5/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/_k/vhkrrz4d6nl6zgzw_hmd4sxh0000gn/T/pip-build-nvl8n3d2/hddm/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/_k/vhkrrz4d6nl6zgzw_hmd4sxh0000gn/T/pip-x493098f-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/_k/vhkrrz4d6nl6zgzw_hmd4sxh0000gn/T/pip-build-nvl8n3d2/hddm/

twiecki commented 7 years ago

@josemceb can you post the full output?

josemceb commented 7 years ago

Apologies, here it is!

Collecting HDDM
  Using cached HDDM-0.6.1.tar.gz
Requirement already satisfied: NumPy>=1.6.0 in /anaconda/envs/Py3.5/lib/python3.5/site-packages (from HDDM)
Requirement already satisfied: SciPy>=0.6.0 in /anaconda/envs/Py3.5/lib/python3.5/site-packages (from HDDM)
Requirement already satisfied: kabuki>=0.6.0 in /anaconda/envs/Py3.5/lib/python3.5/site-packages (from HDDM)
Requirement already satisfied: PyMC>=2.3.3 in /anaconda/envs/Py3.5/lib/python3.5/site-packages (from HDDM)
Requirement already satisfied: pandas>=0.12.0 in /anaconda/envs/Py3.5/lib/python3.5/site-packages (from HDDM)
Requirement already satisfied: patsy in /anaconda/envs/Py3.5/lib/python3.5/site-packages (from HDDM)
Requirement already satisfied: matplotlib>=1.0.0 in /anaconda/envs/Py3.5/lib/python3.5/site-packages (from kabuki>=0.6.0->HDDM)
Requirement already satisfied: pytz>=2011k in /anaconda/envs/Py3.5/lib/python3.5/site-packages (from pandas>=0.12.0->HDDM)
Requirement already satisfied: python-dateutil>=2 in /anaconda/envs/Py3.5/lib/python3.5/site-packages (from pandas>=0.12.0->HDDM)
Requirement already satisfied: six in /anaconda/envs/Py3.5/lib/python3.5/site-packages (from patsy->HDDM)
Requirement already satisfied: cycler>=0.10 in /anaconda/envs/Py3.5/lib/python3.5/site-packages (from matplotlib>=1.0.0->kabuki>=0.6.0->HDDM)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 in /anaconda/envs/Py3.5/lib/python3.5/site-packages (from matplotlib>=1.0.0->kabuki>=0.6.0->HDDM)
Building wheels for collected packages: HDDM
  Running setup.py bdist_wheel for HDDM ... error
  Complete output from command //anaconda/envs/Py3.5/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/_k/vhkrrz4d6nl6zgzw_hmd4sxh0000gn/T/pip-build-f542ng8s/HDDM/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 /var/folders/_k/vhkrrz4d6nl6zgzw_hmd4sxh0000gn/T/tmp8dpdje4mpip-wheel- --python-tag cp35:
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.macosx-10.6-x86_64-3.5
  creating build/lib.macosx-10.6-x86_64-3.5/hddm
  copying hddm/__init__.py -> build/lib.macosx-10.6-x86_64-3.5/hddm
  copying hddm/diag.py -> build/lib.macosx-10.6-x86_64-3.5/hddm
  copying hddm/generate.py -> build/lib.macosx-10.6-x86_64-3.5/hddm
  copying hddm/likelihoods.py -> build/lib.macosx-10.6-x86_64-3.5/hddm
  copying hddm/MPLTraits.py -> build/lib.macosx-10.6-x86_64-3.5/hddm
  copying hddm/MPLTraits_qt.py -> build/lib.macosx-10.6-x86_64-3.5/hddm
  copying hddm/utils.py -> build/lib.macosx-10.6-x86_64-3.5/hddm
  creating build/lib.macosx-10.6-x86_64-3.5/hddm/tests
  copying hddm/tests/__init__.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/tests
  copying hddm/tests/benchmark.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/tests
  copying hddm/tests/matlab_values.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/tests
  copying hddm/tests/test_generate.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/tests
  copying hddm/tests/test_likelihoods.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/tests
  copying hddm/tests/test_models.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/tests
  copying hddm/tests/test_optimization.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/tests
  creating build/lib.macosx-10.6-x86_64-3.5/hddm/models
  copying hddm/models/__init__.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/models
  copying hddm/models/base.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/models
  copying hddm/models/hddm_info.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/models
  copying hddm/models/hddm_regression.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/models
  copying hddm/models/hddm_stimcoding.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/models
  copying hddm/models/hddm_transformed.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/models
  copying hddm/models/hddm_truncated.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/models
  creating build/lib.macosx-10.6-x86_64-3.5/hddm/examples
  copying hddm/examples/__init__.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/examples
  copying hddm/examples/plot_posterior_quantiles.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/examples
  copying hddm/examples/postpred.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/examples
  copying hddm/examples/simple_model.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/examples
  copying hddm/examples/cavanagh_theta_nn.csv -> build/lib.macosx-10.6-x86_64-3.5/hddm/examples
  copying hddm/examples/simple_difficulty.csv -> build/lib.macosx-10.6-x86_64-3.5/hddm/examples
  copying hddm/examples/simple_subjs_difficulty.csv -> build/lib.macosx-10.6-x86_64-3.5/hddm/examples
  copying hddm/examples/simple_subjs_difficulty_single.csv -> build/lib.macosx-10.6-x86_64-3.5/hddm/examples
  copying hddm/examples/simple_difficulty.conf -> build/lib.macosx-10.6-x86_64-3.5/hddm/examples
  running build_ext
  building 'wfpt' extension
  creating build/temp.macosx-10.6-x86_64-3.5
  creating build/temp.macosx-10.6-x86_64-3.5/src
  /usr/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I//anaconda/envs/Py3.5/include -arch x86_64 -I//anaconda/envs/Py3.5/lib/python3.5/site-packages/numpy/core/include -I//anaconda/envs/Py3.5/include/python3.5m -c src/wfpt.c -o build/temp.macosx-10.6-x86_64-3.5/src/wfpt.o
  clang: error: no such file or directory: 'src/wfpt.c'
  clang: error: no input files
  error: command '/usr/bin/clang' failed with exit status 1

  ----------------------------------------
  Failed building wheel for HDDM
  Running setup.py clean for HDDM
Failed to build HDDM
Installing collected packages: HDDM
  Running setup.py install for HDDM ... error
    Complete output from command //anaconda/envs/Py3.5/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/_k/vhkrrz4d6nl6zgzw_hmd4sxh0000gn/T/pip-build-f542ng8s/HDDM/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/_k/vhkrrz4d6nl6zgzw_hmd4sxh0000gn/T/pip-baz18mcy-record/install-record.txt --single-version-externally-managed --compile:
    running install
    running build
    running build_py
    creating build
    creating build/lib.macosx-10.6-x86_64-3.5
    creating build/lib.macosx-10.6-x86_64-3.5/hddm
    copying hddm/__init__.py -> build/lib.macosx-10.6-x86_64-3.5/hddm
    copying hddm/diag.py -> build/lib.macosx-10.6-x86_64-3.5/hddm
    copying hddm/generate.py -> build/lib.macosx-10.6-x86_64-3.5/hddm
    copying hddm/likelihoods.py -> build/lib.macosx-10.6-x86_64-3.5/hddm
    copying hddm/MPLTraits.py -> build/lib.macosx-10.6-x86_64-3.5/hddm
    copying hddm/MPLTraits_qt.py -> build/lib.macosx-10.6-x86_64-3.5/hddm
    copying hddm/utils.py -> build/lib.macosx-10.6-x86_64-3.5/hddm
    creating build/lib.macosx-10.6-x86_64-3.5/hddm/tests
    copying hddm/tests/__init__.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/tests
    copying hddm/tests/benchmark.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/tests
    copying hddm/tests/matlab_values.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/tests
    copying hddm/tests/test_generate.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/tests
    copying hddm/tests/test_likelihoods.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/tests
    copying hddm/tests/test_models.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/tests
    copying hddm/tests/test_optimization.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/tests
    creating build/lib.macosx-10.6-x86_64-3.5/hddm/models
    copying hddm/models/__init__.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/models
    copying hddm/models/base.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/models
    copying hddm/models/hddm_info.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/models
    copying hddm/models/hddm_regression.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/models
    copying hddm/models/hddm_stimcoding.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/models
    copying hddm/models/hddm_transformed.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/models
    copying hddm/models/hddm_truncated.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/models
    creating build/lib.macosx-10.6-x86_64-3.5/hddm/examples
    copying hddm/examples/__init__.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/examples
    copying hddm/examples/plot_posterior_quantiles.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/examples
    copying hddm/examples/postpred.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/examples
    copying hddm/examples/simple_model.py -> build/lib.macosx-10.6-x86_64-3.5/hddm/examples
    copying hddm/examples/cavanagh_theta_nn.csv -> build/lib.macosx-10.6-x86_64-3.5/hddm/examples
    copying hddm/examples/simple_difficulty.csv -> build/lib.macosx-10.6-x86_64-3.5/hddm/examples
    copying hddm/examples/simple_subjs_difficulty.csv -> build/lib.macosx-10.6-x86_64-3.5/hddm/examples
    copying hddm/examples/simple_subjs_difficulty_single.csv -> build/lib.macosx-10.6-x86_64-3.5/hddm/examples
    copying hddm/examples/simple_difficulty.conf -> build/lib.macosx-10.6-x86_64-3.5/hddm/examples
    running build_ext
    building 'wfpt' extension
    creating build/temp.macosx-10.6-x86_64-3.5
    creating build/temp.macosx-10.6-x86_64-3.5/src
    /usr/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I//anaconda/envs/Py3.5/include -arch x86_64 -I//anaconda/envs/Py3.5/lib/python3.5/site-packages/numpy/core/include -I//anaconda/envs/Py3.5/include/python3.5m -c src/wfpt.c -o build/temp.macosx-10.6-x86_64-3.5/src/wfpt.o
    clang: error: no such file or directory: 'src/wfpt.c'
    clang: error: no input files
    error: command '/usr/bin/clang' failed with exit status 1

    ----------------------------------------
Command "//anaconda/envs/Py3.5/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/_k/vhkrrz4d6nl6zgzw_hmd4sxh0000gn/T/pip-build-f542ng8s/HDDM/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/_k/vhkrrz4d6nl6zgzw_hmd4sxh0000gn/T/pip-baz18mcy-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/_k/vhkrrz4d6nl6zgzw_hmd4sxh0000gn/T/pip-build-f542ng8s/HDDM/
ronimaimon commented 6 years ago

I have the exact same issue on my Mac. clang: error: no such file or directory: 'src/wfpt.c'

Did anyone find a way around it?

twiecki commented 6 years ago

Why are you not installing using anaconda?

On Wed, Feb 14, 2018 at 5:49 PM, ronimaimon notifications@github.com wrote:

I have the exact same issue on my Mac. clang: error: no such file or directory: 'src/wfpt.c'

Did anyone find a way around it?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/hddm-devs/hddm/issues/41#issuecomment-365669982, or mute the thread https://github.com/notifications/unsubscribe-auth/AApJmDO7t51SEyWSlG3zvruPbx8STNQmks5tUw6BgaJpZM4MWtAf .

ronimaimon commented 6 years ago

I can install anaconda specifically for this but was hoping to have hddm installed together with the rest of my python packages..

On Wed, Feb 14, 2018 at 4:54 PM, Thomas Wiecki notifications@github.com wrote:

Why are you not installing using anaconda?

On Wed, Feb 14, 2018 at 5:49 PM, ronimaimon notifications@github.com wrote:

I have the exact same issue on my Mac. clang: error: no such file or directory: 'src/wfpt.c'

Did anyone find a way around it?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/hddm-devs/hddm/issues/41#issuecomment-365669982, or mute the thread https://github.com/notifications/unsubscribe-auth/ AApJmDO7t51SEyWSlG3zvruPbx8STNQmks5tUw6BgaJpZM4MWtAf .

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sammosummo commented 6 years ago

Unfortunately having one big python environment for all your needs is not very feasible. This is one of the major gripes about python for many people. I would recommend switching to anaconda permanently and creating virtual envs for your disparate projects. Personally I have a virtual env just for hddm related work.

-- Samuel R. Mathias, Ph.D. Associate Research Scientist (ARS) Neurocognition, Neurocomputation and Neurogenetics (n3) Division Yale University School of Medicine 40 Temple Street, Room 694 New Haven CT 06510 http://www.srmathias.com

From: ronimaimon notifications@github.com Sent: Wednesday, February 14, 2018 11:59:14 AM To: hddm-devs/hddm Cc: Subscribed Subject: Re: [hddm-devs/hddm] Installation problem (#41)

I can install anaconda specifically for this but was hoping to have hddm installed together with the rest of my python packages..

On Wed, Feb 14, 2018 at 4:54 PM, Thomas Wiecki notifications@github.com wrote:

Why are you not installing using anaconda?

On Wed, Feb 14, 2018 at 5:49 PM, ronimaimon notifications@github.com wrote:

I have the exact same issue on my Mac. clang: error: no such file or directory: 'src/wfpt.c'

Did anyone find a way around it?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/hddm-devs/hddm/issues/41#issuecomment-365669982, or mute the thread https://github.com/notifications/unsubscribe-auth/ AApJmDO7t51SEyWSlG3zvruPbx8STNQmks5tUw6BgaJpZM4MWtAf .

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twiecki commented 6 years ago

Yes, that's the best approach. Note that conda environments also work quite well.

On Wed, Feb 14, 2018 at 9:13 PM, Sam Mathias notifications@github.com wrote:

Unfortunately having one big python environment for all your needs is not very feasible. This is one of the major gripes about python for many people. I would recommend switching to anaconda permanently and creating virtual envs for your disparate projects. Personally I have a virtual env just for hddm related work.

-- Samuel R. Mathias, Ph.D. Associate Research Scientist (ARS) Neurocognition, Neurocomputation and Neurogenetics (n3) Division Yale University School of Medicine 40 Temple Street, Room 694 https://maps.google.com/?q=40+Temple+Street,+Room+694+%0D+New+Haven+CT+06510&entry=gmail&source=g New Haven CT 06510 http://www.srmathias.com

From: ronimaimon notifications@github.com Sent: Wednesday, February 14, 2018 11:59:14 AM To: hddm-devs/hddm Cc: Subscribed Subject: Re: [hddm-devs/hddm] Installation problem (#41)

I can install anaconda specifically for this but was hoping to have hddm installed together with the rest of my python packages..

On Wed, Feb 14, 2018 at 4:54 PM, Thomas Wiecki notifications@github.com wrote:

Why are you not installing using anaconda?

On Wed, Feb 14, 2018 at 5:49 PM, ronimaimon notifications@github.com wrote:

I have the exact same issue on my Mac. clang: error: no such file or directory: 'src/wfpt.c'

Did anyone find a way around it?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/hddm-devs/hddm/issues/41#issuecomment-365669982, or mute the thread https://github.com/notifications/unsubscribe-auth/ AApJmDO7t51SEyWSlG3zvruPbx8STNQmks5tUw6BgaJpZM4MWtAf .

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arthurprat commented 6 years ago

I have run in the same problem and I wanted to keep my pip workflow.

Apparently setup.py tries to install wfpt using Cython and 'src/wfpt.pyx', but if it cannot find Cython, it will try to use 'src/wfpt.c'. This file is not there, so it fails. Hence my solution was to install Cython using: pip install Cython

So far it is working. I hope nothing is broken under the hood...

birkin commented 5 years ago

I too had issues installing this in my 'normal' development setup of pip-installing into a virtual-environment on my mac. I wrote up notes detailing steps that worked for me.

cgc commented 5 years ago

Installing Cython first with pip install Cython resolved this issue for me. Might be worth modifying the pip documentation to recommend installing Cython in addition to the other packages? I'm happy to draft that pull request.