Installing HDDM for Windows with numpy error

[atuck...@gmail.com]

Hi all,

When I try to install the hddm modules for Windows using the commands:

pip install kabuki 

pip install hddm

for both I am getting an error RuntimeWarning: ParentModule 'numpy.disutils' not found while handling absolute import

Anybody know how to fix this?

Thank you,

Adrienne

[Thomas Wiecki]

Hi Adrienne,

Windows can be a little painful to set up. I suggest you install the anaconda python distribution instead of using the bare-bones version from python.org. You can find the installer here: http://docs.continuum.io/anaconda/install.html#windows-install and it should have most dependencies (except pymc). After that, can you do:

pip install pymc

pip install kabuki 

pip install hddm

And try again?

Thomas

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[atuck...@gmail.com]

Thank you for you help Thomas!

I uninstalled and resintalled Anaconda-64bit, making it my default python program, and rebooted the computer. Then when I try pip install pymc I get the following error....

Adrienne

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

C:\Anaconda\Scripts\pip-script.py run on 07/23/13 14:30:57

Downloading/unpacking pymc

  Running setup.py egg_info for package pymc

    No optimized BLAS or Lapack libraries found, building from source. This may take a while...

    No optimized BLAS or Lapack libraries found, building from source. This may take a while...

    running egg_info

    running build_src

    build_src

    building extension "pymc.flib" sources

    f2py options: []

      adding 'build\src.win-amd64-2.7\fortranobject.c' to sources.

      adding 'build\src.win-amd64-2.7' to include_dirs.

      adding 'build\src.win-amd64-2.7\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.win-amd64-2.7\fortranobject.c' to sources.

      adding 'build\src.win-amd64-2.7' to include_dirs.

      adding 'build\src.win-amd64-2.7\pymc\gp\linalg_utils-f2pywrappers.f' to sources.

    building extension "pymc.gp.incomplete_chol" sources

    f2py options: []

      adding 'build\src.win-amd64-2.7\fortranobject.c' to sources.

      adding 'build\src.win-amd64-2.7' to include_dirs.

      adding 'build\src.win-amd64-2.7\pymc\gp\incomplete_chol-f2pywrappers.f' to sources.

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

    f2py options: []

      adding 'build\src.win-amd64-2.7\fortranobject.c' to sources.

      adding 'build\src.win-amd64-2.7' to include_dirs.

      adding 'build\src.win-amd64-2.7\pymc\gp\cov_funs\isotropic_cov_funs-f2pywrappers.f' to sources.

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

    f2py options: []

      adding 'build\src.win-amd64-2.7\fortranobject.c' to sources.

      adding 'build\src.win-amd64-2.7' to include_dirs.

    build_src: building npy-pkg config files

    writing pip-egg-info\pymc.egg-info\PKG-INFO

    writing top-level names to pip-egg-info\pymc.egg-info\top_level.txt

    writing dependency_links to pip-egg-info\pymc.egg-info\dependency_links.txt

    warning: manifest_maker: standard file '-c' not found

    

    reading manifest file 'pip-egg-info\pymc.egg-info\SOURCES.txt'

    writing manifest file 'pip-egg-info\pymc.egg-info\SOURCES.txt'

    C:\Anaconda\lib\site-packages\numpy\distutils\system_info.py:564: UserWarning: Specified path C:/Program Files (x86)/Intel/Composer XE/mkl/lib/intel64 is invalid.

      warnings.warn('Specified path %s is invalid.' % d)

    C:\Anaconda\lib\site-packages\numpy\distutils\system_info.py:564: UserWarning: Specified path C:/Program Files (x86)/Intel/Composer XE/compiler/lib/intel64 is invalid.

      warnings.warn('Specified path %s is invalid.' % d)

    C:\Anaconda\lib\site-packages\numpy\distutils\system_info.py:564: UserWarning: Specified path C:/Program Files (x86)/Intel/Composer XE/mkl/include is invalid.

      warnings.warn('Specified path %s is invalid.' % d)

    C:\Anaconda\lib\site-packages\numpy\distutils\system_info.py:1408: UserWarning:

        Atlas (http://math-atlas.sourceforge.net/) libraries not found.

        Directories to search for the libraries can be specified in the

        numpy/distutils/site.cfg file (section [atlas]) or by setting

        the ATLAS environment variable.

      warnings.warn(AtlasNotFoundError.__doc__)

    C:\Anaconda\lib\site-packages\numpy\distutils\system_info.py:1419: UserWarning:

        Lapack (http://www.netlib.org/lapack/) libraries not found.

        Directories to search for the libraries can be specified in the

        numpy/distutils/site.cfg file (section [lapack]) or by setting

        the LAPACK environment variable.

      warnings.warn(LapackNotFoundError.__doc__)

    C:\Anaconda\lib\site-packages\numpy\distutils\system_info.py:1422: UserWarning:

        Lapack (http://www.netlib.org/lapack/) sources not found.

        Directories to search for the sources can be specified in the

        numpy/distutils/site.cfg file (section [lapack_src]) or by setting

        the LAPACK_SRC environment variable.

      warnings.warn(LapackSrcNotFoundError.__doc__)

    C:\Anaconda\lib\site-packages\numpy\distutils\system_info.py:495: UserWarning:

        Lapack (http://www.netlib.org/lapack/) libraries not found.

        Directories to search for the libraries can be specified in the

        numpy/distutils/site.cfg file (section [lapack]) or by setting

        the LAPACK environment variable.

      warnings.warn(self.notfounderror.__doc__)

  Source in c:\users\user\appdata\local\temp\pip-build-user\pymc has version 2.2, which satisfies requirement pymc

Installing collected packages: pymc

  Running setup.py install for pymc

    Running command C:\Anaconda\python.exe -c "import setuptools;__file__='c:\\users\\user\\appdata\\local\\temp\\pip-build-User\\pymc\\setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record c:\users\user\appdata\local\temp\pip-1qrd7q-record\install-record.txt --single-version-externally-managed

    No optimized BLAS or Lapack libraries found, building from source. This may take a while...

    No optimized BLAS or Lapack libraries found, building from source. This may take a while...

    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: []

      adding 'build\src.win-amd64-2.7\fortranobject.c' to sources.

      adding 'build\src.win-amd64-2.7' to include_dirs.

      adding 'build\src.win-amd64-2.7\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.win-amd64-2.7\fortranobject.c' to sources.

      adding 'build\src.win-amd64-2.7' to include_dirs.

      adding 'build\src.win-amd64-2.7\pymc\gp\linalg_utils-f2pywrappers.f' to sources.

    building extension "pymc.gp.incomplete_chol" sources

    f2py options: []

      adding 'build\src.win-amd64-2.7\fortranobject.c' to sources.

      adding 'build\src.win-amd64-2.7' to include_dirs.

      adding 'build\src.win-amd64-2.7\pymc\gp\incomplete_chol-f2pywrappers.f' to sources.

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

    f2py options: []

      adding 'build\src.win-amd64-2.7\fortranobject.c' to sources.

      adding 'build\src.win-amd64-2.7' to include_dirs.

      adding 'build\src.win-amd64-2.7\pymc\gp\cov_funs\isotropic_cov_funs-f2pywrappers.f' to sources.

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

    f2py options: []

      adding 'build\src.win-amd64-2.7\fortranobject.c' to sources.

      adding 'build\src.win-amd64-2.7' to include_dirs.

    build_src: building npy-pkg config files

    running build_py

    running build_ext

    Looking for python27.dll

    Cannot build msvcr library: "msvcr90d.dll" not found

    customize Mingw32CCompiler

    customize Mingw32CCompiler using build_ext

    customize GnuFCompiler

    Could not locate executable g77

    Could not locate executable f77

    customize IntelVisualFCompiler

    Could not locate executable ifort

    Could not locate executable ifl

    customize AbsoftFCompiler

    Could not locate executable f90

    customize CompaqVisualFCompiler

    Could not locate executable DF

    customize IntelItaniumVisualFCompiler

    Could not locate executable efl

    customize Gnu95FCompiler

    Found executable C:\Anaconda\Scripts\gfortran.bat

    Found executable C:\Anaconda\Scripts\gfortran.bat

    C:\Anaconda\lib\site-packages\numpy\distutils\system_info.py:564: UserWarning: Specified path C:/Program Files (x86)/Intel/Composer XE/mkl/lib/intel64 is invalid.

      warnings.warn('Specified path %s is invalid.' % d)

    C:\Anaconda\lib\site-packages\numpy\distutils\system_info.py:564: UserWarning: Specified path C:/Program Files (x86)/Intel/Composer XE/compiler/lib/intel64 is invalid.

      warnings.warn('Specified path %s is invalid.' % d)

    C:\Anaconda\lib\site-packages\numpy\distutils\system_info.py:564: UserWarning: Specified path C:/Program Files (x86)/Intel/Composer XE/mkl/include is invalid.

      warnings.warn('Specified path %s is invalid.' % d)

    C:\Anaconda\lib\site-packages\numpy\distutils\system_info.py:1408: UserWarning:

        Atlas (http://math-atlas.sourceforge.net/) libraries not found.

        Directories to search for the libraries can be specified in the

        numpy/distutils/site.cfg file (section [atlas]) or by setting

        the ATLAS environment variable.

      warnings.warn(AtlasNotFoundError.__doc__)

    C:\Anaconda\lib\site-packages\numpy\distutils\system_info.py:1419: UserWarning:

        Lapack (http://www.netlib.org/lapack/) libraries not found.

        Directories to search for the libraries can be specified in the

        numpy/distutils/site.cfg file (section [lapack]) or by setting

        the LAPACK environment variable.

      warnings.warn(LapackNotFoundError.__doc__)

    C:\Anaconda\lib\site-packages\numpy\distutils\system_info.py:1422: UserWarning:

        Lapack (http://www.netlib.org/lapack/) sources not found.

        Directories to search for the sources can be specified in the

        numpy/distutils/site.cfg file (section [lapack_src]) or by setting

        the LAPACK_SRC environment variable.

      warnings.warn(LapackSrcNotFoundError.__doc__)

    C:\Anaconda\lib\site-packages\numpy\distutils\system_info.py:495: UserWarning:

        Lapack (http://www.netlib.org/lapack/) libraries not found.

        Directories to search for the libraries can be specified in the

        numpy/distutils/site.cfg file (section [lapack]) or by setting

        the LAPACK environment variable.

      warnings.warn(self.notfounderror.__doc__)

    Traceback (most recent call last):

      File "<string>", line 1, in <module>

      File "c:\users\user\appdata\local\temp\pip-build-User\pymc\setup.py", line 134, in <module>

        **(config_dict))

      File "C:\Anaconda\lib\site-packages\numpy\distutils\core.py", line 186, in setup

        return old_setup(**new_attr)

      File "C:\Anaconda\lib\distutils\core.py", line 152, in setup

        dist.run_commands()

      File "C:\Anaconda\lib\distutils\dist.py", line 953, in run_commands

        self.run_command(cmd)

      File "C:\Anaconda\lib\distutils\dist.py", line 972, in run_command

        cmd_obj.run()

      File "C:\Anaconda\lib\site-packages\numpy\distutils\command\install.py", line 57, in run

        r = self.setuptools_run()

      File "C:\Anaconda\lib\site-packages\numpy\distutils\command\install.py", line 31, in setuptools_run

        return old_install_mod._install.run(self)

      File "C:\Anaconda\lib\distutils\command\install.py", line 563, in run

        self.run_command('build')

      File "C:\Anaconda\lib\distutils\cmd.py", line 326, in run_command

        self.distribution.run_command(command)

      File "C:\Anaconda\lib\distutils\dist.py", line 972, in run_command

        cmd_obj.run()

      File "C:\Anaconda\lib\site-packages\numpy\distutils\command\build.py", line 37, in run

        old_build.run(self)

      File "C:\Anaconda\lib\distutils\command\build.py", line 127, in run

        self.run_command(cmd_name)

      File "C:\Anaconda\lib\distutils\cmd.py", line 326, in run_command

        self.distribution.run_command(command)

      File "C:\Anaconda\lib\distutils\dist.py", line 972, in run_command

        cmd_obj.run()

      File "C:\Anaconda\lib\site-packages\numpy\distutils\command\build_ext.py", line 193, in run

        c_compiler=self.compiler)

      File "C:\Anaconda\lib\site-packages\numpy\distutils\fcompiler\__init__.py", line 839, in new_fcompiler

        c_compiler=c_compiler)

      File "C:\Anaconda\lib\site-packages\numpy\distutils\fcompiler\__init__.py", line 814, in get_default_fcompiler

        c_compiler=c_compiler)

      File "C:\Anaconda\lib\site-packages\numpy\distutils\fcompiler\__init__.py", line 763, in _find_existing_fcompiler

        c.customize(dist)

      File "C:\Anaconda\lib\site-packages\numpy\distutils\fcompiler\__init__.py", line 538, in customize

        self.set_libraries(self.get_libraries())

      File "C:\Anaconda\lib\site-packages\numpy\distutils\fcompiler\gnu.py", line 331, in get_libraries

        raise NotImplementedError("Only MS compiler supported with gfortran on win64")

    NotImplementedError: Only MS compiler supported with gfortran on win64

    Complete output from command C:\Anaconda\python.exe -c "import setuptools;__file__='c:\\users\\user\\appdata\\local\\temp\\pip-build-User\\pymc\\setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record c:\users\user\appdata\local\temp\pip-1qrd7q-record\install-record.txt --single-version-externally-managed:

    No optimized BLAS or Lapack libraries found, building from source. This may take a while...

No optimized BLAS or Lapack libraries found, building from source. This may take a while...

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: []

  adding 'build\src.win-amd64-2.7\fortranobject.c' to sources.

  adding 'build\src.win-amd64-2.7' to include_dirs.

  adding 'build\src.win-amd64-2.7\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.win-amd64-2.7\fortranobject.c' to sources.

  adding 'build\src.win-amd64-2.7' to include_dirs.

  adding 'build\src.win-amd64-2.7\pymc\gp\linalg_utils-f2pywrappers.f' to sources.

building extension "pymc.gp.incomplete_chol" sources

f2py options: []

  adding 'build\src.win-amd64-2.7\fortranobject.c' to sources.

  adding 'build\src.win-amd64-2.7' to include_dirs.

  adding 'build\src.win-amd64-2.7\pymc\gp\incomplete_chol-f2pywrappers.f' to sources.

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

f2py options: []

  adding 'build\src.win-amd64-2.7\fortranobject.c' to sources.

  adding 'build\src.win-amd64-2.7' to include_dirs.

  adding 'build\src.win-amd64-2.7\pymc\gp\cov_funs\isotropic_cov_funs-f2pywrappers.f' to sources.

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

f2py options: []

  adding 'build\src.win-amd64-2.7\fortranobject.c' to sources.

  adding 'build\src.win-amd64-2.7' to include_dirs.

build_src: building npy-pkg config files

running build_py

running build_ext

Looking for python27.dll

Cannot build msvcr library: "msvcr90d.dll" not found

customize Mingw32CCompiler

customize Mingw32CCompiler using build_ext

customize GnuFCompiler

Could not locate executable g77

Could not locate executable f77

customize IntelVisualFCompiler

Could not locate executable ifort

Could not locate executable ifl

customize AbsoftFCompiler

Could not locate executable f90

customize CompaqVisualFCompiler

Could not locate executable DF

customize IntelItaniumVisualFCompiler

Could not locate executable efl

customize Gnu95FCompiler

Found executable C:\Anaconda\Scripts\gfortran.bat

Found executable C:\Anaconda\Scripts\gfortran.bat

C:\Anaconda\lib\site-packages\numpy\distutils\system_info.py:564: UserWarning: Specified path C:/Program Files (x86)/Intel/Composer XE/mkl/lib/intel64 is invalid.

  warnings.warn('Specified path %s is invalid.' % d)

C:\Anaconda\lib\site-packages\numpy\distutils\system_info.py:564: UserWarning: Specified path C:/Program Files (x86)/Intel/Composer XE/compiler/lib/intel64 is invalid.

  warnings.warn('Specified path %s is invalid.' % d)

C:\Anaconda\lib\site-packages\numpy\distutils\system_info.py:564: UserWarning: Specified path C:/Program Files (x86)/Intel/Composer XE/mkl/include is invalid.

  warnings.warn('Specified path %s is invalid.' % d)

C:\Anaconda\lib\site-packages\numpy\distutils\system_info.py:1408: UserWarning:

    Atlas (http://math-atlas.sourceforge.net/) libraries not found.

    Directories to search for the libraries can be specified in the

    numpy/distutils/site.cfg file (section [atlas]) or by setting

    the ATLAS environment variable.

  warnings.warn(AtlasNotFoundError.__doc__)

C:\Anaconda\lib\site-packages\numpy\distutils\system_info.py:1419: UserWarning:

    Lapack (http://www.netlib.org/lapack/) libraries not found.

    Directories to search for the libraries can be specified in the

    numpy/distutils/site.cfg file (section [lapack]) or by setting

    the LAPACK environment variable.

  warnings.warn(LapackNotFoundError.__doc__)

C:\Anaconda\lib\site-packages\numpy\distutils\system_info.py:1422: UserWarning:

    Lapack (http://www.netlib.org/lapack/) sources not found.

    Directories to search for the sources can be specified in the

    numpy/distutils/site.cfg file (section [lapack_src]) or by setting

    the LAPACK_SRC environment variable.

  warnings.warn(LapackSrcNotFoundError.__doc__)

C:\Anaconda\lib\site-packages\numpy\distutils\system_info.py:495: UserWarning:

    Lapack (http://www.netlib.org/lapack/) libraries not found.

    Directories to search for the libraries can be specified in the

    numpy/distutils/site.cfg file (section [lapack]) or by setting

    the LAPACK environment variable.

  warnings.warn(self.notfounderror.__doc__)

Traceback (most recent call last):

  File "<string>", line 1, in <module>

  File "c:\users\user\appdata\local\temp\pip-build-User\pymc\setup.py", line 134, in <module>

    **(config_dict))

  File "C:\Anaconda\lib\site-packages\numpy\distutils\core.py", line 186, in setup

    return old_setup(**new_attr)

  File "C:\Anaconda\lib\distutils\core.py", line 152, in setup

    dist.run_commands()

  File "C:\Anaconda\lib\distutils\dist.py", line 953, in run_commands

    self.run_command(cmd)

  File "C:\Anaconda\lib\distutils\dist.py", line 972, in run_command

    cmd_obj.run()

  File "C:\Anaconda\lib\site-packages\numpy\distutils\command\install.py", line 57, in run

    r = self.setuptools_run()

  File "C:\Anaconda\lib\site-packages\numpy\distutils\command\install.py", line 31, in setuptools_run

    return old_install_mod._install.run(self)

  File "C:\Anaconda\lib\distutils\command\install.py", line 563, in run

    self.run_command('build')

  File "C:\Anaconda\lib\distutils\cmd.py", line 326, in run_command

    self.distribution.run_command(command)

  File "C:\Anaconda\lib\distutils\dist.py", line 972, in run_command

    cmd_obj.run()

  File "C:\Anaconda\lib\site-packages\numpy\distutils\command\build.py", line 37, in run

    old_build.run(self)

  File "C:\Anaconda\lib\distutils\command\build.py", line 127, in run

    self.run_command(cmd_name)

  File "C:\Anaconda\lib\distutils\cmd.py", line 326, in run_command

    self.distribution.run_command(command)

  File "C:\Anaconda\lib\distutils\dist.py", line 972, in run_command

    cmd_obj.run()

  File "C:\Anaconda\lib\site-packages\numpy\distutils\command\build_ext.py", line 193, in run

    c_compiler=self.compiler)

  File "C:\Anaconda\lib\site-packages\numpy\distutils\fcompiler\__init__.py", line 839, in new_fcompiler

    c_compiler=c_compiler)

  File "C:\Anaconda\lib\site-packages\numpy\distutils\fcompiler\__init__.py", line 814, in get_default_fcompiler

    c_compiler=c_compiler)

  File "C:\Anaconda\lib\site-packages\numpy\distutils\fcompiler\__init__.py", line 763, in _find_existing_fcompiler

    c.customize(dist)

  File "C:\Anaconda\lib\site-packages\numpy\distutils\fcompiler\__init__.py", line 538, in customize

    self.set_libraries(self.get_libraries())

  File "C:\Anaconda\lib\site-packages\numpy\distutils\fcompiler\gnu.py", line 331, in get_libraries

    raise NotImplementedError("Only MS compiler supported with gfortran on win64")

NotImplementedError: Only MS compiler supported with gfortran on win64

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

Command C:\Anaconda\python.exe -c "import setuptools;__file__='c:\\users\\user\\appdata\\local\\temp\\pip-build-User\\pymc\\setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record c:\users\user\appdata\local\temp\pip-1qrd7q-record\install-record.txt --single-version-externally-managed failed with error code 1 in c:\users\user\appdata\local\temp\pip-build-User\pymc

Exception information:

Traceback (most recent call last):

  File "C:\Anaconda\lib\site-packages\pip\basecommand.py", line 139, in main

    status = self.run(options, args)

  File "C:\Anaconda\lib\site-packages\pip\commands\install.py", line 271, in run

    requirement_set.install(install_options, global_options, root=options.root_path)

  File "C:\Anaconda\lib\site-packages\pip\req.py", line 1185, in install

    requirement.install(install_options, global_options, *args, **kwargs)

  File "C:\Anaconda\lib\site-packages\pip\req.py", line 592, in install

    cwd=self.source_dir, filter_stdout=self._filter_install, show_stdout=False)

  File "C:\Anaconda\lib\site-packages\pip\util.py", line 662, in call_subprocess

    % (command_desc, proc.returncode, cwd))

InstallationError: Command C:\Anaconda\python.exe -c "import setuptools;__file__='c:\\users\\user\\appdata\\local\\temp\\pip-build-User\\pymc\\setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record c:\users\user\appdata\local\temp\pip-1qrd7q-record\install-record.txt --single-version-externally-managed failed with error code 1 in c:\users\user\appdata\local\temp\pip-build-User\pymc

Op maandag 22 juli 2013 21:42:20 UTC+2 schreef Thomas het volgende:

[Thomas Wiecki]

Hi Adrienne,

Can you instead of pip install, try:

conda install pymc

and see if that works? If it does, try the pip install of kabuki and hddm.

Thomas

[atuck...@gmail.com]

Hi Thomas,

Thanks but still out of luck! When I type 

conda install pymc 

it says 'No packages found matching: pymc.'

Adrienne

[Thomas Wiecki]

Bummer. Can you try installing the MS compiler via visual studio express: https://www.microsoft.com/visualstudio/eng/downloads#d-express-windows-desktop

And then type pip install pymc again.

Thomas

[atuck...@gmail.com]

Hi Thomas,

Thanks for sticking with me on this. Turns out I had already installed VisualStudio. Over the past few days I have been installing, uninstalling, and reinstalling but still no dice. 

Adrienne

[Thomas Wiecki]

Hi Adrienne,

I tried compiling under windows but also no luck. I think you could try anaconda win 32 bit instead of 64. And then do conda install pymc.

Thomas

Thomas Wiecki

PhD candidate, Brown University

Quantitative Researcher, Quantopian Inc, Boston

[atuck...@gmail.com]

Progress :) ! With Anaconda 32-bit although I am unable to conda install pymc, I can, however,pip install pymc and I can also pip install kabuki.

Unfortunately I cannot pip install hddm nor can I conda install hddm.

Thank you Thomas,

Adrienne

[Thomas Wiecki]

Great! What's the error message when you do pip install hddm?

Thomas

[atuck...@gmail.com]

Hi Thomas,

The error message is:

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

C:\Anaconda\Scripts\pip-script.py run on 08/01/13 11:16:10

Downloading/unpacking hddm

  Running setup.py egg_info for package hddm

    running egg_info

    writing requirements to pip-egg-info\HDDM.egg-info\requires.txt

    writing pip-egg-info\HDDM.egg-info\PKG-INFO

    writing top-level names to pip-egg-info\HDDM.egg-info\top_level.txt

    writing dependency_links to pip-egg-info\HDDM.egg-info\dependency_links.txt

    warning: manifest_maker: standard file '-c' not found

    

    reading manifest file 'pip-egg-info\HDDM.egg-info\SOURCES.txt'

    writing manifest file 'pip-egg-info\HDDM.egg-info\SOURCES.txt'

  Source in c:\users\user\appdata\local\temp\pip-build-user\hddm has version 0.5, which satisfies requirement hddm

Requirement already satisfied (use --upgrade to upgrade): NumPy>=1.6.0 in c:\anaconda\lib\site-packages (from hddm)

Requirement already satisfied (use --upgrade to upgrade): SciPy>=0.6.0 in c:\anaconda\lib\site-packages (from hddm)

Requirement already satisfied (use --upgrade to upgrade): kabuki>=0.5 in c:\anaconda\lib\site-packages (from hddm)

Requirement already satisfied (use --upgrade to upgrade): PyMC==2.2 in c:\anaconda\lib\site-packages (from hddm)

Requirement already satisfied (use --upgrade to upgrade): pandas>=0.10.0 in c:\anaconda\lib\site-packages (from hddm)

Downloading/unpacking patsy (from hddm)

  Running setup.py egg_info for package patsy

    running egg_info

    writing requirements to pip-egg-info\patsy.egg-info\requires.txt

    writing pip-egg-info\patsy.egg-info\PKG-INFO

    writing top-level names to pip-egg-info\patsy.egg-info\top_level.txt

    writing dependency_links to pip-egg-info\patsy.egg-info\dependency_links.txt

    warning: manifest_maker: standard file '-c' not found

    

    reading manifest file 'pip-egg-info\patsy.egg-info\SOURCES.txt'

    reading manifest template 'MANIFEST.in'

    no previously-included directories found matching 'doc\_build'

    writing manifest file 'pip-egg-info\patsy.egg-info\SOURCES.txt'

  Source in c:\users\user\appdata\local\temp\pip-build-user\patsy has version 0.1.0, which satisfies requirement patsy (from hddm)

Requirement already satisfied (use --upgrade to upgrade): matplotlib>=1.0.0 in c:\anaconda\lib\site-packages (from kabuki>=0.5->hddm)

Installing collected packages: hddm, patsy

  Running setup.py install for hddm

    Running command C:\Anaconda\python.exe -c "import setuptools;__file__='c:\\users\\user\\appdata\\local\\temp\\pip-build-User\\hddm\\setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record c:\users\user\appdata\local\temp\pip-tkfrcb-record\install-record.txt --single-version-externally-managed

    running install

    running build

    running build_py

    running build_ext

    building 'cdfdif_wrapper' extension

    C:\Anaconda\Scripts\gcc.bat -mdll -O -Wall -IC:\Anaconda\lib\site-packages\numpy\core\include -IC:\Anaconda\include -IC:\Anaconda\PC -c src/cdfdif_wrapper.c -o build\temp.win32-2.7\Release\src\cdfdif_wrapper.o

    In file included from C:\Anaconda\lib\site-packages\numpy\core\include/numpy/ndarraytypes.h:1728:0,

                     from C:\Anaconda\lib\site-packages\numpy\core\include/numpy/ndarrayobject.h:17,

                     from C:\Anaconda\lib\site-packages\numpy\core\include/numpy/arrayobject.h:15,

                     from src/cdfdif_wrapper.c:314:

    C:\Anaconda\lib\site-packages\numpy\core\include/numpy/npy_deprecated_api.h:8:9: note: #pragma message: C:\Anaconda\lib\site-packages\numpy\core\include/numpy/npy_deprecated_api.h(8) : Warning Msg: Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION

    src/cdfdif_wrapper.c: In function '__Pyx_RaiseArgtupleInvalid':

    src/cdfdif_wrapper.c:4455:18: warning: unknown conversion type character 'z' in format [-Wformat]

    src/cdfdif_wrapper.c:4455:18: warning: format '%s' expects argument of type 'char *', but argument 5 has type 'Py_ssize_t' [-Wformat]

    src/cdfdif_wrapper.c:4455:18: warning: unknown conversion type character 'z' in format [-Wformat]

    src/cdfdif_wrapper.c:4455:18: warning: too many arguments for format [-Wformat-extra-args]

    src/cdfdif_wrapper.c: In function '__Pyx_BufFmt_ProcessTypeChunk':

    src/cdfdif_wrapper.c:4827:26: warning: unknown conversion type character 'z' in format [-Wformat]

    src/cdfdif_wrapper.c:4827:26: warning: unknown conversion type character 'z' in format [-Wformat]

    src/cdfdif_wrapper.c:4827:26: warning: too many arguments for format [-Wformat-extra-args]

    src/cdfdif_wrapper.c:4879:20: warning: unknown conversion type character 'z' in format [-Wformat]

    src/cdfdif_wrapper.c:4879:20: warning: unknown conversion type character 'z' in format [-Wformat]

    src/cdfdif_wrapper.c:4879:20: warning: too many arguments for format [-Wformat-extra-args]

    src/cdfdif_wrapper.c: In function '__pyx_buffmt_parse_array':

    src/cdfdif_wrapper.c:4939:25: warning: unknown conversion type character 'z' in format [-Wformat]

    src/cdfdif_wrapper.c:4939:25: warning: too many arguments for format [-Wformat-extra-args]

    src/cdfdif_wrapper.c: In function '__Pyx_GetBufferAndValidate':

    src/cdfdif_wrapper.c:5120:7: warning: unknown conversion type character 'z' in format [-Wformat]

    src/cdfdif_wrapper.c:5120:7: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'Py_ssize_t' [-Wformat]

    src/cdfdif_wrapper.c:5120:7: warning: unknown conversion type character 'z' in format [-Wformat]

    src/cdfdif_wrapper.c:5120:7: warning: too many arguments for format [-Wformat-extra-args]

    src/cdfdif_wrapper.c: In function '__Pyx_RaiseTooManyValuesError':

    src/cdfdif_wrapper.c:5323:18: warning: unknown conversion type character 'z' in format [-Wformat]

    src/cdfdif_wrapper.c:5323:18: warning: too many arguments for format [-Wformat-extra-args]

    src/cdfdif_wrapper.c: In function '__Pyx_RaiseNeedMoreValuesError':

    src/cdfdif_wrapper.c:5329:18: warning: unknown conversion type character 'z' in format [-Wformat]

    src/cdfdif_wrapper.c:5329:18: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'Py_ssize_t' [-Wformat]

    src/cdfdif_wrapper.c:5329:18: warning: too many arguments for format [-Wformat-extra-args]

    In file included from C:\Anaconda\lib\site-packages\numpy\core\include/numpy/ndarrayobject.h:26:0,

                     from C:\Anaconda\lib\site-packages\numpy\core\include/numpy/arrayobject.h:15,

                     from src/cdfdif_wrapper.c:314:

    src/cdfdif_wrapper.c: At top level:

    C:\Anaconda\lib\site-packages\numpy\core\include/numpy/__multiarray_api.h:1594:1: warning: '_import_array' defined but not used [-Wunused-function]

    In file included from C:\Anaconda\lib\site-packages\numpy\core\include/numpy/ufuncobject.h:311:0,

                     from src/cdfdif_wrapper.c:315:

    C:\Anaconda\lib\site-packages\numpy\core\include/numpy/__ufunc_api.h:236:1: warning: '_import_umath' defined but not used [-Wunused-function]

    src/cdfdif_wrapper.c: In function '__pyx_pw_14cdfdif_wrapper_1dmat_cdf_array':

    src/cdfdif_wrapper.c:1585:15: warning: '__pyx_v_w_outlier' may be used uninitialized in this function [-Wmaybe-uninitialized]

    src/cdfdif_wrapper.c:1343:10: note: '__pyx_v_w_outlier' was declared here

    src/cdfdif_wrapper.c:1296:110: warning: '__pyx_v_p_outlier' may be used uninitialized in this function [-Wmaybe-uninitialized]

    src/cdfdif_wrapper.c:1342:10: note: '__pyx_v_p_outlier' was declared here

    src/cdfdif_wrapper.c:1651:26: warning: '__pyx_v_st' may be used uninitialized in this function [-Wmaybe-uninitialized]

    src/cdfdif_wrapper.c:1341:10: note: '__pyx_v_st' was declared here

    src/cdfdif_wrapper.c:1649:24: warning: '__pyx_v_t' may be used uninitialized in this function [-Wmaybe-uninitialized]

    src/cdfdif_wrapper.c:1340:10: note: '__pyx_v_t' was declared here

    src/cdfdif_wrapper.c:1823:38: warning: '__pyx_v_sz' may be used uninitialized in this function [-Wmaybe-uninitialized]

    src/cdfdif_wrapper.c:1339:10: note: '__pyx_v_sz' was declared here

    src/cdfdif_wrapper.c:1814:36: warning: '__pyx_v_z' may be used uninitialized in this function [-Wmaybe-uninitialized]

    src/cdfdif_wrapper.c:1338:10: note: '__pyx_v_z' was declared here

    src/cdfdif_wrapper.c:1787:36: warning: '__pyx_v_a' may be used uninitialized in this function [-Wmaybe-uninitialized]

    src/cdfdif_wrapper.c:1337:10: note: '__pyx_v_a' was declared here

    src/cdfdif_wrapper.c:1805:38: warning: '__pyx_v_sv' may be used uninitialized in this function [-Wmaybe-uninitialized]

    src/cdfdif_wrapper.c:1336:10: note: '__pyx_v_sv' was declared here

    src/cdfdif_wrapper.c:1841:36: warning: '__pyx_v_v' may be used uninitialized in this function [-Wmaybe-uninitialized]

    src/cdfdif_wrapper.c:1335:10: note: '__pyx_v_v' was declared here

    C:\Anaconda\Scripts\gcc.bat -mdll -O -Wall -IC:\Anaconda\lib\site-packages\numpy\core\include -IC:\Anaconda\include -IC:\Anaconda\PC -c src/cdfdif.c -o build\temp.win32-2.7\Release\src\cdfdif.o

    src/cdfdif.c: In function 'cdfdif':

    src/cdfdif.c:218:30: warning: 'Fnew' may be used uninitialized in this function [-Wmaybe-uninitialized]

    writing build\temp.win32-2.7\Release\src\cdfdif_wrapper.def

    C:\Anaconda\Scripts\gcc.bat -shared -s build\temp.win32-2.7\Release\src\cdfdif_wrapper.o build\temp.win32-2.7\Release\src\cdfdif.o build\temp.win32-2.7\Release\src\cdfdif_wrapper.def -LC:\Anaconda\libs -LC:\Anaconda\PCbuild -lpython27 -lmsvcr90 -o build\lib.win32-2.7\cdfdif_wrapper.pyd

    build\temp.win32-2.7\Release\src\cdfdif_wrapper.o:cdfdif_wrapper.c:(.text+0x6002): undefined reference to `__imp__cdfdif'

    collect2.exe: error: ld returned 1 exit status

    error: command 'gcc' failed with exit status 1

    Complete output from command C:\Anaconda\python.exe -c "import setuptools;__file__='c:\\users\\user\\appdata\\local\\temp\\pip-build-User\\hddm\\setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record c:\users\user\appdata\local\temp\pip-tkfrcb-record\install-record.txt --single-version-externally-managed:

    running install

running build

running build_py

running build_ext

building 'cdfdif_wrapper' extension

C:\Anaconda\Scripts\gcc.bat -mdll -O -Wall -IC:\Anaconda\lib\site-packages\numpy\core\include -IC:\Anaconda\include -IC:\Anaconda\PC -c src/cdfdif_wrapper.c -o build\temp.win32-2.7\Release\src\cdfdif_wrapper.o

In file included from C:\Anaconda\lib\site-packages\numpy\core\include/numpy/ndarraytypes.h:1728:0,

                 from C:\Anaconda\lib\site-packages\numpy\core\include/numpy/ndarrayobject.h:17,

                 from C:\Anaconda\lib\site-packages\numpy\core\include/numpy/arrayobject.h:15,

                 from src/cdfdif_wrapper.c:314:

C:\Anaconda\lib\site-packages\numpy\core\include/numpy/npy_deprecated_api.h:8:9: note: #pragma message: C:\Anaconda\lib\site-packages\numpy\core\include/numpy/npy_deprecated_api.h(8) : Warning Msg: Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION

src/cdfdif_wrapper.c: In function '__Pyx_RaiseArgtupleInvalid':

src/cdfdif_wrapper.c:4455:18: warning: unknown conversion type character 'z' in format [-Wformat]

src/cdfdif_wrapper.c:4455:18: warning: format '%s' expects argument of type 'char *', but argument 5 has type 'Py_ssize_t' [-Wformat]

src/cdfdif_wrapper.c:4455:18: warning: unknown conversion type character 'z' in format [-Wformat]

src/cdfdif_wrapper.c:4455:18: warning: too many arguments for format [-Wformat-extra-args]

src/cdfdif_wrapper.c: In function '__Pyx_BufFmt_ProcessTypeChunk':

src/cdfdif_wrapper.c:4827:26: warning: unknown conversion type character 'z' in format [-Wformat]

src/cdfdif_wrapper.c:4827:26: warning: unknown conversion type character 'z' in format [-Wformat]

src/cdfdif_wrapper.c:4827:26: warning: too many arguments for format [-Wformat-extra-args]

src/cdfdif_wrapper.c:4879:20: warning: unknown conversion type character 'z' in format [-Wformat]

src/cdfdif_wrapper.c:4879:20: warning: unknown conversion type character 'z' in format [-Wformat]

src/cdfdif_wrapper.c:4879:20: warning: too many arguments for format [-Wformat-extra-args]

src/cdfdif_wrapper.c: In function '__pyx_buffmt_parse_array':

src/cdfdif_wrapper.c:4939:25: warning: unknown conversion type character 'z' in format [-Wformat]

src/cdfdif_wrapper.c:4939:25: warning: too many arguments for format [-Wformat-extra-args]

src/cdfdif_wrapper.c: In function '__Pyx_GetBufferAndValidate':

src/cdfdif_wrapper.c:5120:7: warning: unknown conversion type character 'z' in format [-Wformat]

src/cdfdif_wrapper.c:5120:7: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'Py_ssize_t' [-Wformat]

src/cdfdif_wrapper.c:5120:7: warning: unknown conversion type character 'z' in format [-Wformat]

src/cdfdif_wrapper.c:5120:7: warning: too many arguments for format [-Wformat-extra-args]

src/cdfdif_wrapper.c: In function '__Pyx_RaiseTooManyValuesError':

src/cdfdif_wrapper.c:5323:18: warning: unknown conversion type character 'z' in format [-Wformat]

src/cdfdif_wrapper.c:5323:18: warning: too many arguments for format [-Wformat-extra-args]

src/cdfdif_wrapper.c: In function '__Pyx_RaiseNeedMoreValuesError':

src/cdfdif_wrapper.c:5329:18: warning: unknown conversion type character 'z' in format [-Wformat]

src/cdfdif_wrapper.c:5329:18: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'Py_ssize_t' [-Wformat]

src/cdfdif_wrapper.c:5329:18: warning: too many arguments for format [-Wformat-extra-args]

In file included from C:\Anaconda\lib\site-packages\numpy\core\include/numpy/ndarrayobject.h:26:0,

                 from C:\Anaconda\lib\site-packages\numpy\core\include/numpy/arrayobject.h:15,

                 from src/cdfdif_wrapper.c:314:

src/cdfdif_wrapper.c: At top level:

C:\Anaconda\lib\site-packages\numpy\core\include/numpy/__multiarray_api.h:1594:1: warning: '_import_array' defined but not used [-Wunused-function]

In file included from C:\Anaconda\lib\site-packages\numpy\core\include/numpy/ufuncobject.h:311:0,

                 from src/cdfdif_wrapper.c:315:

C:\Anaconda\lib\site-packages\numpy\core\include/numpy/__ufunc_api.h:236:1: warning: '_import_umath' defined but not used [-Wunused-function]

src/cdfdif_wrapper.c: In function '__pyx_pw_14cdfdif_wrapper_1dmat_cdf_array':

src/cdfdif_wrapper.c:1585:15: warning: '__pyx_v_w_outlier' may be used uninitialized in this function [-Wmaybe-uninitialized]

src/cdfdif_wrapper.c:1343:10: note: '__pyx_v_w_outlier' was declared here

src/cdfdif_wrapper.c:1296:110: warning: '__pyx_v_p_outlier' may be used uninitialized in this function [-Wmaybe-uninitialized]

src/cdfdif_wrapper.c:1342:10: note: '__pyx_v_p_outlier' was declared here

src/cdfdif_wrapper.c:1651:26: warning: '__pyx_v_st' may be used uninitialized in this function [-Wmaybe-uninitialized]

src/cdfdif_wrapper.c:1341:10: note: '__pyx_v_st' was declared here

src/cdfdif_wrapper.c:1649:24: warning: '__pyx_v_t' may be used uninitialized in this function [-Wmaybe-uninitialized]

src/cdfdif_wrapper.c:1340:10: note: '__pyx_v_t' was declared here

src/cdfdif_wrapper.c:1823:38: warning: '__pyx_v_sz' may be used uninitialized in this function [-Wmaybe-uninitialized]

src/cdfdif_wrapper.c:1339:10: note: '__pyx_v_sz' was declared here

src/cdfdif_wrapper.c:1814:36: warning: '__pyx_v_z' may be used uninitialized in this function [-Wmaybe-uninitialized]

src/cdfdif_wrapper.c:1338:10: note: '__pyx_v_z' was declared here

src/cdfdif_wrapper.c:1787:36: warning: '__pyx_v_a' may be used uninitialized in this function [-Wmaybe-uninitialized]

src/cdfdif_wrapper.c:1337:10: note: '__pyx_v_a' was declared here

src/cdfdif_wrapper.c:1805:38: warning: '__pyx_v_sv' may be used uninitialized in this function [-Wmaybe-uninitialized]

src/cdfdif_wrapper.c:1336:10: note: '__pyx_v_sv' was declared here

src/cdfdif_wrapper.c:1841:36: warning: '__pyx_v_v' may be used uninitialized in this function [-Wmaybe-uninitialized]

src/cdfdif_wrapper.c:1335:10: note: '__pyx_v_v' was declared here

C:\Anaconda\Scripts\gcc.bat -mdll -O -Wall -IC:\Anaconda\lib\site-packages\numpy\core\include -IC:\Anaconda\include -IC:\Anaconda\PC -c src/cdfdif.c -o build\temp.win32-2.7\Release\src\cdfdif.o

src/cdfdif.c: In function 'cdfdif':

src/cdfdif.c:218:30: warning: 'Fnew' may be used uninitialized in this function [-Wmaybe-uninitialized]

writing build\temp.win32-2.7\Release\src\cdfdif_wrapper.def

C:\Anaconda\Scripts\gcc.bat -shared -s build\temp.win32-2.7\Release\src\cdfdif_wrapper.o build\temp.win32-2.7\Release\src\cdfdif.o build\temp.win32-2.7\Release\src\cdfdif_wrapper.def -LC:\Anaconda\libs -LC:\Anaconda\PCbuild -lpython27 -lmsvcr90 -o build\lib.win32-2.7\cdfdif_wrapper.pyd

build\temp.win32-2.7\Release\src\cdfdif_wrapper.o:cdfdif_wrapper.c:(.text+0x6002): undefined reference to `__imp__cdfdif'

collect2.exe: error: ld returned 1 exit status

error: command 'gcc' failed with exit status 1

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

Command C:\Anaconda\python.exe -c "import setuptools;__file__='c:\\users\\user\\appdata\\local\\temp\\pip-build-User\\hddm\\setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record c:\users\user\appdata\local\temp\pip-tkfrcb-record\install-record.txt --single-version-externally-managed failed with error code 1 in c:\users\user\appdata\local\temp\pip-build-User\hddm

Exception information:

Traceback (most recent call last):

  File "C:\Anaconda\lib\site-packages\pip\basecommand.py", line 139, in main

    status = self.run(options, args)

  File "C:\Anaconda\lib\site-packages\pip\commands\install.py", line 271, in run

    requirement_set.install(install_options, global_options, root=options.root_path)

  File "C:\Anaconda\lib\site-packages\pip\req.py", line 1185, in install

    requirement.install(install_options, global_options, *args, **kwargs)

  File "C:\Anaconda\lib\site-packages\pip\req.py", line 592, in install

    cwd=self.source_dir, filter_stdout=self._filter_install, show_stdout=False)

  File "C:\Anaconda\lib\site-packages\pip\util.py", line 662, in call_subprocess

    % (command_desc, proc.returncode, cwd))

InstallationError: Command C:\Anaconda\python.exe -c "import setuptools;__file__='c:\\users\\user\\appdata\\local\\temp\\pip-build-User\\hddm\\setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record c:\users\user\appdata\local\temp\pip-tkfrcb-record\install-record.txt --single-version-externally-managed failed with error code 1 in c:\users\user\appdata\local\temp\pip-build-User\hddm

Adrienne

[Thomas Wiecki]

I made an attempt to fix this. Can you try again, using:

pip install -U --no-deps git+https://github.com/hddm-devs/hddm.git@develop

And let me know if that helps.

Thomas

[atuck...@gmail.com]

Alas, no. I also downloaded Git but that didn't change anything.

C:\Anaconda\Scripts\pip-script.py run on 08/01/13 15:50:21

Downloading/unpacking git+https://github.com/hddm-devs/hddm.git@develop

  Cloning https://github.com/hddm-devs/hddm.git (to develop) to c:\users\user\appdata\local\temp\pip-lpow5b-build

Cannot find command 'git'

Exception information:

Traceback (most recent call last):

  File "C:\Anaconda\lib\site-packages\pip\basecommand.py", line 139, in main

    status = self.run(options, args)

  File "C:\Anaconda\lib\site-packages\pip\commands\install.py", line 266, in run

    requirement_set.prepare_files(finder, force_root_egg_info=self.bundle, bundle=self.bundle)

  File "C:\Anaconda\lib\site-packages\pip\req.py", line 1033, in prepare_files

    self.unpack_url(url, location, self.is_download)

  File "C:\Anaconda\lib\site-packages\pip\req.py", line 1154, in unpack_url

    return unpack_vcs_link(link, loc, only_download)

  File "C:\Anaconda\lib\site-packages\pip\download.py", line 373, in unpack_vcs_link

    vcs_backend.unpack(location)

  File "C:\Anaconda\lib\site-packages\pip\vcs\__init__.py", line 240, in unpack

    self.obtain(location)

  File "C:\Anaconda\lib\site-packages\pip\vcs\git.py", line 112, in obtain

    call_subprocess([self.cmd, 'clone', '-q', url, dest])

  File "C:\Anaconda\lib\site-packages\pip\vcs\__init__.py", line 110, in cmd

    command = find_command(self.name)

  File "C:\Anaconda\lib\site-packages\pip\util.py", line 107, in find_command

    raise BadCommand('Cannot find command %r' % cmd)

BadCommand: Cannot find command 'git'

[Thomas Wiecki]

Well, that's a different problem though (apparently anaconda does come with git).

Anyway, you can also just download a zipfile here:
https://github.com/hddm-devs/hddm/archive/develop.zip

and unpack it. Then execute cmd.exe to get a shell, cd into the hddm directory and type:

python setup.py build
python setup.py install

and see if that compiles (and installs).

Thanks for your patience here. The upside is that once this works I will be able to upload a new package with the fix that should install just fine on windows.

Thomas

[atuck...@gmail.com]

Thank you Thomas, it is compiled and installed :) !

Within Anaconda this works:

import pandas as pd

import matplotlib.pyplot as plt

This doesn't work

import hddm
It does say .....version '0.5.1.dev' but then it says .....warning you are trying to PyMC from inside its source....

Import Error: DLL Load Failed: The specified module could not be found.
that will be a neat trick if you can get anything to be just fine on windows :-P....
Adrienne

[Thomas Wiecki]

OK, this is a pymc problem. I assume you did use pip install pymc instead of conda install pymc, right?

In any case, while I investigate and try to upload a compiled version, you might want to give wakari.io a try. Essentially it's an IPython interpreter in your browser so you don't have to set up anything. I prepared environment here:
https://www.wakari.io/sharing/bundle/twiecki/hddm_demo

Which you can try by clicking on Run/Edit this notebook at the top. Let me know if that does or does not work.

Thomas

[AJA]

Hi Thomas (and Adrienne),

I have also been trying to install on Windows and am having many of the same problems. I have tried all the work arounds you suggested to Adrienne with no success. I am not sure if it helps the issue any (probably doesn't) but I did have this working on my Windows computer earlier this year (I think int was hddm version 4.1), and everything seemed to be working just fine. I had to wipe some things of my PC recently and now when I tried to re-install these programs I get the error messages the same as posted above.

Again, not sure if this helps isolate any problems or not but hopefully it does. From what I have seen the program looks and works great!

Thanks

AJA

[Thomas Wiecki]

Hi all,

Sorry for the installation woes. I'm pretty sure that this is unrelated to HDDM as the problems occur with installing pymc.

Anaconda had support for pymc but the current version (1.6) hasn't updated it yet. I opened an issue here:
https://github.com/ContinuumIO/anaconda-issues/issues/7 but it hasn't received any love.

But since this worked with an older anaconda version you could try install anaconda 1.5 instead (with numpy 1.6):
http://repo.continuum.io/archive/Anaconda-1.5.0-Windows-x86.exe

and see if 'conda install pymc' works. If it does, try 'pip install kabuki' and then download hddm develop from: https://github.com/hddm-devs/hddm/archive/develop.zip

and unpack it. Then execute cmd.exe to get a shell, cd into the hddm directory and type:

python setup.py build
python setup.py install

When reporting problems with this, please make sure to include the full error message and which command triggered it.

Thomas

[AJA]

Thanks,

Sorry to be a pain, I didn't want to repeat too many of the same error messages as above. In any case, the older version of anaconda worked in that I could pip install pymc and pip install kabuki. 

However, after downloading the zip file you linked, I get errors when using python setup.py build and python setup.py install.

The error messages from each command are in the attached text file.

thanks again

[Thomas Wiecki]

Try running: setup.py build -c msvc -p win32
to compile hddm. Does that produce a different outcome?

[AJA]

That command gives the following error message

error: Unable to find vcvarsall.bat

...

[Thomas Wiecki]

I might have misinterpreted what the problem was.

Did you install mingw32 by hand? Not sure if there is one that also comes with anaconda and the one you have is incompatible. So maybe try removing that and seeing if the anaconda compiler gets picked up.

Thomas

Thomas Wiecki

[AJA]

Yes, that was absolutely the problem. So now everything has installed (i.e. pip install pymc, pip install kabuki and python setup.py build and install).

However, as mentioned in earlier posts, it is now saying "Warming you are trying to import pymc from within its own source tree" Let me know if you need specifics, but it sounds like you already knew that was the problem.

Andy

...

[Thomas Wiecki]

So I assume this happens no matter from where you launch ipython?

Otherwise, instead of pip install pymc, try conda install pymc (best to run pip uninstall pymc before to clean it up).

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[AJA]

Actually, conda install pymc doesn't work for me. It gives a message along the lines of "can't find a package that meets the requirements".

Sorry I have been uninstalling and re-installing various python packages to see I could find one that works so I don't have the exact error message for you (but can get it if you need it). Like I said I had it working once before and I am certain that I was using enthought rather than andaconda. However, even trying some of the recent installers from enthought isn't producing any results.

...

[Thomas Wiecki]

So the current problem is still the pymc error message, can't import from source directory?

Thomas

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