[Neuroimaging] Dipy installation problem
=?gb2312?B?QWRhbSBSeWJpqL1za2k=?=
adam.rybinski at outlook.com
Thu Dec 10 04:35:09 EST 2015
Hi,I remember having similar problem on Windows, it was while back ago, amd now I'm on linux most of the time.Eventually, the way I ran dipy on Windows was using anaconda 2.7, and then installing compiler for Python 2.7 in Windows https://www.microsoft.com/en-us/download/details.aspx?id=44266
I couldn't find microsoft compiler for Python 3.5---this one is somehow bundled with their Visual Studio Python IDE I think.
So If you don't care that much about Python version, try:
conda create --name python2 python=2.7
activate python2
pip install nibabel dipy (and all other dependencies you need)
I hope it helps,
Adam
> From: matthew.brett at gmail.com
> Date: Wed, 9 Dec 2015 22:01:11 -0800
> To: neuroimaging at python.org
> Subject: Re: [Neuroimaging] Dipy installation problem
>
> Hi,
>
> Thanks for the report.
>
> On Wed, Dec 9, 2015 at 8:33 AM, ÁÖÁxºê <b02207006 at ntu.edu.tw> wrote:
> > Hi, I got a problem while installing Dipy package on my Windows x64 system.
> > I've solved the problem like "unable to find vcvarsall.bat" by solutions
> > online.
> > That is, the distutils.cfg has been made.
> >
> > But now new problem pops up...
> > Error information like£º"TypeError: unoderable types...." and "failed
> > building wheel for dipy."shows
> > and I can not find usable solution online.
> > The followings are the full error information. (but some of this limited by
> > the capacity of CMD I think)
> >
> >
> > ts
> > copying dipy\viz\tests\test_fvtk_utils.py ->
> > build\lib.win32-3.5\dipy\viz\test
> > s
> > copying dipy\viz\tests\test_fvtk_widgets.py ->
> > build\lib.win32-3.5\dipy\viz\te
> > sts
> > copying dipy\viz\tests\test_fvtk_window.py ->
> > build\lib.win32-3.5\dipy\viz\tes
> > ts
> > copying dipy\viz\tests\test_regtools.py ->
> > build\lib.win32-3.5\dipy\viz\tests
> > copying dipy\viz\tests\__init__.py -> build\lib.win32-3.5\dipy\viz\tests
> > creating build\lib.win32-3.5\dipy\testing
> > copying dipy\testing\decorators.py -> build\lib.win32-3.5\dipy\testing
> > copying dipy\testing\memory.py -> build\lib.win32-3.5\dipy\testing
> > copying dipy\testing\spherepoints.py -> build\lib.win32-3.5\dipy\testing
> > copying dipy\testing\__init__.py -> build\lib.win32-3.5\dipy\testing
> > creating build\lib.win32-3.5\dipy\testing\tests
> > copying dipy\testing\tests\test_decorators.py ->
> > build\lib.win32-3.5\dipy\test
> > ing\tests
> > copying dipy\testing\tests\test_memory.py ->
> > build\lib.win32-3.5\dipy\testing\
> > tests
> > copying dipy\testing\tests\__init__.py ->
> > build\lib.win32-3.5\dipy\testing\tes
> > ts
> > creating build\lib.win32-3.5\dipy\boots
> > copying dipy\boots\resampling.py -> build\lib.win32-3.5\dipy\boots
> > copying dipy\boots\__init__.py -> build\lib.win32-3.5\dipy\boots
> > creating build\lib.win32-3.5\dipy\data
> > copying dipy\data\fetcher.py -> build\lib.win32-3.5\dipy\data
> > copying dipy\data\__init__.py -> build\lib.win32-3.5\dipy\data
> > creating build\lib.win32-3.5\dipy\utils
> > copying dipy\utils\arrfuncs.py -> build\lib.win32-3.5\dipy\utils
> > copying dipy\utils\optpkg.py -> build\lib.win32-3.5\dipy\utils
> > copying dipy\utils\six.py -> build\lib.win32-3.5\dipy\utils
> > copying dipy\utils\tripwire.py -> build\lib.win32-3.5\dipy\utils
> > copying dipy\utils\_importlib.py -> build\lib.win32-3.5\dipy\utils
> > copying dipy\utils\__init__.py -> build\lib.win32-3.5\dipy\utils
> > creating build\lib.win32-3.5\dipy\utils\tests
> > copying dipy\utils\tests\test_arrfuncs.py ->
> > build\lib.win32-3.5\dipy\utils\te
> > sts
> > copying dipy\utils\tests\test_tripwire.py ->
> > build\lib.win32-3.5\dipy\utils\te
> > sts
> > copying dipy\utils\tests\__init__.py ->
> > build\lib.win32-3.5\dipy\utils\tests
> > creating build\lib.win32-3.5\dipy\fixes
> > copying dipy\fixes\argparse.py -> build\lib.win32-3.5\dipy\fixes
> > copying dipy\fixes\__init__.py -> build\lib.win32-3.5\dipy\fixes
> > creating build\lib.win32-3.5\dipy\external
> > copying dipy\external\fsl.py -> build\lib.win32-3.5\dipy\external
> > copying dipy\external\__init__.py -> build\lib.win32-3.5\dipy\external
> > creating build\lib.win32-3.5\dipy\external\tests
> > copying dipy\external\tests\__init__.py ->
> > build\lib.win32-3.5\dipy\external\t
> > ests
> > creating build\lib.win32-3.5\dipy\segment
> > copying dipy\segment\clustering.py -> build\lib.win32-3.5\dipy\segment
> > copying dipy\segment\mask.py -> build\lib.win32-3.5\dipy\segment
> > copying dipy\segment\metric.py -> build\lib.win32-3.5\dipy\segment
> > copying dipy\segment\quickbundles.py -> build\lib.win32-3.5\dipy\segment
> > copying dipy\segment\threshold.py -> build\lib.win32-3.5\dipy\segment
> > copying dipy\segment\__init__.py -> build\lib.win32-3.5\dipy\segment
> > creating build\lib.win32-3.5\dipy\segment\benchmarks
> > copying dipy\segment\benchmarks\bench_quickbundles.py ->
> > build\lib.win32-3.5\d
> > ipy\segment\benchmarks
> > copying dipy\segment\benchmarks\__init__.py ->
> > build\lib.win32-3.5\dipy\segmen
> > t\benchmarks
> > creating build\lib.win32-3.5\dipy\segment\tests
> > copying dipy\segment\tests\test_clustering.py ->
> > build\lib.win32-3.5\dipy\segm
> > ent\tests
> > copying dipy\segment\tests\test_feature.py ->
> > build\lib.win32-3.5\dipy\segment
> > \tests
> > copying dipy\segment\tests\test_mask.py ->
> > build\lib.win32-3.5\dipy\segment\te
> > sts
> > copying dipy\segment\tests\test_metric.py ->
> > build\lib.win32-3.5\dipy\segment\
> > tests
> > copying dipy\segment\tests\test_qb.py ->
> > build\lib.win32-3.5\dipy\segment\test
> > s
> > copying dipy\segment\tests\test_quickbundles.py ->
> > build\lib.win32-3.5\dipy\se
> > gment\tests
> > copying dipy\segment\tests\__init__.py ->
> > build\lib.win32-3.5\dipy\segment\tes
> > ts
> > creating build\lib.win32-3.5\dipy\sims
> > copying dipy\sims\phantom.py -> build\lib.win32-3.5\dipy\sims
> > copying dipy\sims\voxel.py -> build\lib.win32-3.5\dipy\sims
> > copying dipy\sims\__init__.py -> build\lib.win32-3.5\dipy\sims
> > creating build\lib.win32-3.5\dipy\sims\tests
> > copying dipy\sims\tests\test_phantom.py ->
> > build\lib.win32-3.5\dipy\sims\tests
> >
> > copying dipy\sims\tests\test_voxel.py ->
> > build\lib.win32-3.5\dipy\sims\tests
> > copying dipy\sims\tests\__init__.py -> build\lib.win32-3.5\dipy\sims\tests
> > creating build\lib.win32-3.5\dipy\denoise
> > copying dipy\denoise\nlmeans.py -> build\lib.win32-3.5\dipy\denoise
> > copying dipy\denoise\noise_estimate.py -> build\lib.win32-3.5\dipy\denoise
> > copying dipy\denoise\__init__.py -> build\lib.win32-3.5\dipy\denoise
> > creating build\lib.win32-3.5\dipy\denoise\tests
> > copying dipy\denoise\tests\test_denoise.py ->
> > build\lib.win32-3.5\dipy\denoise
> > \tests
> > copying dipy\denoise\tests\test_nlmeans.py ->
> > build\lib.win32-3.5\dipy\denoise
> > \tests
> > copying dipy\denoise\tests\test_noise_estimate.py ->
> > build\lib.win32-3.5\dipy\
> > denoise\tests
> > copying dipy\denoise\tests\__init__.py ->
> > build\lib.win32-3.5\dipy\denoise\tes
> > ts
> > creating build\lib.win32-3.5\dipy\data\files
> > copying dipy\data\files\55dir_grad.bval ->
> > build\lib.win32-3.5\dipy\data\files
> >
> > copying dipy\data\files\55dir_grad.bvec ->
> > build\lib.win32-3.5\dipy\data\files
> >
> > copying dipy\data\files\aniso_vox.nii.gz ->
> > build\lib.win32-3.5\dipy\data\file
> > s
> > copying dipy\data\files\C.npy -> build\lib.win32-3.5\dipy\data\files
> > copying dipy\data\files\C1.pkl.gz -> build\lib.win32-3.5\dipy\data\files
> > copying dipy\data\files\C3.pkl.gz -> build\lib.win32-3.5\dipy\data\files
> > copying dipy\data\files\cb_2.npz -> build\lib.win32-3.5\dipy\data\files
> > copying dipy\data\files\circle.npy -> build\lib.win32-3.5\dipy\data\files
> > copying dipy\data\files\dipy_colormaps.json ->
> > build\lib.win32-3.5\dipy\data\f
> > iles
> > copying dipy\data\files\dsi4169_b_table.txt ->
> > build\lib.win32-3.5\dipy\data\f
> > iles
> > copying dipy\data\files\dsi515_b_table.txt ->
> > build\lib.win32-3.5\dipy\data\fi
> > les
> > copying dipy\data\files\eg_3voxels.pkl ->
> > build\lib.win32-3.5\dipy\data\files
> > copying dipy\data\files\evenly_distributed_sphere_362.npz ->
> > build\lib.win32-3
> > .5\dipy\data\files
> > copying dipy\data\files\evenly_distributed_sphere_642.npz ->
> > build\lib.win32-3
> > .5\dipy\data\files
> > copying dipy\data\files\evenly_distributed_sphere_724.npz ->
> > build\lib.win32-3
> > .5\dipy\data\files
> > copying dipy\data\files\fib0.pkl.gz -> build\lib.win32-3.5\dipy\data\files
> > copying dipy\data\files\fib1.pkl.gz -> build\lib.win32-3.5\dipy\data\files
> > copying dipy\data\files\fib2.pkl.gz -> build\lib.win32-3.5\dipy\data\files
> > copying dipy\data\files\func_coef.nii.gz ->
> > build\lib.win32-3.5\dipy\data\file
> > s
> > copying dipy\data\files\func_discrete.nii.gz ->
> > build\lib.win32-3.5\dipy\data\
> > files
> > copying dipy\data\files\grad_514.txt ->
> > build\lib.win32-3.5\dipy\data\files
> > copying dipy\data\files\gtab_3shell.txt ->
> > build\lib.win32-3.5\dipy\data\files
> >
> > copying dipy\data\files\gtab_isbi2013_2shell.txt ->
> > build\lib.win32-3.5\dipy\d
> > ata\files
> > copying dipy\data\files\gtab_taiwan_dsi.txt ->
> > build\lib.win32-3.5\dipy\data\f
> > iles
> > copying dipy\data\files\life_matlab_rmse.npy ->
> > build\lib.win32-3.5\dipy\data\
> > files
> > copying dipy\data\files\life_matlab_weights.npy ->
> > build\lib.win32-3.5\dipy\da
> > ta\files
> > copying dipy\data\files\repulsion100.npz ->
> > build\lib.win32-3.5\dipy\data\file
> > s
> > copying dipy\data\files\repulsion724.npz ->
> > build\lib.win32-3.5\dipy\data\file
> > s
> > copying dipy\data\files\S0_10slices.nii.gz ->
> > build\lib.win32-3.5\dipy\data\fi
> > les
> > copying dipy\data\files\ScannerVectors_GQI101.txt ->
> > build\lib.win32-3.5\dipy\
> > data\files
> > copying dipy\data\files\small_101D.bval ->
> > build\lib.win32-3.5\dipy\data\files
> >
> > copying dipy\data\files\small_101D.bvec ->
> > build\lib.win32-3.5\dipy\data\files
> >
> > copying dipy\data\files\small_101D.nii.gz ->
> > build\lib.win32-3.5\dipy\data\fil
> > es
> > copying dipy\data\files\small_25.bval ->
> > build\lib.win32-3.5\dipy\data\files
> > copying dipy\data\files\small_25.bvec ->
> > build\lib.win32-3.5\dipy\data\files
> > copying dipy\data\files\small_25.nii.gz ->
> > build\lib.win32-3.5\dipy\data\files
> >
> > copying dipy\data\files\small_64D.bvals.npy ->
> > build\lib.win32-3.5\dipy\data\f
> > iles
> > copying dipy\data\files\small_64D.gradients.npy ->
> > build\lib.win32-3.5\dipy\da
> > ta\files
> > copying dipy\data\files\small_64D.nii ->
> > build\lib.win32-3.5\dipy\data\files
> > copying dipy\data\files\sphere_grad.txt ->
> > build\lib.win32-3.5\dipy\data\files
> >
> > copying dipy\data\files\t1_coronal_slice.npy ->
> > build\lib.win32-3.5\dipy\data\
> > files
> > copying dipy\data\files\test_piesno.nii.gz ->
> > build\lib.win32-3.5\dipy\data\fi
> > les
> > copying dipy\data\files\tracks300.trk ->
> > build\lib.win32-3.5\dipy\data\files
> > running build_ext
> > Traceback (most recent call last):
> > File "<string>", line 1, in <module>
> > File
> > "C:\Users\andylin\AppData\Local\Temp\pip-build-8ygf1kth\dipy\setup.py",
> > line 241, in <module>
> > main(**extra_setuptools_args)
> > File
> > "C:\Users\andylin\AppData\Local\Temp\pip-build-8ygf1kth\dipy\setup.py",
> > line 234, in main
> > **extra_args
> > File "C:\Users\andylin\Anaconda3\lib\distutils\core.py", line 148, in
> > setup
> > dist.run_commands()
> > File "C:\Users\andylin\Anaconda3\lib\distutils\dist.py", line 955, in
> > run_co
> > mmands
> > self.run_command(cmd)
> > File "C:\Users\andylin\Anaconda3\lib\distutils\dist.py", line 974, in
> > run_co
> > mmand
> > cmd_obj.run()
> > File
> > "C:\Users\andylin\Anaconda3\lib\site-packages\wheel\bdist_wheel.py", li
> > ne 176, in run
> > self.run_command('build')
> > File "C:\Users\andylin\Anaconda3\lib\distutils\cmd.py", line 313, in
> > run_com
> > mand
> > self.distribution.run_command(command)
> > File "C:\Users\andylin\Anaconda3\lib\distutils\dist.py", line 974, in
> > run_co
> > mmand
> > cmd_obj.run()
> > File "C:\Users\andylin\Anaconda3\lib\distutils\command\build.py", line
> > 135,
> > in run
> > self.run_command(cmd_name)
> > File "C:\Users\andylin\Anaconda3\lib\distutils\cmd.py", line 313, in
> > run_com
> > mand
> > self.distribution.run_command(command)
> > File "C:\Users\andylin\Anaconda3\lib\distutils\dist.py", line 974, in
> > run_co
> > mmand
> > cmd_obj.run()
> > File "C:\Users\andylin\Anaconda3\lib\distutils\command\build_ext.py",
> > line 3
> > 07, in run
> > force=self.force)
> > File "C:\Users\andylin\Anaconda3\lib\distutils\ccompiler.py", line 1031,
> > in
> > new_compiler
> > return klass(None, dry_run, force)
> > File "C:\Users\andylin\Anaconda3\lib\distutils\cygwinccompiler.py", line
> > 282
> > , in __init__
> > CygwinCCompiler.__init__ (self, verbose, dry_run, force)
> > File "C:\Users\andylin\Anaconda3\lib\distutils\cygwinccompiler.py", line
> > 126
> > , in __init__
> > if self.ld_version >= "2.10.90":
> > TypeError: unorderable types: NoneType() >= str()
> >
> > ----------------------------------------
> > Failed building wheel for dipy
> > Failed to build dipy
> > Installing collected packages: dipy
> > Running setup.py install for dipy
> > Complete output from command C:\Users\andylin\Anaconda3\python.exe -c
> > "impor
> > t setuptools,
> > tokenize;__file__='C:\\Users\\andylin\\AppData\\Local\\Temp\\pip-b
> > uild-8ygf1kth\\dipy\\setup.py';exec(compile(getattr(tokenize, 'open',
> > open)(__fi
> > le__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record
> > C:\User
> > s\andylin\AppData\Local\Temp\pip-r_4d6qec-record\install-record.txt
> > --single-ver
> > sion-externally-managed --compile:
> > running install
> > running build
> > running build_py
> > running build_ext
> > Traceback (most recent call last):
> > File "<string>", line 1, in <module>
> > File
> > "C:\Users\andylin\AppData\Local\Temp\pip-build-8ygf1kth\dipy\setup.py
> > ", line 241, in <module>
> > main(**extra_setuptools_args)
> > File
> > "C:\Users\andylin\AppData\Local\Temp\pip-build-8ygf1kth\dipy\setup.py
> > ", line 234, in main
> > **extra_args
> > File "C:\Users\andylin\Anaconda3\lib\distutils\core.py", line 148, in
> > setu
> > p
> > dist.run_commands()
> > File "C:\Users\andylin\Anaconda3\lib\distutils\dist.py", line 955, in
> > run_
> > commands
> > self.run_command(cmd)
> > File "C:\Users\andylin\Anaconda3\lib\distutils\dist.py", line 974, in
> > run_
> > command
> > cmd_obj.run()
> > File
> > "C:\Users\andylin\AppData\Local\Temp\pip-build-8ygf1kth\dipy\setup.py
> > ", line 153, in run
> > install.install.run(self)
> > File
> > "C:\Users\andylin\Anaconda3\lib\site-packages\setuptools-18.5-py3.5.e
> > gg\setuptools\command\install.py", line 61, in run
> > File "C:\Users\andylin\Anaconda3\lib\distutils\command\install.py",
> > line 5
> > 39, in run
> > self.run_command('build')
> > File "C:\Users\andylin\Anaconda3\lib\distutils\cmd.py", line 313, in
> > run_c
> > ommand
> > self.distribution.run_command(command)
> > File "C:\Users\andylin\Anaconda3\lib\distutils\dist.py", line 974, in
> > run_
> > command
> > cmd_obj.run()
> > File "C:\Users\andylin\Anaconda3\lib\distutils\command\build.py", line
> > 135
> > , in run
> > self.run_command(cmd_name)
> > File "C:\Users\andylin\Anaconda3\lib\distutils\cmd.py", line 313, in
> > run_c
> > ommand
> > self.distribution.run_command(command)
> > File "C:\Users\andylin\Anaconda3\lib\distutils\dist.py", line 974, in
> > run_
> > command
> > cmd_obj.run()
> > File "C:\Users\andylin\Anaconda3\lib\distutils\command\build_ext.py",
> > line
> > 307, in run
> > force=self.force)
> > File "C:\Users\andylin\Anaconda3\lib\distutils\ccompiler.py", line
> > 1031, i
> > n new_compiler
> > return klass(None, dry_run, force)
> > File "C:\Users\andylin\Anaconda3\lib\distutils\cygwinccompiler.py",
> > line 2
> > 82, in __init__
> > CygwinCCompiler.__init__ (self, verbose, dry_run, force)
> > File "C:\Users\andylin\Anaconda3\lib\distutils\cygwinccompiler.py",
> > line 1
> > 26, in __init__
> > if self.ld_version >= "2.10.90":
> > TypeError: unorderable types: NoneType() >= str()
> >
> > ----------------------------------------
> > Command "C:\Users\andylin\Anaconda3\python.exe -c "import setuptools,
> > tokenize;_
> > _file__='C:\\Users\\andylin\\AppData\\Local\\Temp\\pip-build-8ygf1kth\\dipy\\set
> > up.py';exec(compile(getattr(tokenize, 'open',
> > open)(__file__).read().replace('\r
> > \n', '\n'), __file__, 'exec'))" install --record
> > C:\Users\andylin\AppData\Local\
> > Temp\pip-r_4d6qec-record\install-record.txt
> > --single-version-externally-managed
> > --compile" failed with error code 1 in
> > C:\Users\andylin\AppData\Local\Temp\pip-b
> > uild-8ygf1kth\dipy
> >
> > C:\Users\andylin\Anaconda3>
>
> I'm afraid I don't personally use Anaconda, so I haven't seen an error
> like this.
>
> Have you tried installing any other Python packages that need compilation?
>
> Best,
>
> Matthew
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
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