[Neuroimaging] Dipy installation problem
Matthew Brett
matthew.brett at gmail.com
Thu Dec 10 01:01:11 EST 2015
Hi,
Thanks for the report.
On Wed, Dec 9, 2015 at 8:33 AM, 林義宏 <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："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
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