Hi all,
I am having a problem in installing whitematteranalysis with pip as follows;
(base) C:\Users\kidokoro_win> pip install git+https://github.com/SlicerDMRI/whitematteranalysis.git
Collecting git+https://github.com/SlicerDMRI/whitematteranalysis.git
Cloning GitHub - SlicerDMRI/whitematteranalysis: White matter tractography clustering and more... to c:\users\kidokoro_win\appdata\local\temp\pip-req-build-w2zcv6au
Running command git clone --filter=blob:none --quiet GitHub - SlicerDMRI/whitematteranalysis: White matter tractography clustering and more... ‘C:\Users\kidokoro_win\AppData\Local\Temp\pip-req-build-w2zcv6au’
Resolved GitHub - SlicerDMRI/whitematteranalysis: White matter tractography clustering and more... to commit 5bbe6a17fc37e68530fb578476339943e5cc57c4
Preparing metadata (setup.py) … done
Collecting cython
Using cached Cython-0.29.33-py2.py3-none-any.whl (987 kB)
Requirement already satisfied: numpy in c:\users\kidokoro_win\miniconda3\lib\site-packages (from WhiteMatterAnalysis==0.3.0) (1.23.5)
Requirement already satisfied: setuptools in c:\users\kidokoro_win\miniconda3\lib\site-packages (from WhiteMatterAnalysis==0.3.0) (65.6.3)
Collecting scipy
Downloading scipy-1.10.1-cp310-cp310-win_amd64.whl (42.5 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 42.5/42.5 MB 10.4 MB/s eta 0:00:00
Collecting vtk
Downloading vtk-9.2.6-cp310-cp310-win_amd64.whl (48.8 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.8/48.8 MB 10.7 MB/s eta 0:00:00
Requirement already satisfied: joblib in c:\users\kidokoro_win\miniconda3\lib\site-packages (from WhiteMatterAnalysis==0.3.0) (1.2.0)
Collecting statsmodels
Downloading statsmodels-0.13.5-cp310-cp310-win_amd64.whl (9.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.1/9.1 MB 11.5 MB/s eta 0:00:00
Collecting xlrd
Downloading xlrd-2.0.1-py2.py3-none-any.whl (96 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 96.5/96.5 kB 5.8 MB/s eta 0:00:00
Collecting matplotlib
Downloading matplotlib-3.7.1-cp310-cp310-win_amd64.whl (7.6 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.6/7.6 MB 11.6 MB/s eta 0:00:00
Collecting nibabel
Downloading nibabel-5.0.1-py3-none-any.whl (3.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 11.0 MB/s eta 0:00:00
Requirement already satisfied: packaging>=20.0 in c:\users\kidokoro_win\miniconda3\lib\site-packages (from matplotlib->WhiteMatterAnalysis==0.3.0) (22.0)
Requirement already satisfied: python-dateutil>=2.7 in c:\users\kidokoro_win\miniconda3\lib\site-packages (from matplotlib->WhiteMatterAnalysis==0.3.0) (2.8.2)
Requirement already satisfied: pillow>=6.2.0 in c:\users\kidokoro_win\miniconda3\lib\site-packages (from matplotlib->WhiteMatterAnalysis==0.3.0) (9.4.0)
Collecting fonttools>=4.22.0
Downloading fonttools-4.39.0-py3-none-any.whl (1.0 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.0/1.0 MB 8.0 MB/s eta 0:00:00
Collecting contourpy>=1.0.1
Downloading contourpy-1.0.7-cp310-cp310-win_amd64.whl (162 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 163.0/163.0 kB 10.2 MB/s eta 0:00:00
Collecting kiwisolver>=1.0.1
Downloading kiwisolver-1.4.4-cp310-cp310-win_amd64.whl (55 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 55.3/55.3 kB ? eta 0:00:00
Collecting pyparsing>=2.3.1
Downloading pyparsing-3.0.9-py3-none-any.whl (98 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.3/98.3 kB 5.5 MB/s eta 0:00:00
Collecting cycler>=0.10
Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB)
Collecting patsy>=0.5.2
Downloading patsy-0.5.3-py2.py3-none-any.whl (233 kB)
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Collecting pandas>=0.25
Downloading pandas-1.5.3-cp310-cp310-win_amd64.whl (10.4 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.4/10.4 MB 11.5 MB/s eta 0:00:00
Requirement already satisfied: pytz>=2020.1 in c:\users\kidokoro_win\miniconda3\lib\site-packages (from pandas>=0.25->statsmodels->WhiteMatterAnalysis==0.3.0) (2022.7)
Requirement already satisfied: six in c:\users\kidokoro_win\miniconda3\lib\site-packages (from patsy>=0.5.2->statsmodels->WhiteMatterAnalysis==0.3.0) (1.16.0)
Building wheels for collected packages: WhiteMatterAnalysis
Building wheel for WhiteMatterAnalysis (setup.py) … error
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [38 lines of output]
C:\Users\kidokoro_win\miniconda3\lib\site-packages\setuptools\installer.py:27: SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer.
warnings.warn(
running bdist_wheel
running build
running build_py
creating build
creating build\lib.win-amd64-cpython-310
creating build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\cluster.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\congeal_multisubject.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\congeal_to_atlas.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\fibers.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\filter.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\io.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\laterality.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\mrml.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\register.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\register_two_subjects.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\register_two_subjects_nonrigid.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\register_two_subjects_nonrigid_bsplines.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\relative_distance.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\render.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\similarity.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\tract_measurement.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis_init_.py → build\lib.win-amd64-cpython-310\whitematteranalysis
running build_ext
cythoning whitematteranalysis/fibers.pyx to whitematteranalysis\fibers.c
c:\users\kidokoro_win\appdata\local\temp\pip-req-build-w2zcv6au.eggs\cython-0.29.33-py3.10.egg\Cython\Compiler\Main.py:369: FutureWarning: Cython directive ‘language_level’ not set, using 2 for now (Py2). This will change in a later release! File: C:\Users\kidokoro_win\AppData\Local\Temp\pip-req-build-w2zcv6au\whitematteranalysis\fibers.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning whitematteranalysis/similarity.pyx to whitematteranalysis\similarity.c
c:\users\kidokoro_win\appdata\local\temp\pip-req-build-w2zcv6au.eggs\cython-0.29.33-py3.10.egg\Cython\Compiler\Main.py:369: FutureWarning: Cython directive ‘language_level’ not set, using 2 for now (Py2). This will change in a later release! File: C:\Users\kidokoro_win\AppData\Local\Temp\pip-req-build-w2zcv6au\whitematteranalysis\similarity.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
building ‘whitematteranalysis.fibers’ extension
creating build\temp.win-amd64-cpython-310
creating build\temp.win-amd64-cpython-310\Release
creating build\temp.win-amd64-cpython-310\Release\whitematteranalysis
cl.exe /c /nologo /O2 /W3 /GL /DNDEBUG /MD -IC:\Users\kidokoro_win\miniconda3\lib\site-packages\numpy\core\include -IC:\Users\kidokoro_win\miniconda3\include -IC:\Users\kidokoro_win\miniconda3\Include /Tcwhitematteranalysis\fibers.c /Fobuild\temp.win-amd64-cpython-310\Release\whitematteranalysis\fibers.obj
error: command ‘cl.exe’ failed: None
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for WhiteMatterAnalysis
Running setup.py clean for WhiteMatterAnalysis
Failed to build WhiteMatterAnalysis
Installing collected packages: xlrd, scipy, pyparsing, patsy, nibabel, kiwisolver, fonttools, cython, cycler, contourpy, pandas, matplotlib, vtk, statsmodels, WhiteMatterAnalysis
Running setup.py install for WhiteMatterAnalysis … error
error: subprocess-exited-with-error
× Running setup.py install for WhiteMatterAnalysis did not run successfully.
│ exit code: 1
╰─> [34 lines of output]
running install
C:\Users\kidokoro_win\miniconda3\lib\site-packages\setuptools\command\install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build
running build_py
creating build
creating build\lib.win-amd64-cpython-310
creating build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\cluster.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\congeal_multisubject.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\congeal_to_atlas.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\fibers.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\filter.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\io.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\laterality.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\mrml.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\register.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\register_two_subjects.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\register_two_subjects_nonrigid.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\register_two_subjects_nonrigid_bsplines.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\relative_distance.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\render.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\similarity.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis\tract_measurement.py → build\lib.win-amd64-cpython-310\whitematteranalysis
copying whitematteranalysis_init_.py → build\lib.win-amd64-cpython-310\whitematteranalysis
running build_ext
skipping ‘whitematteranalysis\fibers.c’ Cython extension (up-to-date)
skipping ‘whitematteranalysis\similarity.c’ Cython extension (up-to-date)
building ‘whitematteranalysis.fibers’ extension
creating build\temp.win-amd64-cpython-310
creating build\temp.win-amd64-cpython-310\Release
creating build\temp.win-amd64-cpython-310\Release\whitematteranalysis
cl.exe /c /nologo /O2 /W3 /GL /DNDEBUG /MD -IC:\Users\kidokoro_win\miniconda3\lib\site-packages\numpy\core\include -IC:\Users\kidokoro_win\miniconda3\include -IC:\Users\kidokoro_win\miniconda3\Include /Tcwhitematteranalysis\fibers.c /Fobuild\temp.win-amd64-cpython-310\Release\whitematteranalysis\fibers.obj
error: command ‘cl.exe’ failed: None
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure
× Encountered error while trying to install package.
╰─> WhiteMatterAnalysis
note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.
Could anyone tell me how to solve this?
I tried Python 3.7 and 3.8 as well, but the result was the same. Because I am a begginer user for Python, I might make a easy mistake at the first step.
And I am going to use SlicerWMA for white matter analysis.
Any advice would be appreciated.
Fumi