[Rtk-users] RTK for Python : installation failed

Mon Apr 1 10:44:48 EDT 2019

Hi RTK users,

We have an installation which failed, although we followed the following
commands for Python :

python -m pip install --upgrade pip
python -m pip install --upgrade --pre itk
python -m pip install itk-rtk

it failed after : python -m pip install --upgrade --pre itk

the error message is at the end of this email.

Do you have any idea of what we are doing wrong?

Thanks,

Yannick

____________________________

 <http://www.surgiqual-institute.com/> SQI_Logo_Mail

Yannick Grondin, PhD

Radiation Physics R&D Engineer

 <http://www.surgiqual-institute.com/> http://www.surgiqual-institute.com/

+33 (0) 4 58 00 38 08

Collecting itk

  Using cached
https://files.pythonhosted.org/packages/69/e3/4b25d14a0637696193a57ca5838c5e
465b31024935eace2457188d8c9071/itk-5.0rc1.tar.gz

Building wheels for collected packages: itk

  Building wheel for itk (setup.py): started

  Building wheel for itk (setup.py): still running...

  Building wheel for itk (setup.py): finished with status 'error'

  Complete output from command D:\Softwares\python\python.exe -u -c "import
setuptools,
tokenize;__file__='C:\\Users\\kouka\\AppData\\Local\\Temp\\pip-install-byycn
ry8\\itk\\setup.py';f=getattr(tokenize, 'open',
open)(__file__);code=f.read().replace('\r\n',
'\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d
C:\Users\kouka\AppData\Local\Temp\pip-wheel-g_09lifp --python-tag cp37:

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

  -- Trying "Ninja" generator

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

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

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

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

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

  -------

  --

  Not searching for unused variables given on the command line.

  -- The C compiler identification is MSVC 19.16.27027.1

  -- Check for working C compiler:
D:/Softwares/visualstudio/VC/Tools/MSVC/14.16.27023/bin/Hostx86/x86/cl.exe

  -- Check for working C compiler:
D:/Softwares/visualstudio/VC/Tools/MSVC/14.16.27023/bin/Hostx86/x86/cl.exe
-- works

  -- Detecting C compiler ABI info

  -- Detecting C compiler ABI info - done

  -- Detecting C compile features

  -- Detecting C compile features - done

  -- The CXX compiler identification is MSVC 19.16.27027.1

  -- Check for working CXX compiler:
D:/Softwares/visualstudio/VC/Tools/MSVC/14.16.27023/bin/Hostx86/x86/cl.exe

  -- Check for working CXX compiler:
D:/Softwares/visualstudio/VC/Tools/MSVC/14.16.27023/bin/Hostx86/x86/cl.exe
-- works

  -- Detecting CXX compiler ABI info

  -- Detecting CXX compiler ABI info - done

  -- Detecting CXX compile features

  -- Detecting CXX compile features - done

  -- Configuring done

  -- Generating done

  -- Build files have been written to:
C:/Users/kouka/AppData/Local/Temp/pip-install-byycnry8/itk/_cmake_test_compi
le/build

  --

  -------

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

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

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

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

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

  -- Trying "Ninja" generator - success

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

  -- SuperBuild - ITKPythonPackage_WHEEL_NAME:itk

  -- SuperBuild -

  -- SuperBuild - ITK-source-download

  -- SuperBuild -   ITK_SOURCE_DIR:
C:/Users/kouka/AppData/Local/Temp/pip-install-byycnry8/itk/_skbuild/win32-3.
7/cmake-build/ITKs

  -- SuperBuild - ITK-source-download[OK]

  -- SuperBuild -

  -- SuperBuild - Searching for python

  -- SuperBuild -   PYTHON_INCLUDE_DIR: D:/Softwares/python/Include

  -- SuperBuild -   PYTHON_LIBRARY: D:/Softwares/python/libs/python37.lib

  -- SuperBuild -   PYTHON_EXECUTABLE: D:/Softwares/python/python.exe

  -- SuperBuild - Searching for python[OK]

  -- SuperBuild -   DOXYGEN_EXECUTABLE:

  -- ITK CMake Cache Args -

  -- SuperBuild -

  -- SuperBuild - ITK => Requires ITK-source-download

  -- SuperBuild -   ITK_BINARY_DIR:
C:/Users/kouka/AppData/Local/Temp/pip-install-byycnry8/itk/_skbuild/win32-3.
7/cmake-build/ITKb

  -- SuperBuild - ITK[OK]

  -- SuperBuild -

  -- SuperBuild - ITKPythonPackage => Requires ITK

  -- SuperBuild - ITKPythonPackage[OK]

  -- Configuring done

  -- Generating done

  -- Build files have been written to:
C:/Users/kouka/AppData/Local/Temp/pip-install-byycnry8/itk/_skbuild/win32-3.
7/cmake-build

  [1/25] Creating directories for 'ITK-source-download'

  [1/25] Performing download step (git clone) for 'ITK-source-download'

  Cloning into 'ITKs'...

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  Checking out files: 100% (15746/15746), done.

  Note: checking out '3a11b90d06513'.

  You are in 'detached HEAD' state. You can look around, make experimental

  changes and commit them, and you can discard any commits you make in this

  state without impacting any branches by performing another checkout.

  If you want to create a new branch to retain commits you create, you may

  do so (now or later) by using -b with the checkout command again. Example:

    git checkout -b <new-branch-name>

  HEAD is now at 3a11b90d06 COMP: Avoid duplicate wrapping of
VectorContainer with unsigned short

  [3/25] No patch step for 'ITK-source-download'

  [4/25] Performing update step for 'ITK-source-download'

  [5/25] No configure step for 'ITK-source-download'

  [6/25] No build step for 'ITK-source-download'

  [7/25] No install step for 'ITK-source-download'

  [8/25] Completed 'ITK-source-download'

  [9/25] Creating directories for 'ITK'

  [9/25] No download step for 'ITK'

  [10/25] No update step for 'ITK'

  [11/25] No patch step for 'ITK'

  [12/25] Performing configure step for 'ITK'

  -- The CXX compiler identification is MSVC 19.16.27027.1

  -- The C compiler identification is MSVC 19.16.27027.1

  -- Check for working CXX compiler:
D:/Softwares/visualstudio/VC/Tools/MSVC/14.16.27023/bin/Hostx86/x86/cl.exe

  -- Check for working CXX compiler:
D:/Softwares/visualstudio/VC/Tools/MSVC/14.16.27023/bin/Hostx86/x86/cl.exe
-- works

  -- Detecting CXX compiler ABI info

  -- Detecting CXX compiler ABI info - done

  -- Detecting CXX compile features

  -- Detecting CXX compile features - done

  -- Check for working C compiler:
D:/Softwares/visualstudio/VC/Tools/MSVC/14.16.27023/bin/Hostx86/x86/cl.exe

  -- Check for working C compiler:
D:/Softwares/visualstudio/VC/Tools/MSVC/14.16.27023/bin/Hostx86/x86/cl.exe
-- works

  -- Detecting C compiler ABI info

  -- Detecting C compiler ABI info - done

  -- Detecting C compile features

  -- Detecting C compile features - done

  CMake Error at CMakeLists.txt:109 (message):

    ITK source code directory path length is too long (94 > 50).Please move
the

    ITK source code directory to a directory with a shorter path.

  -- Configuring incomplete, errors occurred!

  See also
"C:/Users/kouka/AppData/Local/Temp/pip-install-byycnry8/itk/_skbuild/win32-3
.7/cmake-build/ITKb/CMakeFiles/CMakeOutput.log".

  FAILED: ITKp/src/ITK-stamp/ITK-configure

  cmd.exe /C "cd /D
C:\Users\kouka\AppData\Local\Temp\pip-install-byycnry8\itk\_skbuild\win32-3.
7\cmake-build\ITKb && D:\Softwares\cmake\bin\cmake.exe
-DBUILD_TESTING:BOOL=OFF
-DCMAKE_INSTALL_PREFIX:PATH=C:/Users/kouka/AppData/Local/Temp/pip-install-by
ycnry8/itk/_skbuild/win32-3.7/cmake-install
-DPY_SITE_PACKAGES_PATH:PATH=C:/Users/kouka/AppData/Local/Temp/pip-install-b
yycnry8/itk/_skbuild/win32-3.7/cmake-install
-DWRAP_ITK_INSTALL_COMPONENT_IDENTIFIER:STRING=PythonWheel
-DWRAP_ITK_INSTALL_COMPONENT_PER_MODULE:BOOL=OFF -DITK_LEGACY_SILENT:BOOL=ON
-DITK_WRAP_PYTHON:BOOL=ON -DITK_WRAP_PYTHON_LEGACY:BOOL=OFF
-DITK_WRAP_unsigned_short:BOOL=ON -DITK_WRAP_DOC:BOOL=ON
-DDOXYGEN_EXECUTABLE:FILEPATH=
-DPYTHON_INCLUDE_DIR:PATH=D:/Softwares/python/Include
-DPYTHON_LIBRARY:FILEPATH=D:/Softwares/python/libs/python37.lib
-DPYTHON_EXECUTABLE:FILEPATH=D:/Softwares/python/python.exe
-DCMAKE_BUILD_TYPE:STRING=Release
-DCMAKE_MAKE_PROGRAM:FILEPATH=D:/Softwares/visualstudio/Common7/IDE/CommonEx
tensions/Microsoft/CMake/Ninja/ninja.exe -GNinja
C:/Users/kouka/AppData/Local/Temp/pip-install-byycnry8/itk/_skbuild/win32-3.
7/cmake-build/ITKs && D:\Softwares\cmake\bin\cmake.exe -E touch
C:/Users/kouka/AppData/Local/Temp/pip-install-byycnry8/itk/_skbuild/win32-3.
7/cmake-build/ITKp/src/ITK-stamp/ITK-configure"

  ninja: build stopped: subcommand failed.

  Traceback (most recent call last):

    File "D:\Softwares\python\lib\site-packages\skbuild\setuptools_wrap.py",
line 578, in setup

      cmkr.make(make_args, env=env)

    File "D:\Softwares\python\lib\site-packages\skbuild\cmaker.py", line
482, in make

      os.path.abspath(CMAKE_BUILD_DIR())))

  An error occurred while building with CMake.

    Command:

      "cmake" "--build" "." "--target" "install" "--config" "Release" "--"

    Source directory:

      C:\Users\kouka\AppData\Local\Temp\pip-install-byycnry8\itk

    Working directory:

C:\Users\kouka\AppData\Local\Temp\pip-install-byycnry8\itk\_skbuild\win32-3.
7\cmake-build

  Please see CMake's output for more information.

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

  Running setup.py clean for itk

  Complete output from command D:\Softwares\python\python.exe -u -c "import
setuptools,
tokenize;__file__='C:\\Users\\kouka\\AppData\\Local\\Temp\\pip-install-byycn
ry8\\itk\\setup.py';f=getattr(tokenize, 'open',
open)(__file__);code=f.read().replace('\r\n',
'\n');f.close();exec(compile(code, __file__, 'exec'))" clean --all:

  running clean

  '_skbuild\win32-3.7\setuptools\lib' does not exist -- can't clean it

  '_skbuild\win32-3.7\setuptools\bdist.win32' does not exist -- can't clean
it

  '_skbuild\win32-3.7\setuptools\scripts-3.7' does not exist -- can't clean
it

  removing '_skbuild\win32-3.7\setuptools'

  removing '_skbuild\win32-3.7\cmake-install'

  removing '_skbuild\win32-3.7\cmake-build'

  error: [WinError 5] Access is denied:
'_skbuild\\win32-3.7\\cmake-build\\ITKs\\.git\\objects\\pack\\pack-debda3808
782fb53135b9fc9cb82b15868dc57b0.idx'

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

Failed to build itk

Installing collected packages: itk

  Running setup.py install for itk: started

    Running setup.py install for itk: still running...

    Running setup.py install for itk: finished with status 'error'

    Complete output from command D:\Softwares\python\python.exe -u -c
"import setuptools,
tokenize;__file__='C:\\Users\\kouka\\AppData\\Local\\Temp\\pip-install-byycn
ry8\\itk\\setup.py';f=getattr(tokenize, 'open',
open)(__file__);code=f.read().replace('\r\n',
'\n');f.close();exec(compile(code, __file__, 'exec'))" install --record
C:\Users\kouka\AppData\Local\Temp\pip-record-ri4o36nk\install-record.txt
--single-version-externally-managed --compile:

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

    -- Trying "Ninja" generator

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

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

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

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

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

    -------

   --

    Not searching for unused variables given on the command line.

    -- The C compiler identification is MSVC 19.16.27027.1

    -- Check for working C compiler:
D:/Softwares/visualstudio/VC/Tools/MSVC/14.16.27023/bin/Hostx86/x86/cl.exe

    -- Check for working C compiler:
D:/Softwares/visualstudio/VC/Tools/MSVC/14.16.27023/bin/Hostx86/x86/cl.exe
-- works

    -- Detecting C compiler ABI info

    -- Detecting C compiler ABI info - done

    -- Detecting C compile features

    -- Detecting C compile features - done

    -- The CXX compiler identification is MSVC 19.16.27027.1

    -- Check for working CXX compiler:
D:/Softwares/visualstudio/VC/Tools/MSVC/14.16.27023/bin/Hostx86/x86/cl.exe

    -- Check for working CXX compiler:
D:/Softwares/visualstudio/VC/Tools/MSVC/14.16.27023/bin/Hostx86/x86/cl.exe
-- works

    -- Detecting CXX compiler ABI info

    -- Detecting CXX compiler ABI info - done

    -- Detecting CXX compile features

    -- Detecting CXX compile features - done

    -- Configuring done

    -- Generating done

    -- Build files have been written to:
C:/Users/kouka/AppData/Local/Temp/pip-install-byycnry8/itk/_cmake_test_compi
le/build

    --

    -------

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

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

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

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

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

    -- Trying "Ninja" generator - success

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

    -- SuperBuild - ITKPythonPackage_WHEEL_NAME:itk

    -- SuperBuild -

    -- SuperBuild - ITK-source-download

    -- SuperBuild -   ITK_SOURCE_DIR:
C:/Users/kouka/AppData/Local/Temp/pip-install-byycnry8/itk/_skbuild/win32-3.
7/cmake-build/ITKs

    -- SuperBuild - ITK-source-download[OK]

    -- SuperBuild -

    -- SuperBuild - Searching for python

    -- SuperBuild -   PYTHON_INCLUDE_DIR: D:/Softwares/python/Include

    -- SuperBuild -   PYTHON_LIBRARY: D:/Softwares/python/libs/python37.lib

    -- SuperBuild -   PYTHON_EXECUTABLE: D:/Softwares/python/python.exe

    -- SuperBuild - Searching for python[OK]

    -- SuperBuild -   DOXYGEN_EXECUTABLE:

    -- ITK CMake Cache Args -

    -- SuperBuild -

    -- SuperBuild - ITK => Requires ITK-source-download

    -- SuperBuild -   ITK_BINARY_DIR:
C:/Users/kouka/AppData/Local/Temp/pip-install-byycnry8/itk/_skbuild/win32-3.
7/cmake-build/ITKb

    -- SuperBuild - ITK[OK]

    -- SuperBuild -

    -- SuperBuild - ITKPythonPackage => Requires ITK

    -- SuperBuild - ITKPythonPackage[OK]

    -- Configuring done

    -- Generating done

    -- Build files have been written to:
C:/Users/kouka/AppData/Local/Temp/pip-install-byycnry8/itk/_skbuild/win32-3.
7/cmake-build

    [1/25] Creating directories for 'ITK-source-download'

    [1/25] Performing download step (git clone) for 'ITK-source-download'

    Cloning into 'ITKs'...

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    Checking out files: 100% (15746/15746), done.

    Note: checking out '3a11b90d06513'.

    You are in 'detached HEAD' state. You can look around, make experimental

    changes and commit them, and you can discard any commits you make in
this

    state without impacting any branches by performing another checkout.

    If you want to create a new branch to retain commits you create, you may

    do so (now or later) by using -b with the checkout command again.
Example:

      git checkout -b <new-branch-name>

    HEAD is now at 3a11b90d06 COMP: Avoid duplicate wrapping of
VectorContainer with unsigned short

    [3/25] No patch step for 'ITK-source-download'

    [4/25] Performing update step for 'ITK-source-download'

    [5/25] No configure step for 'ITK-source-download'

    [6/25] No build step for 'ITK-source-download'

    [7/25] No install step for 'ITK-source-download'

    [8/25] Completed 'ITK-source-download'

    [9/25] Creating directories for 'ITK'

    [9/25] No download step for 'ITK'

    [10/25] No update step for 'ITK'

    [11/25] No patch step for 'ITK'

    [12/25] Performing configure step for 'ITK'

    -- The CXX compiler identification is MSVC 19.16.27027.1

    -- The C compiler identification is MSVC 19.16.27027.1

    -- Check for working CXX compiler:
D:/Softwares/visualstudio/VC/Tools/MSVC/14.16.27023/bin/Hostx86/x86/cl.exe

    -- Check for working CXX compiler:
D:/Softwares/visualstudio/VC/Tools/MSVC/14.16.27023/bin/Hostx86/x86/cl.exe
-- works

    -- Detecting CXX compiler ABI info

    -- Detecting CXX compiler ABI info - done

    -- Detecting CXX compile features

    -- Detecting CXX compile features - done

    -- Check for working C compiler:
D:/Softwares/visualstudio/VC/Tools/MSVC/14.16.27023/bin/Hostx86/x86/cl.exe

    -- Check for working C compiler:
D:/Softwares/visualstudio/VC/Tools/MSVC/14.16.27023/bin/Hostx86/x86/cl.exe
-- works

    -- Detecting C compiler ABI info

    -- Detecting C compiler ABI info - done

    -- Detecting C compile features

    -- Detecting C compile features - done

    CMake Error at CMakeLists.txt:109 (message):

      ITK source code directory path length is too long (94 > 50).Please
move the

      ITK source code directory to a directory with a shorter path.

    -- Configuring incomplete, errors occurred!

    See also
"C:/Users/kouka/AppData/Local/Temp/pip-install-byycnry8/itk/_skbuild/win32-3
.7/cmake-build/ITKb/CMakeFiles/CMakeOutput.log".

    FAILED: ITKp/src/ITK-stamp/ITK-configure

    cmd.exe /C "cd /D
C:\Users\kouka\AppData\Local\Temp\pip-install-byycnry8\itk\_skbuild\win32-3.
7\cmake-build\ITKb && D:\Softwares\cmake\bin\cmake.exe
-DBUILD_TESTING:BOOL=OFF
-DCMAKE_INSTALL_PREFIX:PATH=C:/Users/kouka/AppData/Local/Temp/pip-install-by
ycnry8/itk/_skbuild/win32-3.7/cmake-install
-DPY_SITE_PACKAGES_PATH:PATH=C:/Users/kouka/AppData/Local/Temp/pip-install-b
yycnry8/itk/_skbuild/win32-3.7/cmake-install
-DWRAP_ITK_INSTALL_COMPONENT_IDENTIFIER:STRING=PythonWheel
-DWRAP_ITK_INSTALL_COMPONENT_PER_MODULE:BOOL=OFF -DITK_LEGACY_SILENT:BOOL=ON
-DITK_WRAP_PYTHON:BOOL=ON -DITK_WRAP_PYTHON_LEGACY:BOOL=OFF
-DITK_WRAP_unsigned_short:BOOL=ON -DITK_WRAP_DOC:BOOL=ON
-DDOXYGEN_EXECUTABLE:FILEPATH=
-DPYTHON_INCLUDE_DIR:PATH=D:/Softwares/python/Include
-DPYTHON_LIBRARY:FILEPATH=D:/Softwares/python/libs/python37.lib
-DPYTHON_EXECUTABLE:FILEPATH=D:/Softwares/python/python.exe
-DCMAKE_BUILD_TYPE:STRING=Release
-DCMAKE_MAKE_PROGRAM:FILEPATH=D:/Softwares/visualstudio/Common7/IDE/CommonEx
tensions/Microsoft/CMake/Ninja/ninja.exe -GNinja
C:/Users/kouka/AppData/Local/Temp/pip-install-byycnry8/itk/_skbuild/win32-3.
7/cmake-build/ITKs && D:\Softwares\cmake\bin\cmake.exe -E touch
C:/Users/kouka/AppData/Local/Temp/pip-install-byycnry8/itk/_skbuild/win32-3.
7/cmake-build/ITKp/src/ITK-stamp/ITK-configure"

    ninja: build stopped: subcommand failed.

    Traceback (most recent call last):

      File
"D:\Softwares\python\lib\site-packages\skbuild\setuptools_wrap.py", line
578, in setup

        cmkr.make(make_args, env=env)

      File "D:\Softwares\python\lib\site-packages\skbuild\cmaker.py", line
482, in make

        os.path.abspath(CMAKE_BUILD_DIR())))

    An error occurred while building with CMake.

      Command:

        "cmake" "--build" "." "--target" "install" "--config" "Release" "--"

      Source directory:

        C:\Users\kouka\AppData\Local\Temp\pip-install-byycnry8\itk

      Working directory:

C:\Users\kouka\AppData\Local\Temp\pip-install-byycnry8\itk\_skbuild\win32-3.
7\cmake-build

    Please see CMake's output for more information.

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

  Failed building wheel for itk

  Failed cleaning build dir for itk

Command "D:\Softwares\python\python.exe -u -c "import setuptools,
tokenize;__file__='C:\\Users\\kouka\\AppData\\Local\\Temp\\pip-install-byycn
ry8\\itk\\setup.py';f=getattr(tokenize, 'open',
open)(__file__);code=f.read().replace('\r\n',
'\n');f.close();exec(compile(code, __file__, 'exec'))" install --record
C:\Users\kouka\AppData\Local\Temp\pip-record-ri4o36nk\install-record.txt
--single-version-externally-managed --compile" failed with error code 1 in
C:\Users\kouka\AppData\Local\Temp\pip-install-byycnry8\itk\

---
L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast.
https://www.avast.com/antivirus
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