Hi, I am trying to install pygco package in Slicer 4.11 The package installs well in regular python 3.6, 3.7 environment. But withing Slicer 4.13 installation is failing while building the wheel file. Is there any solution?
Below is the error message inside python interactor window:
pip_install(‘pygco’)
Requirement already satisfied: pygco in c:\users\usrA147\appdata\local\na-mic\slicer 4.11.20200930\lib\python\lib\site-packages (0.0.16)
Requirement already satisfied: cython in c:\users\usrA147\appdata\local\na-mic\slicer 4.11.20200930\lib\python\lib\site-packages (from pygco) (0.29.21)
command: ‘C:\Users\usrA147\AppData\Local\NA-MIC\Slicer 4.11.20200930\bin\python-real.exe’ -u -c ‘import sys, setuptools, tokenize; sys.argv[0] = ‘"’“‘C:\Users\usrA147\AppData\Local\Temp\pip-install-yyvbemew\pygco\setup.py’”’“‘; file=’”‘“‘C:\Users\usrA147\AppData\Local\Temp\pip-install-yyvbemew\pygco\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\usrA147\AppData\Local\Temp\pip-wheel-2mzmu_b6’
cwd: C:\Users\usrA147\AppData\Local\Temp\pip-install-yyvbemew\pygco
Complete output (16 lines):
running bdist_wheel
running build
running build_ext
cythoning gco_python.pyx to gco_python.cpp
C:\Users\usrA147\AppData\Local\NA-MIC\Slicer 4.11.20200930\lib\Python\Lib\site-packages\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\usrA147\AppData\Local\Temp\pip-install-yyvbemew\pygco\gco_python.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
building ‘pygco’ extension
creating build
creating build\temp.win-amd64-3.6
creating build\temp.win-amd64-3.6\Release
creating build\temp.win-amd64-3.6\Release\gco_src
C:\Program Files (x86)\Microsoft Visual Studio\2017\BuildTools\VC\Tools\MSVC\14.16.27023\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -Igco_src “-IC:\Users\usrA147\AppData\Local\NA-MIC\Slicer 4.11.20200930\lib\Python\Lib\site-packages\numpy\core\include” “-IC:\Users\usrA147\AppData\Local\NA-MIC\Slicer 4.11.20200930\lib\Python\include” “-IC:\Users\usrA147\AppData\Local\NA-MIC\Slicer 4.11.20200930\lib\Python\include” “-IC:\Program Files (x86)\Microsoft Visual Studio\2017\BuildTools\VC\Tools\MSVC\14.16.27023\include” “-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.6.1\include\um” “-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\ucrt” “-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\shared” “-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\um” “-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\winrt” “-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\cppwinrt” /EHsc /Tpgco_python.cpp /Fobuild\temp.win-amd64-3.6\Release\gco_python.obj -fpermissive
cl : Command line warning D9002 : ignoring unknown option ‘-fpermissive’
gco_python.cpp
gco_python.cpp(4): fatal error C1083: Cannot open include file: ‘Python.h’: No such file or directory
error: command ‘C:\Program Files (x86)\Microsoft Visual Studio\2017\BuildTools\VC\Tools\MSVC\14.16.27023\bin\HostX86\x64\cl.exe’ failed with exit status 2
ERROR: Failed building wheel for pygco
Running setup.py clean for pygco
Failed to build pygco
Installing collected packages: pygco
Running setup.py install for pygco: started
Running setup.py install for pygco: finished with status ‘error’
ERROR: Command errored out with exit status 1:
command: ‘C:\Users\usrA147\AppData\Local\NA-MIC\Slicer 4.11.20200930\bin\python-real.exe’ -u -c ‘import sys, setuptools, tokenize; sys.argv[0] = ‘"’“‘C:\Users\usrA147\AppData\Local\Temp\pip-install-yyvbemew\pygco\setup.py’”’“‘; file=’”‘“‘C:\Users\usrA147\AppData\Local\Temp\pip-install-yyvbemew\pygco\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\usrA147\AppData\Local\Temp\pip-record-j0rrv1q1\install-record.txt’ --single-version-externally-managed --compile --install-headers ‘C:\Users\usrA147\AppData\Local\NA-MIC\Slicer 4.11.20200930\lib\Python\Include\pygco’
cwd: C:\Users\usrA147\AppData\Local\Temp\pip-install-yyvbemew\pygco
Complete output (14 lines):
running install
running build
running build_ext
skipping ‘gco_python.cpp’ Cython extension (up-to-date)
building ‘pygco’ extension
creating build
creating build\temp.win-amd64-3.6
creating build\temp.win-amd64-3.6\Release
creating build\temp.win-amd64-3.6\Release\gco_src
C:\Program Files (x86)\Microsoft Visual Studio\2017\BuildTools\VC\Tools\MSVC\14.16.27023\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -Igco_src “-IC:\Users\usrA147\AppData\Local\NA-MIC\Slicer 4.11.20200930\lib\Python\Lib\site-packages\numpy\core\include” “-IC:\Users\usrA147\AppData\Local\NA-MIC\Slicer 4.11.20200930\lib\Python\include” “-IC:\Users\usrA147\AppData\Local\NA-MIC\Slicer 4.11.20200930\lib\Python\include” “-IC:\Program Files (x86)\Microsoft Visual Studio\2017\BuildTools\VC\Tools\MSVC\14.16.27023\include” “-IC:\Program Files (x86)\Windows Kits\NETFXSDK\4.6.1\include\um” “-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\ucrt” “-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\shared” “-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\um” “-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\winrt” “-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\cppwinrt” /EHsc /Tpgco_python.cpp /Fobuild\temp.win-amd64-3.6\Release\gco_python.obj -fpermissive
cl : Command line warning D9002 : ignoring unknown option ‘-fpermissive’
gco_python.cpp
gco_python.cpp(4): fatal error C1083: Cannot open include file: ‘Python.h’: No such file or directory
error: command ‘C:\Program Files (x86)\Microsoft Visual Studio\2017\BuildTools\VC\Tools\MSVC\14.16.27023\bin\HostX86\x64\cl.exe’ failed with exit status 2
----------------------------------------
ERROR: Command errored out with exit status 1: ‘C:\Users\usrA147\AppData\Local\NA-MIC\Slicer 4.11.20200930\bin\python-real.exe’ -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '”‘“‘C:\Users\usrA147\AppData\Local\Temp\pip-install-yyvbemew\pygco\setup.py’”’“‘; file=’”‘“‘C:\Users\usrA147\AppData\Local\Temp\pip-install-yyvbemew\pygco\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\usrA147\AppData\Local\Temp\pip-record-j0rrv1q1\install-record.txt’ --single-version-externally-managed --compile --install-headers ‘C:\Users\usrA147\AppData\Local\NA-MIC\Slicer 4.11.20200930\lib\Python\Include\pygco’ Check the logs for full command output.
WARNING: You are using pip version 20.1.1; however, version 21.0.1 is available.
You should consider upgrading via the ‘C:\Users\usrA147\AppData\Local\NA-MIC\Slicer 4.11.20200930\bin\python-real.exe -m pip install --upgrade pip’ command.
Traceback (most recent call last):
File “”, line 1, in
File “C:\Users\usrA147\AppData\Local\NA-MIC\Slicer 4.11.20200930\bin\Python\slicer\util.py”, line 2569, in pip_install
_executePythonModule(‘pip’, args)
File “C:\Users\usrA147\AppData\Local\NA-MIC\Slicer 4.11.20200930\bin\Python\slicer\util.py”, line 2545, in _executePythonModule
logProcessOutput(proc)
File “C:\Users\usrA147\AppData\Local\NA-MIC\Slicer 4.11.20200930\bin\Python\slicer\util.py”, line 2517, in logProcessOutput
raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command ‘[‘C:/Users/usrA147/AppData/Local/NA-MIC/Slicer 4.11.20200930/bin/…/bin\PythonSlicer.EXE’, ‘-m’, ‘pip’, ‘install’, ‘pygco’]’ returned non-zero exit status 1.