Установка пакета amici Python — компилятор C не может создать простую тестовую программу
Я пытаюсь установить пакет Python AMICI. Я следую руководству на этой странице: https://amici.readthedocs.io/en/latest/python_installation.html .
Я хотел бы использовать AMICI для создания проблемы SBML в PyPesto, используя формат PEtab.
Я использую Python 3.9 и установил компилятор MSVC C, доступный в инструментах сборки Visual Studio.
Ниже приведена ошибка, которую я получаю при попытке установить AMICI с помощью команды pip install amici:
`
(venv) C:\Users\ana.valinhas\Documents\Python Scripts\MechanisticModelTransfectionPEtab>pip install amici
Collecting amici
Using cached amici-0.18.1.tar.gz (1.1 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting cmake-build-extension==0.5.1 (from amici)
Using cached cmake_build_extension-0.5.1-py3-none-any.whl (13 kB)
Requirement already satisfied: sympy>=1.9 in c:\users\ana.valinhas\documents\python scripts\mechanisticmodeltransfectionpetab\venv\lib\site-packages (from amici) (1.12)
Requirement already satisfied: python-libsbml in c:\users\ana.valinhas\documents\python scripts\mechanisticmodeltransfectionpetab\venv\lib\site-packages (from amici) (5.20.1)
Requirement already satisfied: h5py in c:\users\ana.valinhas\documents\python scripts\mechanisticmodeltransfectionpetab\venv\lib\site-packages (from amici) (3.8.0)
Requirement already satisfied: pandas>=2.0.2 in c:\users\ana.valinhas\documents\python scripts\mechanisticmodeltransfectionpetab\venv\lib\site-packages (from amici) (2.0.2)
Collecting wurlitzer (from amici)
Using cached wurlitzer-3.0.3-py3-none-any.whl (7.3 kB)
Collecting toposort (from amici)
Using cached toposort-1.10-py3-none-any.whl (8.5 kB)
Requirement already satisfied: setuptools>=48 in c:\users\ana.valinhas\documents\python scripts\mechanisticmodeltransfectionpetab\venv\lib\site-packages (from amici) (68.0.0)
Requirement already satisfied: mpmath in c:\users\ana.valinhas\documents\python scripts\mechanisticmodeltransfectionpetab\venv\lib\site-packages (from amici) (1.3.0)
Requirement already satisfied: numpy>=1.19.3 in c:\users\ana.valinhas\documents\python scripts\mechanisticmodeltransfectionpetab\venv\lib\site-packages (from amici) (1.24.3)
Requirement already satisfied: cmake in c:\users\ana.valinhas\documents\python scripts\mechanisticmodeltransfectionpetab\venv\lib\site-packages (from cmake-build-extension==0.5.1->amici) (3.26.4)
Collecting ninja (from cmake-build-extension==0.5.1->amici)
Using cached ninja-1.11.1-py2.py3-none-win_amd64.whl (313 kB)
Requirement already satisfied: GitPython in c:\users\ana.valinhas\documents\python scripts\mechanisticmodeltransfectionpetab\venv\lib\site-packages (from cmake-build-extension==0.5.1->amici) (3.1.31)
Requirement already satisfied: setuptools-scm in c:\users\ana.valinhas\documents\python scripts\mechanisticmodeltransfectionpetab\venv\lib\site-packages (from cmake-build-extension==0.5.1->amici) (7.1.0)
Requirement already satisfied: python-dateutil>=2.8.2 in c:\users\ana.valinhas\documents\python scripts\mechanisticmodeltransfectionpetab\venv\lib\site-packages (from pandas>=2.0.2->amici) (2.8.2)
Requirement already satisfied: pytz>=2020.1 in c:\users\ana.valinhas\documents\python scripts\mechanisticmodeltransfectionpetab\venv\lib\site-packages (from pandas>=2.0.2->amici) (2023.3)
Requirement already satisfied: tzdata>=2022.1 in c:\users\ana.valinhas\documents\python scripts\mechanisticmodeltransfectionpetab\venv\lib\site-packages (from pandas>=2.0.2->amici) (2023.3)
Requirement already satisfied: six>=1.5 in c:\users\ana.valinhas\documents\python scripts\mechanisticmodeltransfectionpetab\venv\lib\site-packages (from python-dateutil>=2.8.2->pandas>=2.0.2->amici) (1.16.0)
Requirement already satisfied: gitdb<5,>=4.0.1 in c:\users\ana.valinhas\documents\python scripts\mechanisticmodeltransfectionpetab\venv\lib\site-packages (from GitPython->cmake-build-extension==0.5.1->amici) (4.0.10)
Requirement already satisfied: packaging>=20.0 in c:\users\ana.valinhas\documents\python scripts\mechanisticmodeltransfectionpetab\venv\lib\site-packages (from setuptools-scm->cmake-build-extension==0.5.1->amici) (23.1)
Requirement already satisfied: typing-extensions in c:\users\ana.valinhas\documents\python scripts\mechanisticmodeltransfectionpetab\venv\lib\site-packages (from setuptools-scm->cmake-build-extension==0.5.1->amici) (4.6.3)
Requirement already satisfied: tomli>=1.0.0 in c:\users\ana.valinhas\documents\python scripts\mechanisticmodeltransfectionpetab\venv\lib\site-packages (from setuptools-scm->cmake-build-extension==0.5.1->amici) (2.0.1)
Requirement already satisfied: smmap<6,>=3.0.1 in c:\users\ana.valinhas\documents\python scripts\mechanisticmodeltransfectionpetab\venv\lib\site-packages (from gitdb<5,>=4.0.1->GitPython->cmake-build-extension==0.5.1->amici) (5.0.0)
Building wheels for collected packages: amici
Building wheel for amici (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for amici (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [119 lines of output]
running AmiciInstall
running bdist_wheel
running build
running build_py
running AmiciBuildPy
running build_ext
------------------------------ SuiteSparse_config ------------------------------
-- Building SuiteSparse_config version: v7.0.1 (Jan 20, 2023)
-- Source: C:/Users/ana.valinhas/AppData/pip-install-g2gatndu/amici_36641f72bf1a4f5eab8decde7d536cce/amici/ThirdParty/SuiteSparse/SuiteSparse_config
-- Build: C:/Users/ana.valinhas/AppData/pip-install-g2gatndu/amici_36641f72bf1a4f5eab8decde7d536cce/build/temp.win-amd64-cpython-39/Release_SuiteSparse_config
-- The C compiler identification is MSVC 19.36.32534.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - failed
-- Check for working C compiler: C:/Program Files (x86)/Microsoft Visual Studio/2022/BuildTools/VC/Tools/MSVC/14.36.32532/bin/Hostx64/x64/cl.exe
-- Check for working C compiler: C:/Program Files (x86)/Microsoft Visual Studio/2022/BuildTools/VC/Tools/MSVC/14.36.32532/bin/Hostx64/x64/cl.exe - broken
CMake Error at C:/Users/ana.valinhas/AppData/pip-build-env-aqngm_ut/overlay/Lib/site-packages/cmake/data/share/cmake-3.26/Modules/CMakeTestCCompiler.cmake:67 (message):
The C compiler
"C:/Program Files (x86)/Microsoft Visual Studio/2022/BuildTools/VC/Tools/MSVC/14.36.32532/bin/Hostx64/x64/cl.exe"
is not able to compile a simple test program.
It fails with the following output:
Change Dir: C:/Users/ana.valinhas/AppData/pip-install-g2gatndu/amici_36641f72bf1a4f5eab8decde7d536cce/build/temp.win-amd64-cpython-39/Release_SuiteSparse_config/CMakeFiles/CMakeScratch/TryCompile-y0eyq7
Run Build Command(s):C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Scripts\ninja.EXE -v cmTC_3f0da && [1/2] C:\PROGRA~2\MIB055~1\2022\BUILDT~1\VC\Tools\MSVC\1436~1.325\bin\Hostx64\x64\cl.exe /nologo /DWIN
32 /D_WINDOWS /Zi /Ob0 /Od /RTC1 -MDd /showIncludes /FoCMakeFiles\cmTC_3f0da.dir\testCCompiler.c.obj /FdCMakeFiles\cmTC_3f0da.dir\ /FS -c C:\Users\ana.valinhas\AppData\pip-install-g2gatndu\amici_36641f72bf1a4f5eab8decde7d536cce\bui
ld\temp.win-amd64-cpython-39\Release_SuiteSparse_config\CMakeFiles\CMakeScratch\TryCompile-y0eyq7\testCCompiler.c
[2/2] cmd.exe /C "cd . && C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\cmake\data\bin\cmake.exe -E vs_link_exe --intdir=CMakeFiles\cmTC_3f0da.dir --rc=C:\PROGRA~2\WI3CF2~1\10\bin\100220~1.
0\x64\rc.exe --mt=C:\PROGRA~2\WI3CF2~1\10\bin\100220~1.0\x64\mt.exe --manifests -- C:\PROGRA~2\MIB055~1\2022\BUILDT~1\VC\Tools\MSVC\1436~1.325\bin\Hostx64\x64\link.exe /nologo CMakeFiles\cmTC_3f0da.dir\testCCompiler.c.obj /out:cmT
C_3f0da.exe /implib:cmTC_3f0da.lib /pdb:cmTC_3f0da.pdb /version:0.0 /machine:x64 /debug /INCREMENTAL /subsystem:console kernel32.lib user32.lib gdi32.lib winspool.lib shell32.lib ole32.lib oleaut32.lib uuid.lib comdlg32.lib advapi
32.lib && cd ."
FAILED: cmTC_3f0da.exe
cmd.exe /C "cd . && C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\cmake\data\bin\cmake.exe -E vs_link_exe --intdir=CMakeFiles\cmTC_3f0da.dir --rc=C:\PROGRA~2\WI3CF2~1\10\bin\100220~1.0\x64\
rc.exe --mt=C:\PROGRA~2\WI3CF2~1\10\bin\100220~1.0\x64\mt.exe --manifests -- C:\PROGRA~2\MIB055~1\2022\BUILDT~1\VC\Tools\MSVC\1436~1.325\bin\Hostx64\x64\link.exe /nologo CMakeFiles\cmTC_3f0da.dir\testCCompiler.c.obj /out:cmTC_3f0d
a.exe /implib:cmTC_3f0da.lib /pdb:cmTC_3f0da.pdb /version:0.0 /machine:x64 /debug /INCREMENTAL /subsystem:console kernel32.lib user32.lib gdi32.lib winspool.lib shell32.lib ole32.lib oleaut32.lib uuid.lib comdlg32.lib advapi32.lib
&& cd ."
LINK Pass 1: command "C:\PROGRA~2\MIB055~1\2022\BUILDT~1\VC\Tools\MSVC\1436~1.325\bin\Hostx64\x64\link.exe /nologo CMakeFiles\cmTC_3f0da.dir\testCCompiler.c.obj /out:cmTC_3f0da.exe /implib:cmTC_3f0da.lib /pdb:cmTC_3f0da.pd
b /version:0.0 /machine:x64 /debug /INCREMENTAL /subsystem:console kernel32.lib user32.lib gdi32.lib winspool.lib shell32.lib ole32.lib oleaut32.lib uuid.lib comdlg32.lib advapi32.lib /MANIFEST /MANIFESTFILE:CMakeFiles\cmTC_3f0da.di
r/intermediate.manifest CMakeFiles\cmTC_3f0da.dir/manifest.res" failed (exit code 1104) with the following output:
LINK : fatal error LNK1104: cannot open file 'kernel32.lib'
ninja: build stopped: subcommand failed.
CMake will not be able to correctly generate this project.
Call Stack (most recent call first):
cmake_modules/SuiteSparsePolicy.cmake:93 (enable_language)
CMakeLists.txt:34 (include)
-- Configuring incomplete, errors occurred!
running AmiciBuildCMakeExtension
==> Configuring:
$ cmake -S C:\Users\ana.valinhas\AppData\pip-install-g2gatndu\amici_36641f72bf1a4f5eab8decde7d536cce\amici\ThirdParty\SuiteSparse\SuiteSparse_config -B C:\Users\ana.valinhas\AppData\pip-install-g2gatndu\amici_36641f72bf1a4f5ea
b8decde7d536cce\build\temp.win-amd64-cpython-39\Release_SuiteSparse_config -GNinja -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX:PATH=C:\Users\ana.valinhas\AppData\pip-install-g2gatndu\amici_36641f72bf1a4f5eab8decde7d536cce\buil
d\lib.win-amd64-cpython-39\amici -DCMAKE_MAKE_PROGRAM=C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Scripts\ninja.EXE -DCMAKE_VERBOSE_MAKEFILE=ON -DBLA_VENDOR=All -DENABLE_CUDA=FALSE -DNFORTRAN=TRUE
==> Building:
$ cmake --build C:\Users\ana.valinhas\AppData\pip-install-g2gatndu\amici_36641f72bf1a4f5eab8decde7d536cce\build\temp.win-amd64-cpython-39\Release_SuiteSparse_config --config Release
==> Installing:
$ cmake --install C:\Users\ana.valinhas\AppData\pip-install-g2gatndu\amici_36641f72bf1a4f5eab8decde7d536cce\build\temp.win-amd64-cpython-39\Release_SuiteSparse_config
Traceback (most recent call last):
File "C:\Users\ana.valinhas\Documents\Python Scripts\MechanisticModelTransfectionPEtab\venv\lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 353, in <module>
main()
File "C:\Users\ana.valinhas\Documents\Python Scripts\MechanisticModelTransfectionPEtab\venv\lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "C:\Users\ana.valinhas\Documents\Python Scripts\MechanisticModelTransfectionPEtab\venv\lib\site-packages\pip\_vendor\pyproject_hooks\_in_process\_in_process.py", line 251, in build_wheel
return _build_backend().build_wheel(wheel_directory, config_settings,
File "C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\setuptools\build_meta.py", line 416, in build_wheel
return self._build_with_temp_dir(['bdist_wheel'], '.whl',
File "C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\setuptools\build_meta.py", line 401, in _build_with_temp_dir
self.run_setup()
File "C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\setuptools\build_meta.py", line 338, in run_setup
exec(code, locals())
File "<string>", line 175, in <module>
File "<string>", line 159, in main
File "C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\setuptools\__init__.py", line 107, in setup
return distutils.core.setup(**attrs)
File "C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\setuptools\_distutils\core.py", line 185, in setup
return run_commands(dist)
File "C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\setuptools\_distutils\core.py", line 201, in run_commands
dist.run_commands()
File "C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\setuptools\_distutils\dist.py", line 969, in run_commands
self.run_command(cmd)
File "C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\setuptools\dist.py", line 1234, in run_command
super().run_command(command)
File "C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\setuptools\_distutils\dist.py", line 988, in run_command
cmd_obj.run()
File "C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\wheel\bdist_wheel.py", line 343, in run
self.run_command("build")
File "C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\setuptools\_distutils\cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\setuptools\dist.py", line 1234, in run_command
super().run_command(command)
File "C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\setuptools\_distutils\dist.py", line 988, in run_command
cmd_obj.run()
File "C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\setuptools\_distutils\command\build.py", line 131, in run
self.run_command(cmd_name)
File "C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\setuptools\_distutils\cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\setuptools\dist.py", line 1234, in run_command
super().run_command(command)
File "C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\setuptools\_distutils\dist.py", line 988, in run_command
cmd_obj.run()
File "C:\Users\ana.valinhas\AppData\pip-install-g2gatndu\amici_36641f72bf1a4f5eab8decde7d536cce\amici\custom_commands.py", line 124, in run
self.run_command("build_ext")
File "C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\setuptools\_distutils\cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\setuptools\dist.py", line 1234, in run_command
super().run_command(command)
File "C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\setuptools\_distutils\dist.py", line 988, in run_command
cmd_obj.run()
File "C:\Users\ana.valinhas\AppData\pip-install-g2gatndu\amici_36641f72bf1a4f5eab8decde7d536cce\amici\custom_commands.py", line 150, in run
result = super().run()
File "C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\cmake_build_extension\build_extension.py", line 113, in run
self.build_extension(ext)
File "C:\Users\ana.valinhas\AppData\pip-install-g2gatndu\amici_36641f72bf1a4f5eab8decde7d536cce\amici\custom_commands.py", line 177, in build_extension
super().build_extension(ext)
File "C:\Users\ana.valinhas\AppData\pip-build-env-aqngm_ut\overlay\Lib\site-packages\cmake_build_extension\build_extension.py", line 229, in build_extension
subprocess.check_call(configure_command)
File "C:\Users\ana.valinhas\AppData\Local\Programs\Python\Python39\lib\subprocess.py", line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['cmake', '-S', 'C:\\Users\\ana.valinhas\\AppData\\pip-install-g2gatndu\\amici_36641f72bf1a4f5eab8decde7d536cce\\amici\\ThirdParty\\SuiteSparse\\SuiteSparse_config', '-B', 'C:\\Users\\an
a.valinhas\\AppData\\pip-install-g2gatndu\\amici_36641f72bf1a4f5eab8decde7d536cce\\build\\temp.win-amd64-cpython-39\\Release_SuiteSparse_config', '-GNinja', '-DCMAKE_BUILD_TYPE=Release', '-DCMAKE_INSTALL_PREFIX:PATH=C:\\Users\\ana.v
alinhas\\AppData\\pip-install-g2gatndu\\amici_36641f72bf1a4f5eab8decde7d536cce\\build\\lib.win-amd64-cpython-39\\amici', '-DCMAKE_MAKE_PROGRAM=C:\\Users\\ana.valinhas\\AppData\\pip-build-env-aqngm_ut\\overlay\\Scripts\\ninja.EXE', '
-DCMAKE_VERBOSE_MAKEFILE=ON', '-DBLA_VENDOR=All', '-DENABLE_CUDA=FALSE', '-DNFORTRAN=TRUE']' returned non-zero exit status 1.
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for amici
Failed to build amici
ERROR: Could not build wheels for amici, which is required to install pyproject.toml-based projects
`
Некоторые способы устранения неполадок, которые я пробовал до сих пор:
- добавлено местоположение cl.exe компилятора в переменную PATH
- добавлено расположение Windows 10 SDK mt.exe в переменную PATH
- установите переменную CC непосредственно в pycharm в файл cl.exe компилятора.
- Установлены/обновлены все зависимости для AMICI.
- В системе отключена переменная длины MAX_PATH.
При просмотре ошибки кажется, что CMAKE не может сохранить временный файл, созданный при запуске теста на компиляторе.
Кто-нибудь сталкивался с подобной проблемой? Буду признателен, если кто-нибудь подскажет, что делать дальше.
1 ответ
Ошибка связана с тем, что путь, по которому происходит сборка, превышает «стандартный» предел в Windows.
Никаких обещаний, но вы можете попробовать включить длинные пути в самой Windows — некоторые документы можно найти здесь: https://www.microfocus.com/documentation/filr/filr-4/filr-desktop/t47bx2ogpfz7.html
Или как альтернатива; ты можешь попробовать пройти-b c:/buildtmp/или что-то похожее на вашеpip install. Это поместит фактический каталог сборки почти в корень вашего диска C, чтобы, когда cmake генерирует цели и пытается их скомпилировать, максимальный предел длины пути не будет превышен.