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I am a new learner for rppg and python and I am using conda env create --file https://raw.githubusercontent.com/phuselab/pyVHR/master/pyVHR_env.yml to create a new environment. However, this error exists every time, even if I have installed fortran and cmake. Can anyone give me a tip?
`numpy.distutils` is deprecated since NumPy 1.23.0, as a result
of the deprecation of `distutils` itself. It will be removed for
Python >= 3.12. For older Python versions it will remain present.
It is recommended to use `setuptools < 60.0` for those Python versions.
For more details, see:
https://numpy.org/devdocs/reference/distutils_status_migration.html
from numpy.distutils.core import setup
running bdist_wheel
running build
running config_cc
INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
INFO: build_src
INFO: building py_modules sources
INFO: building extension "libforbdf" sources
INFO: f2py options: []
INFO: adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9\fortranobject.c' to sources.
INFO: adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9' to include_dirs.
INFO: adding 'build\src.win-amd64-3.9\libforbdf-f2pywrappers.f' to sources.
INFO: build_src: building npy-pkg config files
D:\miniconda\envs\pyvhr\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_py
creating build\lib.win-amd64-cpython-39
copying pybdf.py -> build\lib.win-amd64-cpython-39
running build_ext
INFO: No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
INFO: customize MSVCCompiler
INFO: customize MSVCCompiler using build_ext
INFO: CCompilerOpt.cc_test_flags[1073] : testing flags (/O2)
error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/
INFO: CCompilerOpt.cache_flush[857] : write cache to path -> C:\Users\26567\AppData\Local\Temp\pip-install-lsm0gmuc\pybdf_a7971f41fb3a45e98bde2a7da8b96c7e\build\temp.win-amd64-cpython-39\Release\ccompiler_opt_cache_ext.py
what do you mean by typing every packages to install?
as in, every time you encountered an error when running the notebook demo code, you installed the missing packages?
for example i cant get past pip install cupy, takes like +20 mins to install on colab and throws an error then
I am a new learner for rppg and python and I am using conda env create --file https://raw.githubusercontent.com/phuselab/pyVHR/master/pyVHR_env.yml to create a new environment. However, this error exists every time, even if I have installed fortran and cmake. Can anyone give me a tip?
Failed to build pybdf
Installing collected packages: rpds-py, attrs, six, referencing, zipp, traitlets, pywin32, python-dateutil, platformdirs, jsonschema-specifications, tornado, pyzmq, jupyter-core, jsonschema, importlib-metadata, fastjsonschema, arrow, webencodings, webcolors, uri-template, soupsieve, rfc3986-validator, rfc3339-validator, pywinpty, nbformat, MarkupSafe, jupyter-client, jsonpointer, isoduration, fqdn, wcwidth, tinycss2, terminado, sniffio, pyyaml, python-json-logger, pygments, parso, pandocfilters, nbclient, mistune, jupyterlab-pygments, jinja2, exceptiongroup, defusedxml, bleach, beautifulsoup4, argon2-cffi-bindings, websocket-client, Send2Trash, prompt-toolkit, prometheus-client, pickleshare, overrides, nbconvert, matplotlib-inline, jupyter-server-terminals, jupyter-events, jedi, decorator, colorama, backcall, argon2-cffi, anyio, pyasn1, psutil, nest-asyncio, jupyter-server, ipython, debugpy, comm, rsa, pyasn1-modules, oauthlib, numpy, notebook-shim, ipython-genutils, ipykernel, cachetools, requests-oauthlib, pytz, pyparsing, nbclassic, kiwisolver, google-auth, fonttools, cycler, contourpy, werkzeug, threadpoolctl, tensorboard-plugin-wit, tensorboard-data-server, protobuf, patsy, pandas, notebook, matplotlib, markdown, joblib, grpcio, google-auth-oauthlib, future, absl-py, wrapt, widgetsnbextension, uncertainties, typing-extensions, tifffile, termcolor, tensorflow-estimator, tensorboard, tenacity, statsmodels, shortuuid, seaborn, scikit-learn, PyWavelets, opt-einsum, opencv-python, opencv-contrib-python, networkx, keras-preprocessing, keras-nightly, jupyterlab-widgets, imageio, h5py, google-pasta, gast, flatbuffers, bidict, baycomp, astunparse, asteval, tqdm, tensorflow, scikit-posthocs, scikit-image, PySimpleGUI, pybdf, plotly, mediapipe, lmfit, ipywidgets, biosppy, autorank, asposestorage
Attempting uninstall: six
Found existing installation: six 1.16.0
Uninstalling six-1.16.0:
Successfully uninstalled six-1.16.0
Attempting uninstall: numpy
Found existing installation: numpy 1.23.5
Uninstalling numpy-1.23.5:
Successfully uninstalled numpy-1.23.5
Attempting uninstall: typing-extensions
Found existing installation: typing-extensions 4.4.0
Uninstalling typing-extensions-4.4.0:
Successfully uninstalled typing-extensions-4.4.0
Running setup.py install for pybdf: started
Running setup.py install for pybdf: finished with status 'error'
Pip subprocess error:
ERROR: Command errored out with exit status 1:
command: 'D:\miniconda\envs\pyvhr\python.exe' -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\26567\AppData\Local\Temp\pip-install-lsm0gmuc\pybdf_a7971f41fb3a45e98bde2a7da8b96c7e\setup.py'"'"'; file='"'"'C:\Users\26567\AppData\Local\Temp\pip-install-lsm0gmuc\pybdf_a7971f41fb3a45e98bde2a7da8b96c7e\setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d 'C:\Users\26567\AppData\Local\Temp\pip-wheel-xfklkjz4'
cwd: C:\Users\26567\AppData\Local\Temp\pip-install-lsm0gmuc\pybdf_a7971f41fb3a45e98bde2a7da8b96c7e
Complete output (38 lines):
C:\Users\26567\AppData\Local\Temp\pip-install-lsm0gmuc\pybdf_a7971f41fb3a45e98bde2a7da8b96c7e\setup.py:4: DeprecationWarning:
running bdist_wheel
running build
running config_cc
INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
INFO: build_src
INFO: building py_modules sources
INFO: building extension "libforbdf" sources
INFO: f2py options: []
INFO: adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9\fortranobject.c' to sources.
INFO: adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9' to include_dirs.
INFO: adding 'build\src.win-amd64-3.9\libforbdf-f2pywrappers.f' to sources.
INFO: build_src: building npy-pkg config files
D:\miniconda\envs\pyvhr\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_py
creating build\lib.win-amd64-cpython-39
copying pybdf.py -> build\lib.win-amd64-cpython-39
running build_ext
INFO: No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
INFO: customize MSVCCompiler
INFO: customize MSVCCompiler using build_ext
INFO: CCompilerOpt.cc_test_flags[1073] : testing flags (/O2)
error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/
INFO: CCompilerOpt.cache_flush[857] : write cache to path -> C:\Users\26567\AppData\Local\Temp\pip-install-lsm0gmuc\pybdf_a7971f41fb3a45e98bde2a7da8b96c7e\build\temp.win-amd64-cpython-39\Release\ccompiler_opt_cache_ext.py
ERROR: Failed building wheel for pybdf
ERROR: Command errored out with exit status 1:
command: 'D:\miniconda\envs\pyvhr\python.exe' -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\26567\AppData\Local\Temp\pip-install-lsm0gmuc\pybdf_a7971f41fb3a45e98bde2a7da8b96c7e\setup.py'"'"'; file='"'"'C:\Users\26567\AppData\Local\Temp\pip-install-lsm0gmuc\pybdf_a7971f41fb3a45e98bde2a7da8b96c7e\setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record 'C:\Users\26567\AppData\Local\Temp\pip-record-tg5mubtn\install-record.txt' --single-version-externally-managed --compile --install-headers 'D:\miniconda\envs\pyvhr\Include\pybdf'
cwd: C:\Users\26567\AppData\Local\Temp\pip-install-lsm0gmuc\pybdf_a7971f41fb3a45e98bde2a7da8b96c7e
Complete output (101 lines):
running install
D:\miniconda\envs\pyvhr\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 config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building py_modules sources
building extension "libforbdf" sources
f2py options: []
adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9\fortranobject.c' to sources.
adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9' to include_dirs.
copying D:\miniconda\envs\pyvhr\lib\site-packages\numpy\f2py\src\fortranobject.c -> build\src.win-amd64-3.9\build\src.win-amd64-3.9
copying D:\miniconda\envs\pyvhr\lib\site-packages\numpy\f2py\src\fortranobject.h -> build\src.win-amd64-3.9\build\src.win-amd64-3.9
adding 'build\src.win-amd64-3.9\libforbdf-f2pywrappers.f' to sources.
build_src: building npy-pkg config files
running build_py
creating build\lib.win-amd64-cpython-39
copying pybdf.py -> build\lib.win-amd64-cpython-39
running build_ext
No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
customize MSVCCompiler
customize MSVCCompiler using build_ext
get_default_fcompiler: matching types: '['gnu', 'intelv', 'absoft', 'compaqv', 'intelev', 'gnu95', 'g95', 'intelvem', 'intelem', 'flang']'
customize GnuFCompiler
Could not locate executable g77
Could not locate executable f77
customize IntelVisualFCompiler
Could not locate executable ifort
Could not locate executable ifl
customize AbsoftFCompiler
Could not locate executable f90
customize CompaqVisualFCompiler
Could not locate executable DF
customize IntelItaniumVisualFCompiler
Could not locate executable efl
customize Gnu95FCompiler
Found executable D:\Mingwfortran\bin\gfortran.exe
Using built-in specs.
COLLECT_GCC=D:\Mingwfortran\bin\gfortran.exe
COLLECT_LTO_WRAPPER=d:/mingwfortran/bin/../libexec/gcc/mingw32/6.3.0/lto-wrapper.exe
Target: mingw32
Configured with: ../src/gcc-6.3.0/configure --build=x86_64-pc-linux-gnu --host=mingw32 --with-gmp=/mingw --with-mpfr=/mingw --with-mpc=/mingw --with-isl=/mingw --prefix=/mingw --disable-win32-registry --target=mingw32 --with-arch=i586 --enable-languages=c,c++,objc,obj-c++,fortran,ada --with-pkgversion='MinGW.org GCC-6.3.0-1' --enable-static --enable-shared --enable-threads --with-dwarf2 --disable-sjlj-exceptions --enable-version-specific-runtime-libs --with-libiconv-prefix=/mingw --with-libintl-prefix=/mingw --enable-libstdcxx-debug --with-tune=generic --enable-libgomp --disable-libvtv --enable-nls
Thread model: win32
gcc version 6.3.0 (MinGW.org GCC-6.3.0-1)
customize Gnu95FCompiler
Using built-in specs.
COLLECT_GCC=D:\Mingwfortran\bin\gfortran.exe
COLLECT_LTO_WRAPPER=d:/mingwfortran/bin/../libexec/gcc/mingw32/6.3.0/lto-wrapper.exe
Target: mingw32
Configured with: ../src/gcc-6.3.0/configure --build=x86_64-pc-linux-gnu --host=mingw32 --with-gmp=/mingw --with-mpfr=/mingw --with-mpc=/mingw --with-isl=/mingw --prefix=/mingw --disable-win32-registry --target=mingw32 --with-arch=i586 --enable-languages=c,c++,objc,obj-c++,fortran,ada --with-pkgversion='MinGW.org GCC-6.3.0-1' --enable-static --enable-shared --enable-threads --with-dwarf2 --disable-sjlj-exceptions --enable-version-specific-runtime-libs --with-libiconv-prefix=/mingw --with-libintl-prefix=/mingw --enable-libstdcxx-debug --with-tune=generic --enable-libgomp --disable-libvtv --enable-nls
Thread model: win32
gcc version 6.3.0 (MinGW.org GCC-6.3.0-1)
customize Gnu95FCompiler using build_ext
building 'libforbdf' extension
compiling C sources
creating build\temp.win-amd64-cpython-39\Release\build
creating build\temp.win-amd64-cpython-39\Release\build\src.win-amd64-3.9
creating build\temp.win-amd64-cpython-39\Release\build\src.win-amd64-3.9\build
creating build\temp.win-amd64-cpython-39\Release\build\src.win-amd64-3.9\build\src.win-amd64-3.9
D:\miniconda\envs\pyvhr\lib\site-packages\setuptools_distutils_msvccompiler.py:546: UserWarning: Fallback spawn triggered. Please update distutils monkeypatch.
warnings.warn("Fallback spawn triggered. Please update distutils monkeypatch.")
D:\visualc++\ide\VC\Tools\MSVC\14.36.32532\bin\HostX86\x64\cl.exe /c /nologo /O2 /W3 /GL /DNDEBUG /MD -Ibuild\src.win-amd64-3.9\build\src.win-amd64-3.9 -ID:\miniconda\envs\pyvhr\lib\site-packages\numpy\core\include -ID:\miniconda\envs\pyvhr\include -ID:\miniconda\envs\pyvhr\Include -ID:\visualc++\ide\VC\Tools\MSVC\14.36.32532\include -ID:\visualc++\ide\VC\Tools\MSVC\14.36.32532\ATLMFC\include -ID:\visualc++\ide\VC\Auxiliary\VS\include -IC:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\ucrt -IC:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\um -IC:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\shared -IC:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\winrt -IC:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\cppwinrt -IC:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE -IC:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\ucrt -IC:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\shared -IC:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\um -IC:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\winrt /Tcbuild\src.win-amd64-3.9\libforbdfmodule.c /Fobuild\temp.win-amd64-cpython-39\Release\build\src.win-amd64-3.9\libforbdfmodule.obj
D:\visualc++\ide\VC\Tools\MSVC\14.36.32532\bin\HostX86\x64\cl.exe /c /nologo /O2 /W3 /GL /DNDEBUG /MD -Ibuild\src.win-amd64-3.9\build\src.win-amd64-3.9 -ID:\miniconda\envs\pyvhr\lib\site-packages\numpy\core\include -ID:\miniconda\envs\pyvhr\include -ID:\miniconda\envs\pyvhr\Include -ID:\visualc++\ide\VC\Tools\MSVC\14.36.32532\include -ID:\visualc++\ide\VC\Tools\MSVC\14.36.32532\ATLMFC\include -ID:\visualc++\ide\VC\Auxiliary\VS\include -IC:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\ucrt -IC:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\um -IC:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\shared -IC:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\winrt -IC:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\cppwinrt -IC:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE -IC:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\ucrt -IC:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\shared -IC:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\um -IC:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\winrt /Tcbuild\src.win-amd64-3.9\build\src.win-amd64-3.9\fortranobject.c /Fobuild\temp.win-amd64-cpython-39\Release\build\src.win-amd64-3.9\build\src.win-amd64-3.9\fortranobject.obj
compiling Fortran sources
Fortran f77 compiler: D:\Mingwfortran\bin\gfortran.exe -Wall -g -ffixed-form -fno-second-underscore -O3 -funroll-loops
Fortran f90 compiler: D:\Mingwfortran\bin\gfortran.exe -Wall -g -fno-second-underscore -O3 -funroll-loops
Fortran fix compiler: D:\Mingwfortran\bin\gfortran.exe -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -O3 -funroll-loops
compile options: '-Ibuild\src.win-amd64-3.9\build\src.win-amd64-3.9 -ID:\miniconda\envs\pyvhr\lib\site-packages\numpy\core\include -ID:\miniconda\envs\pyvhr\include -ID:\miniconda\envs\pyvhr\Include -c'
gfortran.exe:f90: libforbdf.f95
libforbdf.f95:44:44:
ERROR: Command errored out with exit status 1: 'D:\miniconda\envs\pyvhr\python.exe' -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\26567\AppData\Local\Temp\pip-install-lsm0gmuc\pybdf_a7971f41fb3a45e98bde2a7da8b96c7e\setup.py'"'"'; file='"'"'C:\Users\26567\AppData\Local\Temp\pip-install-lsm0gmuc\pybdf_a7971f41fb3a45e98bde2a7da8b96c7e\setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record 'C:\Users\26567\AppData\Local\Temp\pip-record-tg5mubtn\install-record.txt' --single-version-externally-managed --compile --install-headers 'D:\miniconda\envs\pyvhr\Include\pybdf' Check the logs for full command output.
failed
CondaEnvException: Pip failed
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