Closed weantony closed 3 years ago
Hi weantony,
you can try to install the packages individually to see if that solves it, even though it's fairly unlikely:
pip install numpy
Installing numpy first and then pynumpress makes sense I think
pip install pynumpress
Installing pynumpress without the version specified may help as well.
But in the end it looks mostly like a Windows issue and I'm not sure how to fix that.
Maybe someone else has a idea?
Hi weantony,
may be related to the the PATH variable, which has to be edited.
Chekc this out: https://stackoverflow.com/questions/48091017/c1083-cannot-open-include-file-python-h-no-such-file-or-directory
Cheers, Johannes
Hi weantony,
you can try to install the packages individually to see if that solves it, even though it's fairly unlikely:
pip install numpy
Installing numpy first and then pynumpress makes sense I thinkpip install pynumpress
Installing pynumpress without the version specified may help as well. But in the end it looks mostly like a Windows issue and I'm not sure how to fix that. Maybe someone else has a idea?
Hi StSchulze
Thank you very much for your suggestion. I tried to install pynum and pynumpress seperately. I think the problem comes from installing pynumpress. The error message listed below is what I got from installing pynumpress. It looks quite similar to what I got from installing requirements.txt. However, I am still trying to figure out what the problem is.
C:\Users\weant>python -m pip install pynumpress
Collecting pynumpress
Using cached pynumpress-0.0.5.tar.gz (110 kB)
Requirement already satisfied: numpy in c:\users\weant\appdata\roaming\python\python38\site-packages (from pynumpress) (1.19.2)
Building wheels for collected packages: pynumpress
Building wheel for pynumpress (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: 'C:\Users\weant\AppData\Local\Programs\Python\Python38\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\weant\\AppData\\Local\\Temp\\pip-install-y79a4pyb\\pynumpress\\setup.py'"'"'; __file__='"'"'C:\\Users\\weant\\AppData\\Local\\Temp\\pip-install-y79a4pyb\\pynumpress\\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\weant\AppData\Local\Temp\pip-wheel-2kqpjacb'
cwd: C:\Users\weant\AppData\Local\Temp\pip-install-y79a4pyb\pynumpress\
Complete output (16 lines):
running bdist_wheel
running build
running build_py
creating build
creating build\lib.win-amd64-3.8
creating build\lib.win-amd64-3.8\pynumpress
copying pynumpress\__init__.py -> build\lib.win-amd64-3.8\pynumpress
running build_ext
building 'pynumpress.pynumpress' extension
creating build\temp.win-amd64-3.8
creating build\temp.win-amd64-3.8\Release
creating build\temp.win-amd64-3.8\Release\pynumpress
C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.27.29110\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -I.\pynumpress -IC:\Users\weant\AppData\Roaming\Python\Python38\site-packages\numpy\core\include -IC:\Users\weant\AppData\Roaming\Python\Python38\site-packages\numpy\core\include -IC:\Users\weant\AppData\Local\Programs\Python\Python38\include -IC:\Users\weant\AppData\Local\Programs\Python\Python38\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.27.29110\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EHsc /Tppynumpress/pynumpress.cpp /Fobuild\temp.win-amd64-3.8\Release\pynumpress/pynumpress.obj /EHsc
pynumpress.cpp
pynumpress/pynumpress.cpp(30): fatal error C1083: Cannot open include file: 'Python.h': No such file or directory
error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio\\2019\\BuildTools\\VC\\Tools\\MSVC\\14.27.29110\\bin\\HostX86\\x64\\cl.exe' failed with exit status 2
----------------------------------------
ERROR: Failed building wheel for pynumpress
Running setup.py clean for pynumpress
Failed to build pynumpress
Installing collected packages: pynumpress
Running setup.py install for pynumpress ... error
ERROR: Command errored out with exit status 1:
command: 'C:\Users\weant\AppData\Local\Programs\Python\Python38\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\weant\\AppData\\Local\\Temp\\pip-install-y79a4pyb\\pynumpress\\setup.py'"'"'; __file__='"'"'C:\\Users\\weant\\AppData\\Local\\Temp\\pip-install-y79a4pyb\\pynumpress\\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\weant\AppData\Local\Temp\pip-record-pn4i6w2m\install-record.txt' --single-version-externally-managed --compile --install-headers 'C:\Users\weant\AppData\Local\Programs\Python\Python38\Include\pynumpress'
cwd: C:\Users\weant\AppData\Local\Temp\pip-install-y79a4pyb\pynumpress\
Complete output (16 lines):
running install
running build
running build_py
creating build
creating build\lib.win-amd64-3.8
creating build\lib.win-amd64-3.8\pynumpress
copying pynumpress\__init__.py -> build\lib.win-amd64-3.8\pynumpress
running build_ext
building 'pynumpress.pynumpress' extension
creating build\temp.win-amd64-3.8
creating build\temp.win-amd64-3.8\Release
creating build\temp.win-amd64-3.8\Release\pynumpress
C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.27.29110\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -I.\pynumpress -IC:\Users\weant\AppData\Roaming\Python\Python38\site-packages\numpy\core\include -IC:\Users\weant\AppData\Roaming\Python\Python38\site-packages\numpy\core\include -IC:\Users\weant\AppData\Local\Programs\Python\Python38\include -IC:\Users\weant\AppData\Local\Programs\Python\Python38\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.27.29110\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EHsc /Tppynumpress/pynumpress.cpp /Fobuild\temp.win-amd64-3.8\Release\pynumpress/pynumpress.obj /EHsc
pynumpress.cpp
pynumpress/pynumpress.cpp(30): fatal error C1083: Cannot open include file: 'Python.h': No such file or directory
error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio\\2019\\BuildTools\\VC\\Tools\\MSVC\\14.27.29110\\bin\\HostX86\\x64\\cl.exe' failed with exit status 2
----------------------------------------
ERROR: Command errored out with exit status 1: 'C:\Users\weant\AppData\Local\Programs\Python\Python38\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\weant\\AppData\\Local\\Temp\\pip-install-y79a4pyb\\pynumpress\\setup.py'"'"'; __file__='"'"'C:\\Users\\weant\\AppData\\Local\\Temp\\pip-install-y79a4pyb\\pynumpress\\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\weant\AppData\Local\Temp\pip-record-pn4i6w2m\install-record.txt' --single-version-externally-managed --compile --install-headers 'C:\Users\weant\AppData\Local\Programs\Python\Python38\Include\pynumpress' Check the logs for full command output.
Hi,
have you tried the suggestion of @JB-MS ? If that doesn't work either, you might want to open an issue in the pynumpress repo directly. I'm tagging @mobiusklein in case he has a quick fix for it?
Best, Stefan
I haven't encountered this problem on Windows before. It looks like the include path is being specified correctly, but let's check. If you go to C:\Users\weant\AppData\Local\Programs\Python\Python38\include
, do you see the file Python.h
in that folder?
Hi,
have you tried the suggestion of @JB-MS ? If that doesn't work either, you might want to open an issue in the pynumpress repo directly. I'm tagging @mobiusklein in case he has a quick fix for it?
Best, Stefan
Hi StSchulze,
Thank you very much for the reply. I am really sorry I am not able to make very quick reponse because my knowledge related to programing and CS is very limited. I tried to read the suggestion of JB-MS, but I honestly still can't understand the contend of it. Instead I tried to installed python and visual studio 2019 in the same way on another laptop with win 10 Enterprise. After trying pip install install -r requirements.txt, the error became Preparing wheel metadata... error. But pynumpress was successfully installed. So I guess the problem why I can't install pynumpress is related to certain setting or path somewhere. I am still trying to figure things out.
Thank you very much for reaching out and help.
I haven't encountered this problem on Windows before. It looks like the include path is being specified correctly, but let's check. If you go to
C:\Users\weant\AppData\Local\Programs\Python\Python38\include
, do you see the filePython.h
in that folder?
Hi mobiusklein,
I didn't even find a filefolder named inclue in C:\Users\weant\AppData\Local\Programs\Python\Python38. I can find this folder and python.h on my other labtop which install python. Do I need to remove and install python on my pc or just add something to it please? Thank you very much for reaching out and help.
I've just uploaded a Python 3.8 Windows wheel for pynumpress
, so you should be able to install that at least without needing to make any changes to your system now.
That you can't find C:\Users\weant\AppData\Local\Programs\Python\Python38\include
explains why building pynumpress
failed. I can't imagine why the folder would be missing, either. In theory, you could just copy over the include folder from another known good copy of Python 3.8, but this assumes no other part of your Python installation is unexpectedly missing.
The include
folder isn't necessary unless you need to install a package with a C extension from source again, like you're trying to do with pynumpress
.
I've just uploaded a Python 3.8 Windows wheel for
pynumpress
, so you should be able to install that at least without needing to make any changes to your system now.That you can't find
C:\Users\weant\AppData\Local\Programs\Python\Python38\include
explains why buildingpynumpress
failed. I can't imagine why the folder would be missing, either. In theory, you could just copy over the include folder from another known good copy of Python 3.8, but this assumes no other part of your Python installation is unexpectedly missing.The
include
folder isn't necessary unless you need to install a package with a C extension from source again, like you're trying to do withpynumpress
.
Hi mobiusklein,
Thank you so much. I tried python -m pip install pynumpress again and nothing changed. But I think I should reinstall the python first to make it right first. I'll let you know if there's any progress on that. Thank you so much for your help.
I've just uploaded a Python 3.8 Windows wheel for
pynumpress
, so you should be able to install that at least without needing to make any changes to your system now.That you can't find
C:\Users\weant\AppData\Local\Programs\Python\Python38\include
explains why buildingpynumpress
failed. I can't imagine why the folder would be missing, either. In theory, you could just copy over the include folder from another known good copy of Python 3.8, but this assumes no other part of your Python installation is unexpectedly missing.The
include
folder isn't necessary unless you need to install a package with a C extension from source again, like you're trying to do withpynumpress
.
Hi mobiusklein,
I have reinstalled python 3.8.0 and include filefolder showed up. The installation of requirements.txt and setup.py are successfully finished. Thank you very much for all your kindness help. May I further ask what does tox mean in test the package and correct installation please? It seems the tox file in pymzML could not just run by python code. Thank you again for your help.
Happy to help.
tox
is a tool for testing automating testing Python programs across multiple Python versions/environments. It's useful for proving that the program. I don't think you need to worry about it for the moment, unless you plan to make substantial changes to pymzML itself.
Happy to help.
tox
is a tool for testing automating testing Python programs across multiple Python versions/environments. It's useful for proving that the program. I don't think you need to worry about it for the moment, unless you plan to make substantial changes to pymzML itself.
Thank you very much again.
Hi @weantony,
Is your problem resolved and can we close this issue? And Thanks @mobiusklein for fixing this so fast again!
Best, Manuel
Hi @weantony,
Is your problem resolved and can we close this issue? And Thanks @mobiusklein for fixing this so fast again!
Best, Manuel
Hi MKoester,
Thank you all very much, the problem is resolved and can be closed. Your effort really helped a lot.
Best Regards, Jian Yu
Hi Everyone,
I am a beginner in python. I got some problem in installing requirements.txt file. Could someone give some advice please? The entile code is listed below. It looks like there are two errors. The first one is failed to build wheel for pynumpress and the second one is failed to run setup.py for pynumpress. I did have installed visual studio 2019 and wheel already.
Thank you very much in advance.