This error originates from a subprocess

[SaraNiknamHesar]

Hello I have this problem when I am trying to install the ontogpt and use pip install ontogpt

please help me it has been 3 days I am trying to use it but I can't

[caufieldjh]

Hi @SaraNiknamHesar - if you're on a Windows system then this may be the same issue as here: #387
The solution in that case is to install the MS C++ build tools from https://visualstudio.microsoft.com/visual-cpp-build-tools/

[SaraNiknamHesar]

I still have the same problem and I already read and did this solution you suggested but still the problem. the version of my python is 3.10 I tried it on 3.11 3.12 3.13 it did not work I cloned it and then installed oak, I even set the API, but it still didn't recognize Ontogpt. I tried all the ways that I thought would work, but all of them end up with this error.
I provided the whole error because I really don't know what to do and at the end, it mentioned to update pip, I have tried that too, but it didn't work. I installed wheel myself and updated it, unfortunately nothing happened. I even tried to run adeft separately, but I still got the same error.
////////////////////////////////error text
pip install ontogpt
Collecting ontogpt
Using cached ontogpt-1.0.7-py3-none-any.whl (1.3 MB)
Collecting toml<0.11.0,>=0.10.2
Using cached toml-0.10.2-py2.py3-none-any.whl (16 kB)
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Collecting linkml-owl<0.4.0,>=0.3.0
Using cached linkml_owl-0.3.0-py3-none-any.whl (17 kB)
Collecting requests-cache>=1.2.0
Using cached requests_cache-1.2.1-py3-none-any.whl (61 kB)
Requirement already satisfied: click>=8.1.3 in c:\users\lenovo\appdata\local\programs\python\python310\lib\site-packages (from ontogpt) (8.1.7)
Collecting linkml<2.0.0,>=1.8.3
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Requirement already satisfied: requests<3.0.0,>=2.31.0 in c:\users\lenovo\appdata\local\programs\python\python310\lib\site-packages (from ontogpt) (2.32.3)
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Requirement already satisfied: colorama in c:\users\lenovo\appdata\local\programs\python\python310\lib\site-packages (from click>=8.1.3->ontogpt) (0.4.6)
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Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing wheel metadata ... done
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Using cached botocore-1.35.57-py3-none-any.whl (12.7 MB)
Collecting s3transfer<0.11.0,>=0.10.0
Using cached s3transfer-0.10.3-py3-none-any.whl (82 kB)
Collecting wrapt<2,>=1.10
Using cached wrapt-1.16.0-cp310-cp310-win_amd64.whl (37 kB)
Collecting sortedcontainers<3.0,>=2.0
Using cached sortedcontainers-2.4.0-py2.py3-none-any.whl (29 kB)
Collecting arrow>=0.15.0
Using cached arrow-1.3.0-py3-none-any.whl (66 kB)
Collecting types-python-dateutil>=2.8.10
Using cached types_python_dateutil-2.9.0.20241003-py3-none-any.whl (9.7 kB)
Collecting jsonpath-ng
Using cached jsonpath_ng-1.7.0-py3-none-any.whl
Collecting jsonpatch
Using cached jsonpatch-1.33-py2.py3-none-any.whl (12 kB)
Collecting ply
Using cached ply-3.11-py2.py3-none-any.whl (49 kB)
Collecting et-xmlfile
Using cached et_xmlfile-2.0.0-py3-none-any.whl (18 kB)
Collecting rdflib-jsonld==0.6.1
Using cached rdflib_jsonld-0.6.1-py2.py3-none-any.whl (16 kB)
WARNING: scipy 1.14.1 does not provide the extra 'scipy'
Collecting huggingface-hub<1.0,>=0.16.4
Using cached huggingface_hub-0.26.2-py3-none-any.whl (447 kB)
Requirement already satisfied: filelock in c:\users\lenovo\appdata\local\programs\python\python310\lib\site-packages (from huggingface-hub<1.0,>=0.16.4->tokenizers->litellm<2.0.0,>=1.44.28->ontogpt) (3.16.1)
Collecting fsspec>=2023.5.0
Using cached fsspec-2024.10.0-py3-none-any.whl (179 kB)
Building wheels for collected packages: antlr4-python3-runtime, cfgraph, pytest-logging, ratelimit, wikipedia, wikipedia-api, adeft, docopt, intervaltree
Building wheel for antlr4-python3-runtime (setup.py) ... done
Created wheel for antlr4-python3-runtime: filename=antlr4_python3_runtime-4.9.3-py3-none-any.whl size=144586 sha256=c20a49374bf1ec70a5cb501e506462ac986ff2a4a2288bbafdff74c7dfbfb6ab
Stored in directory: c:\users\lenovo\appdata\local\pip\cache\wheels\12\93\dd\1f6a127edc45659556564c5730f6d4e300888f4bca2d4c5a88
Building wheel for cfgraph (setup.py) ... done
Created wheel for cfgraph: filename=CFGraph-0.2.1-py3-none-any.whl size=2240 sha256=d2f08a44271f4b6b9e819f48c7c93aa7dea6d038f503b6e3d7275f2c7d46aec8
Stored in directory: c:\users\lenovo\appdata\local\pip\cache\wheels\26\bd\ce\f40398ab2be182fe27806de6f27185f2dc207241061f7095df
Building wheel for pytest-logging (setup.py) ... done
Created wheel for pytest-logging: filename=pytest_logging-2015.11.4-py3-none-any.whl size=4376 sha256=efbf48979b6d9591db966e9b728467de0957782ca61c7ce1e890068979863bfb
Stored in directory: c:\users\lenovo\appdata\local\pip\cache\wheels\cd\ab\3d\9fdfd7c440f382fb6db4e3ce2d8b7922e6aacf613aa3cb44b9
Building wheel for ratelimit (setup.py) ... done
Created wheel for ratelimit: filename=ratelimit-2.2.1-py3-none-any.whl size=5944 sha256=9dcef25a80370a5656c042d93d94ca84dbb9a9390e76566dbf39fbe78f3e4a9f
Stored in directory: c:\users\lenovo\appdata\local\pip\cache\wheels\27\5f\ba\e972a56dcbf5de9f2b7d2b2a710113970bd173c4dcd3d2c902
Building wheel for wikipedia (setup.py) ... done
Created wheel for wikipedia: filename=wikipedia-1.4.0-py3-none-any.whl size=11723 sha256=de9e31cfa92a18aba7d05294cb5bf9d5662d7b1c823b1afe872df34c45380c6b
Stored in directory: c:\users\lenovo\appdata\local\pip\cache\wheels\5e\b6\c5\93f3dec388ae76edc830cb42901bb0232504dfc0df02fc50de
Building wheel for wikipedia-api (setup.py) ... done
Created wheel for wikipedia-api: filename=Wikipedia_API-0.7.1-py3-none-any.whl size=14403 sha256=cece2b0649c5ba700ed8c8ff3b7f154843b85b46c2cd31abd59745cdcf1ffc57
Stored in directory: c:\users\lenovo\appdata\local\pip\cache\wheels\4c\96\18\b9201cc3e8b47b02b510460210cfd832ccf10c0c4dd0522962
Building wheel for adeft (PEP 517) ... error
ERROR: Command errored out with exit status 1:
command: 'C:\Users\Lenovo\AppData\Local\Programs\Python\Python310\python.exe' 'C:\Users\Lenovo\AppData\Local\Programs\Python\Python310\lib\site-packages\pip_vendor\pep517\in_process_in_process.py' build_wheel 'C:\Users\Lenovo\AppData\Local\Temp\tmpkjl6jxk7'
cwd: C:\Users\Lenovo\AppData\Local\Temp\pip-install-crreu1wq\adeft_be9318e6728e465f8c6135208dae5f30
Complete output (54 lines):
running bdist_wheel
running build
running build_py
creating build\lib.win-amd64-cpython-310\adeft
copying src\adeft\disambiguate.py -> build\lib.win-amd64-cpython-310\adeft
copying src\adeft\discover.py -> build\lib.win-amd64-cpython-310\adeft
copying src\adeft\locations.py -> build\lib.win-amd64-cpython-310\adeft
copying src\adeft\recognize.py -> build\lib.win-amd64-cpython-310\adeft
copying src\adeft\util.py -> build\lib.win-amd64-cpython-310\adeft
copying src\adeft_init_.py -> build\lib.win-amd64-cpython-310\adeft
creating build\lib.win-amd64-cpython-310\adeft\download
copying src\adeft\download\download.py -> build\lib.win-amd64-cpython-310\adeft\download
copying src\adeft\download_init_.py -> build\lib.win-amd64-cpython-310\adeft\download
copying src\adeft\download_main_.py -> build\lib.win-amd64-cpython-310\adeft\download
creating build\lib.win-amd64-cpython-310\adeft\gui
copying src\adeft\gui_init_.py -> build\lib.win-amd64-cpython-310\adeft\gui
creating build\lib.win-amd64-cpython-310\adeft\modeling
copying src\adeft\modeling\classify.py -> build\lib.win-amd64-cpython-310\adeft\modeling
copying src\adeft\modeling\label.py -> build\lib.win-amd64-cpython-310\adeft\modeling
copying src\adeft\modeling_init_.py -> build\lib.win-amd64-cpython-310\adeft\modeling
creating build\lib.win-amd64-cpython-310\adeft\nlp
copying src\adeft\nlp\nlp.py -> build\lib.win-amd64-cpython-310\adeft\nlp
copying src\adeft\nlp_init_.py -> build\lib.win-amd64-cpython-310\adeft\nlp
creating build\lib.win-amd64-cpython-310\adeft\score
copying src\adeft\score\score.py -> build\lib.win-amd64-cpython-310\adeft\score
copying src\adeft\score_init_.py -> build\lib.win-amd64-cpython-310\adeft\score
creating build\lib.win-amd64-cpython-310\adeft\gui\ground
copying src\adeft\gui\ground\ground.py -> build\lib.win-amd64-cpython-310\adeft\gui\ground
copying src\adeft\gui\ground_init_.py -> build\lib.win-amd64-cpython-310\adeft\gui\ground
running egg_info
writing src\adeft.egg-info\PKG-INFO
writing dependency_links to src\adeft.egg-info\dependency_links.txt
writing requirements to src\adeft.egg-info\requires.txt
writing top-level names to src\adeft.egg-info\top_level.txt
reading manifest file 'src\adeft.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'src\adeft.egg-info\SOURCES.txt'
copying src\adeft\nlp\stopwords.json -> build\lib.win-amd64-cpython-310\adeft\nlp
copying src\adeft\score_score.c -> build\lib.win-amd64-cpython-310\adeft\score
copying src\adeft\score_score.pyx -> build\lib.win-amd64-cpython-310\adeft\score
copying src\adeft\score\permutations.pyx -> build\lib.win-amd64-cpython-310\adeft\score
creating build\lib.win-amd64-cpython-310\adeft\gui\ground\static
copying src\adeft\gui\ground\static\ground.css -> build\lib.win-amd64-cpython-310\adeft\gui\ground\static
copying src\adeft\gui\ground\static\scripts.js -> build\lib.win-amd64-cpython-310\adeft\gui\ground\static
creating build\lib.win-amd64-cpython-310\adeft\gui\ground\templates
copying src\adeft\gui\ground\templates\input.jinja2 -> build\lib.win-amd64-cpython-310\adeft\gui\ground\templates
running build_ext
building 'adeft.score._score' extension
creating build\temp.win-amd64-cpython-310\Release\src\adeft\score
"C:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Tools\MSVC\14.41.34120\bin\HostX86\x64\cl.exe" /c /nologo /O2 /W3 /GL /DNDEBUG /MD -IC:\Users\Lenovo\AppData\Local\Programs\Python\Python310\include -IC:\Users\Lenovo\AppData\Local\Programs\Python\Python310\Include "-IC:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Tools\MSVC\14.41.34120\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Auxiliary\VS\include" /Tcsrc/adeft/score/_score.c /Fobuild\temp.win-amd64-cpython-310\Release\src/adeft/score/_score.obj
_score.c
C:\Users\Lenovo\AppData\Local\Programs\Python\Python310\include\pyconfig.h(59): fatal error C1083: Cannot open include file: 'io.h': No such file or directory
error: command 'C:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Tools\MSVC\14.41.34120\bin\HostX86\x64\cl.exe' failed with exit code 2

ERROR: Failed building wheel for adeft
Building wheel for docopt (setup.py) ... done
Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13791 sha256=66620b9dcf6c8f439c0558621618a1ade37596280091e4ce70617b2d297ecf2c
Stored in directory: c:\users\lenovo\appdata\local\pip\cache\wheels\fc\ab\d4\5da2067ac95b36618c629a5f93f809425700506f72c9732fac
Building wheel for intervaltree (setup.py) ... done
Created wheel for intervaltree: filename=intervaltree-3.1.0-py2.py3-none-any.whl size=26140 sha256=cc3cef8f8aa0b5720fa3d230598d962313b89b5b09a4525616770f3cf5bf89d9
Stored in directory: c:\users\lenovo\appdata\local\pip\cache\wheels\fa\80\8c\43488a924a046b733b64de3fac99252674c892a4c3801c0a61
Successfully built antlr4-python3-runtime cfgraph pytest-logging ratelimit wikipedia wikipedia-api docopt intervaltree
Failed to build adeft
ERROR: Could not build wheels for adeft which use PEP 517 and cannot be installed directly
WARNING: You are using pip version 21.2.3; however, version 24.3.1 is available.
You should consider upgrading via the 'C:\Users\Lenovo\AppData\Local\Programs\Python\Python310\python.exe -m pip install --upgrade pip' command.

[caufieldjh]

OK, does this work:

python -m pip install --no-use-pep517 adeft

[caufieldjh]

Another solution here would be to use a Docker container - I don't have one ready to go for OntoGPT but have an open issue for it in #176.

[caufieldjh]

I think this is the main error, though:

C:\Users\Lenovo\AppData\Local\Programs\Python\Python310\include\pyconfig.h(59): fatal error C1083: Cannot open include file: 'io.h': No such file or directory

That should be installed along with the build tools, so I'm not sure why it can't be found on your system.

[SaraNiknamHesar]

The first solution didn't work and I have to check the second one because I don't know Docker, but for the third issue, yes, this is one of the errors that I tried to find an answer for, but no results were obtained. If you could give a solution for this, I would be grateful. I need it a lot to be able to work with this tool, please don't close the issue so that I can test the second solution, because now Europe is night, thanks

[SaraNiknamHesar]

I finally be able to solve the problem but again I countered with another problem and I am using the API key from open api I tried to see in the troubleshooting of the complete document about this problem but it was written that this error can be due to various reasons. I tried to look for the file that specifies the version of the models to change it to 4, but unfortunately I couldn't find it.
I have to add that I got an API from the purchased version of GPT chat and tested it, and I got an API from the regular version and tested it, but it didn't work.

[caufieldjh]

Hi @SaraNiknamHesar - I hid your comment to avoid sharing your API key.
The original comment text is below.

I finally be able to solve the problem but again I countered with another problem and I am using the API key from open api I tried to see in the troubleshooting of the complete document about this problem but it was written that this error can be due to various reasons. I tried to look for the file that specifies the version of the models to change it to 4, but unfortunately I couldn't find it.
I have to add that I got an API from the purchased version of GPT chat and tested it, and I got an API from the regular version and tested it, but it didn't work.

[caufieldjh]

You may want to set your API key as an environment variable - before running ontogpt - like so:

export OPENAI_API_KEY="key-goes-here"

[SaraNiknamHesar]

I did it, but I still have the same problem, isn't there a way to do this manually in the codes???

[SaraNiknamHesar]

With your advice, I used the command you gave and even tried both ways mentioned in the link I posted, but I didn't get an answer. Is there a solution? I want to use this model in my presentation and I am really stuck in solving its problems.

https://help.openai.com/en/articles/5112595-best-practices-for-api-key-safety

[caufieldjh]

Hi @SaraNiknamHesar,
If you have tried the export command (or in the Windows command prompt, setx, as mentioned in the OpenAI docs link you provided) and you're still getting an error with ontogpt, then try this one:

runoak set-apikey -e openai <your openai api key>

If that still doesn't help, you may want to verify that your API key is working with some demo code (like this: https://platform.openai.com/docs/quickstart) or with another package (like this: https://github.com/simonw/llm). It's possible that for some reason your API key is restricted to some services or models. You could also try a different model in the demo code or with OntoGPT itself - for OntoGPT, use the -m argument with a model name, like

ontogpt extract -i example.txt -t drug -m gpt-4o-mini

[SaraNiknamHesar]

Hi unfortunately I couldn't fix it and it didn't work for me actually i really like that to use this also for my project but I can't what can I do for it?