niekdejonge
commented
4 months ago This is not an issue with MS2Query specific, but with installing Scipy. Based on some quick googling, you likely are working on a 32 bit installation of python, this is not supported by Scipy anymore. It then tries to compile it, which requires a lot of other stuff (C++ compilers and others) which you likely don't have installed. Got it from this other issue: https://github.com/danielgatis/rembg/issues/377 So I think the best fix is to reinstall python, but use the 64 bit installation. But maybe do a bit more googling first, since I did not see this issue before myself.
TOTOZAFY
Collecting ms2query Using cached ms2query-1.4.0-py3-none-any.whl.metadata (24 kB) Requirement already satisfied: matchms>=0.24.0 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from ms2query) (0.24.4) Requirement already satisfied: numpy in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from ms2query) (1.24.4) Collecting spec2vec>=0.6.0 (from ms2query) Using cached spec2vec-0.8.0-py3-none-any.whl.metadata (15 kB) Collecting h5py (from ms2query) Using cached h5py-3.11.0-cp311-cp311-win_amd64.whl.metadata (2.5 kB) Collecting pyarrow (from ms2query) Using cached pyarrow-16.1.0-cp311-cp311-win_amd64.whl.metadata (3.1 kB) Requirement already satisfied: scikit-learn in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from ms2query) (1.4.2) Collecting ms2deepscore==0.5.0 (from ms2query) Using cached ms2deepscore-0.5.0-py3-none-any.whl.metadata (7.5 kB) Collecting gensim>=4.0.0 (from ms2query) Using cached gensim-4.3.2-cp311-cp311-win_amd64.whl.metadata (8.5 kB) Requirement already satisfied: pandas in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from ms2query) (2.2.2) Requirement already satisfied: tqdm in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from ms2query) (4.66.4) Requirement already satisfied: matplotlib in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from ms2query) (3.7.2) Collecting skl2onnx (from ms2query) Using cached skl2onnx-1.16.0-py2.py3-none-any.whl.metadata (3.2 kB) Collecting onnxruntime<1.16 (from ms2query) Using cached onnxruntime-1.15.1-cp311-cp311-win_amd64.whl.metadata (4.1 kB) Requirement already satisfied: numba in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from ms2deepscore==0.5.0->ms2query) (0.57.1) Collecting tensorflow (from ms2deepscore==0.5.0->ms2query) Using cached tensorflow-2.16.1-cp311-cp311-win_amd64.whl.metadata (3.5 kB) Requirement already satisfied: scipy>=1.7.0 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from gensim>=4.0.0->ms2query) (1.10.1) Collecting smart-open>=1.8.1 (from gensim>=4.0.0->ms2query) Using cached smart_open-7.0.4-py3-none-any.whl.metadata (23 kB) Requirement already satisfied: deprecated<2.0.0,>=1.2.14 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from matchms>=0.24.0->ms2query) (1.2.14) Requirement already satisfied: lxml<5.0.0,>=4.9.3 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from matchms>=0.24.0->ms2query) (4.9.4) Requirement already satisfied: networkx<4.0,>=3.1 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from matchms>=0.24.0->ms2query) (3.3) Requirement already satisfied: pickydict<0.5.0,>=0.4.0 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from matchms>=0.24.0->ms2query) (0.4.0) Requirement already satisfied: pillow!=9.4.0 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from matchms>=0.24.0->ms2query) (10.3.0) Requirement already satisfied: pubchempy in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from matchms>=0.24.0->ms2query) (1.0.4) Requirement already satisfied: pyteomics<5.0,>=4.6 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from matchms>=0.24.0->ms2query) (4.7.2) Requirement already satisfied: pyyaml<7.0.0,>=6.0.1 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from matchms>=0.24.0->ms2query) (6.0.1) Requirement already satisfied: rdkit<2024.0.0,>=2023.3.2 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from matchms>=0.24.0->ms2query) (2023.9.6) Requirement already satisfied: requests<3.0.0,>=2.31.0 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from matchms>=0.24.0->ms2query) (2.31.0) Requirement already satisfied: sparsestack<0.5.0,>=0.4.1 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from matchms>=0.24.0->ms2query) (0.4.1) Requirement already satisfied: contourpy>=1.0.1 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from matplotlib->ms2query) (1.2.1) Requirement already satisfied: cycler>=0.10 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from matplotlib->ms2query) (0.12.1) Requirement already satisfied: fonttools>=4.22.0 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from matplotlib->ms2query) (4.51.0) Requirement already satisfied: kiwisolver>=1.0.1 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from matplotlib->ms2query) (1.4.5) Requirement already satisfied: packaging>=20.0 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from matplotlib->ms2query) (24.0) Requirement already satisfied: pyparsing<3.1,>=2.3.1 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from matplotlib->ms2query) (3.0.9) Requirement already satisfied: python-dateutil>=2.7 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from matplotlib->ms2query) (2.9.0.post0) Collecting coloredlogs (from onnxruntime<1.16->ms2query) Using cached coloredlogs-15.0.1-py2.py3-none-any.whl.metadata (12 kB) Collecting flatbuffers (from onnxruntime<1.16->ms2query) Using cached flatbuffers-24.3.25-py2.py3-none-any.whl.metadata (850 bytes) Collecting protobuf (from onnxruntime<1.16->ms2query) Using cached protobuf-5.26.1-cp310-abi3-win_amd64.whl.metadata (592 bytes) Requirement already satisfied: sympy in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from onnxruntime<1.16->ms2query) (1.12) Requirement already satisfied: pytz>=2020.1 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from pandas->ms2query) (2024.1) Requirement already satisfied: tzdata>=2022.7 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from pandas->ms2query) (2024.1) Requirement already satisfied: colorama in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from tqdm->ms2query) (0.4.6) Requirement already satisfied: joblib>=1.2.0 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from scikit-learn->ms2query) (1.4.2) Requirement already satisfied: threadpoolctl>=2.0.0 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from scikit-learn->ms2query) (3.5.0) Collecting onnx>=1.2.1 (from skl2onnx->ms2query) Using cached onnx-1.16.0-cp311-cp311-win_amd64.whl.metadata (16 kB) Collecting onnxconverter-common>=1.7.0 (from skl2onnx->ms2query) Using cached onnxconverter_common-1.14.0-py2.py3-none-any.whl.metadata (4.2 kB) Requirement already satisfied: wrapt<2,>=1.10 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from deprecated<2.0.0,>=1.2.14->matchms>=0.24.0->ms2query) (1.16.0) Requirement already satisfied: llvmlite<0.41,>=0.40.0dev0 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from numba->ms2deepscore==0.5.0->ms2query) (0.40.1) Collecting protobuf (from onnxruntime<1.16->ms2query) Using cached protobuf-3.20.2-py2.py3-none-any.whl.metadata (720 bytes) Requirement already satisfied: six>=1.5 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from python-dateutil>=2.7->matplotlib->ms2query) (1.16.0) Requirement already satisfied: charset-normalizer<4,>=2 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from requests<3.0.0,>=2.31.0->matchms>=0.24.0->ms2query) (3.3.2) Requirement already satisfied: idna<4,>=2.5 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from requests<3.0.0,>=2.31.0->matchms>=0.24.0->ms2query) (3.7) Requirement already satisfied: urllib3<3,>=1.21.1 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from requests<3.0.0,>=2.31.0->matchms>=0.24.0->ms2query) (2.2.1) Requirement already satisfied: certifi>=2017.4.17 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from requests<3.0.0,>=2.31.0->matchms>=0.24.0->ms2query) (2024.2.2) Collecting humanfriendly>=9.1 (from coloredlogs->onnxruntime<1.16->ms2query) Using cached humanfriendly-10.0-py2.py3-none-any.whl.metadata (9.2 kB) Requirement already satisfied: mpmath>=0.19 in c:\users\jean\miniconda\envs\matchms\lib\site-packages (from sympy->onnxruntime<1.16->ms2query) (1.3.0) Collecting tensorflow-intel==2.16.1 (from tensorflow->ms2deepscore==0.5.0->ms2query) Using cached tensorflow_intel-2.16.1-cp311-cp311-win_amd64.whl.metadata (5.0 kB) Collecting absl-py>=1.0.0 (from tensorflow-intel==2.16.1->tensorflow->ms2deepscore==0.5.0->ms2query) Using cached absl_py-2.1.0-py3-none-any.whl.metadata (2.3 kB) Collecting astunparse>=1.6.0 (from tensorflow-intel==2.16.1->tensorflow->ms2deepscore==0.5.0->ms2query) Using cached astunparse-1.6.3-py2.py3-none-any.whl.metadata (4.4 kB) Collecting gast!=0.5.0,!=0.5.1,!=0.5.2,>=0.2.1 (from tensorflow-intel==2.16.1->tensorflow->ms2deepscore==0.5.0->ms2query) Using cached gast-0.5.4-py3-none-any.whl.metadata (1.3 kB) Collecting google-pasta>=0.1.1 (from tensorflow-intel==2.16.1->tensorflow->ms2deepscore==0.5.0->ms2query) Using cached google_pasta-0.2.0-py3-none-any.whl.metadata (814 bytes) Collecting libclang>=13.0.0 (from tensorflow-intel==2.16.1->tensorflow->ms2deepscore==0.5.0->ms2query) Using cached libclang-18.1.1-py2.py3-none-win_amd64.whl.metadata (5.3 kB) Collecting ml-dtypes~=0.3.1 (from tensorflow-intel==2.16.1->tensorflow->ms2deepscore==0.5.0->ms2query) Using cached ml_dtypes-0.3.2-cp311-cp311-win_amd64.whl.metadata (20 kB) Collecting opt-einsum>=2.3.2 (from tensorflow-intel==2.16.1->tensorflow->ms2deepscore==0.5.0->ms2query) Using cached opt_einsum-3.3.0-py3-none-any.whl.metadata (6.5 kB) INFO: pip is looking at multiple versions of tensorflow-intel to determine which version is compatible with other requirements. This could take a while. Collecting tensorflow (from ms2deepscore==0.5.0->ms2query) Using cached tensorflow-2.15.1-cp311-cp311-win_amd64.whl.metadata (3.4 kB) Collecting tensorflow-intel==2.15.1 (from tensorflow->ms2deepscore==0.5.0->ms2query) Using cached tensorflow_intel-2.15.1-cp311-cp311-win_amd64.whl.metadata (4.9 kB) Collecting tensorflow (from ms2deepscore==0.5.0->ms2query) Using cached tensorflow-2.15.0-cp311-cp311-win_amd64.whl.metadata (3.6 kB) Collecting tensorflow-intel==2.15.0 (from tensorflow->ms2deepscore==0.5.0->ms2query) Using cached tensorflow_intel-2.15.0-cp311-cp311-win_amd64.whl.metadata (5.1 kB) Collecting ml-dtypes~=0.2.0 (from tensorflow-intel==2.15.0->tensorflow->ms2deepscore==0.5.0->ms2query) Using cached ml_dtypes-0.2.0-cp311-cp311-win_amd64.whl.metadata (20 kB) Collecting tensorflow (from ms2deepscore==0.5.0->ms2query) Using cached tensorflow-2.14.1-cp311-cp311-win_amd64.whl.metadata (3.3 kB) Collecting tensorflow-intel==2.14.1 (from tensorflow->ms2deepscore==0.5.0->ms2query) Using cached tensorflow_intel-2.14.1-cp311-cp311-win_amd64.whl.metadata (4.8 kB) Collecting tensorflow (from ms2deepscore==0.5.0->ms2query) Using cached tensorflow-2.14.0-cp311-cp311-win_amd64.whl.metadata (3.3 kB) Collecting tensorflow-intel==2.14.0 (from tensorflow->ms2deepscore==0.5.0->ms2query) Using cached tensorflow_intel-2.14.0-cp311-cp311-win_amd64.whl.metadata (4.8 kB) Collecting tensorflow (from ms2deepscore==0.5.0->ms2query) Using cached tensorflow-2.13.1-cp311-cp311-win_amd64.whl.metadata (2.6 kB) Collecting tensorflow-intel==2.13.1 (from tensorflow->ms2deepscore==0.5.0->ms2query) Using cached tensorflow_intel-2.13.1-cp311-cp311-win_amd64.whl.metadata (4.1 kB) Collecting gast<=0.4.0,>=0.2.1 (from tensorflow-intel==2.13.1->tensorflow->ms2deepscore==0.5.0->ms2query) Using cached gast-0.4.0-py3-none-any.whl.metadata (1.1 kB) Collecting numpy (from ms2query) Using cached numpy-1.24.3-cp311-cp311-win_amd64.whl.metadata (5.6 kB) Collecting tensorflow (from ms2deepscore==0.5.0->ms2query) Using cached tensorflow-2.13.0-cp311-cp311-win_amd64.whl.metadata (2.6 kB) Collecting tensorflow-intel==2.13.0 (from tensorflow->ms2deepscore==0.5.0->ms2query) Using cached tensorflow_intel-2.13.0-cp311-cp311-win_amd64.whl.metadata (4.1 kB) Collecting tensorflow (from ms2deepscore==0.5.0->ms2query) Using cached tensorflow-2.12.1-cp311-cp311-win_amd64.whl.metadata (2.5 kB) Collecting tensorflow-intel==2.12.1 (from tensorflow->ms2deepscore==0.5.0->ms2query) Using cached tensorflow_intel-2.12.1-cp311-cp311-win_amd64.whl.metadata (4.1 kB) Collecting jax>=0.3.15 (from tensorflow-intel==2.12.1->tensorflow->ms2deepscore==0.5.0->ms2query) Using cached jax-0.4.28-py3-none-any.whl.metadata (23 kB) INFO: pip is still looking at multiple versions of tensorflow-intel to determine which version is compatible with other requirements. This could take a while. Collecting tensorflow (from ms2deepscore==0.5.0->ms2query) Using cached tensorflow-2.12.0-cp311-cp311-win_amd64.whl.metadata (2.5 kB) Collecting tensorflow-intel==2.12.0 (from tensorflow->ms2deepscore==0.5.0->ms2query) Using cached tensorflow_intel-2.12.0-cp311-cp311-win_amd64.whl.metadata (4.1 kB) Collecting sparsestack<0.5.0,>=0.4.1 (from matchms>=0.24.0->ms2query) Using cached sparsestack-0.4.1-py3-none-any.whl.metadata (5.0 kB) INFO: This is taking longer than usual. You might need to provide the dependency resolver with stricter constraints to reduce runtime. See https://pip.pypa.io/warnings/backtracking for guidance. If you want to abort this run, press Ctrl + C. Collecting scipy>=1.7.0 (from gensim>=4.0.0->ms2query) Using cached scipy-1.10.1-cp311-cp311-win_amd64.whl.metadata (58 kB) Using cached scipy-1.10.0-cp311-cp311-win_amd64.whl.metadata (58 kB) Using cached scipy-1.9.3-cp311-cp311-win_amd64.whl.metadata (58 kB) Using cached scipy-1.9.2-cp311-cp311-win_amd64.whl.metadata (58 kB) Using cached scipy-1.9.1.tar.gz (42.0 MB) Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'error' Note: you may need to restart the kernel to use updated packages.
ERROR START IN THIS STEP error: subprocess-exited-with-error
Getting requirements to build wheel did not run successfully. exit code: 1
[55 lines of output] The Meson build system Version: 0.62.2 Source dir: C:\Users\Jean\AppData\Local\Temp\pip-install-2n7u2xrr\scipy_c4ddaa89fd5c484285268f848d94d2b3 Build dir: C:\Users\Jean\AppData\Local\Temp\pip-install-2n7u2xrr\scipy_c4ddaa89fd5c484285268f848d94d2b3.mesonpy-nd1ej9w9\build Build type: native build Project name: SciPy Project version: 1.9.1 WARNING: Failed to activate VS environment: Could not find C:\Program Files (x86)\Microsoft Visual Studio\Installer\vswhere.exe
....\meson.build:1:0: ERROR: Unknown compiler(s): [['icl'], ['cl'], ['cc'], ['gcc'], ['clang'], ['clang-cl'], ['pgcc']] The following exception(s) were encountered: Running "icl " gave "[WinError 2] Le fichier spécifié est introuvable" Running "cl /?" gave "[WinError 2] Le fichier spécifié est introuvable" Running "cc --version" gave "[WinError 2] Le fichier spécifié est introuvable" Running "gcc --version" gave "[WinError 2] Le fichier spécifié est introuvable" Running "clang --version" gave "[WinError 2] Le fichier spécifié est introuvable" Running "clang-cl /?" gave "[WinError 2] Le fichier spécifié est introuvable" Running "pgcc --version" gave "[WinError 2] Le fichier spécifié est introuvable"
A full log can be found at C:\Users\Jean\AppData\Local\Temp\pip-install-2n7u2xrr\scipy_c4ddaa89fd5c484285268f848d94d2b3.mesonpy-nd1ej9w9\build\meson-logs\meson-log.txt
meson setup --native-file=C:\Users\Jean\AppData\Local\Temp\pip-install-2n7u2xrr\scipy_c4ddaa89fd5c484285268f848d94d2b3.mesonpy-native-file.ini -Ddebug=false -Doptimization=2 --prefix=C:\Users\Jean\miniconda\envs\matchms C:\Users\Jean\AppData\Local\Temp\pip-install-2n7u2xrr\scipy_c4ddaa89fd5c484285268f848d94d2b3 C:\Users\Jean\AppData\Local\Temp\pip-install-2n7u2xrr\scipy_c4ddaa89fd5c484285268f848d94d2b3.mesonpy-nd1ej9w9\build Traceback (most recent call last): File "C:\Users\Jean\miniconda\envs\matchms\Lib\site-packages\pip_vendor\pyproject_hooks_in_process_in_process.py", line 353, in
main()
File "C:\Users\Jean\miniconda\envs\matchms\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\Jean\miniconda\envs\matchms\Lib\site-packages\pip_vendor\pyproject_hooks_in_process_in_process.py", line 118, in get_requires_for_build_wheel
return hook(config_settings)
^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Jean\AppData\Local\Temp\pip-build-env-w1llbkt9\overlay\Lib\site-packages\mesonpy__init__.py", line 969, in get_requires_for_build_wheel
with _project(config_settings) as project:
File "C:\Users\Jean\miniconda\envs\matchms\Lib\contextlib.py", line 137, in enter
return next(self.gen)
^^^^^^^^^^^^^^
File "C:\Users\Jean\AppData\Local\Temp\pip-build-env-w1llbkt9\overlay\Lib\site-packages\mesonpy__init__.py", line 948, in _project
with Project.with_temp_working_dir(
File "C:\Users\Jean\miniconda\envs\matchms\Lib\contextlib.py", line 137, in enter
return next(self.gen)
^^^^^^^^^^^^^^
File "C:\Users\Jean\AppData\Local\Temp\pip-build-env-w1llbkt9\overlay\Lib\site-packages\mesonpy__init__.py", line 777, in with_temp_working_dir
yield cls(source_dir, tmpdir, build_dir)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Jean\AppData\Local\Temp\pip-build-env-w1llbkt9\overlay\Lib\site-packages\mesonpy__init__.py", line 682, in init
self._configure(reconfigure=bool(build_dir) and not native_file_mismatch)
File "C:\Users\Jean\AppData\Local\Temp\pip-build-env-w1llbkt9\overlay\Lib\site-packages\mesonpy__init__.py", line 713, in _configure
self._meson(
File "C:\Users\Jean\AppData\Local\Temp\pip-build-env-w1llbkt9\overlay\Lib\site-packages\mesonpy__init__.py", line 696, in _meson
return self._proc('meson', args)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Jean\AppData\Local\Temp\pip-build-env-w1llbkt9\overlay\Lib\site-packages\mesonpy__init__.py", line 691, in _proc
subprocess.check_call(list(args))
File "C:\Users\Jean\miniconda\envs\matchms\Lib\subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['meson', 'setup', '--native-file=C:\Users\Jean\AppData\Local\Temp\pip-install-2n7u2xrr\scipy_c4ddaa89fd5c484285268f848d94d2b3\.mesonpy-native-file.ini', '-Ddebug=false', '-Doptimization=2', '--prefix=C:\Users\Jean\miniconda\envs\matchms', 'C:\Users\Jean\AppData\Local\Temp\pip-install-2n7u2xrr\scipy_c4ddaa89fd5c484285268f848d94d2b3', 'C:\Users\Jean\AppData\Local\Temp\pip-install-2n7u2xrr\scipy_c4ddaa89fd5c484285268f848d94d2b3\.mesonpy-nd1ej9w9\build']' 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: subprocess-exited-with-error
Getting requirements to build wheel did not run successfully. exit code: 1
See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
WHAT CAN I DO TO FIX THIS PROBLEM ?