Environment creation fails with Python version >3.12 #196
Description
Applies To
- Notebooks (.ipynb files)
- Interactive Window and/or Cell Scripts (.py files with #%% markers)
What happened?
Attempted to create environment with Python 3.13.9 - creation appears to proceed normally, but deepnote_toolkit installation fails due to lack of Python 3.13 wheel for clickhouse-driver (see attached logs)
VS Code Version
1.105.1
Jupyter Extension Version
1.1.3
Jupyter logs
Visual Studio Code (1.105.1, undefined, desktop)
Jupyter Extension Version: 1.1.3.
Python Extension Version: 2025.16.0.
Python Environment Extension Version: 1.10.0.
Pylance Extension Version: 2025.9.1.
Platform: win32 (x64).
10:07:35.803 [info] Setting up kernel using configuration: Python 3.13 (Data Science) (be679997-ac8f-4298-880a-500e4d41ee44)
10:07:35.803 [info] Ensuring server is running for configuration be679997-ac8f-4298-880a-500e4d41ee44
10:07:35.804 [info] Ensuring deepnote-toolkit is installed in venv for environment be679997-ac8f-4298-880a-500e4d41ee44...
10:07:35.804 [info] Ensuring virtual environment at ~\AppData\Roaming\Code\User\globalStorage\deepnote.vscode-deepnote\deepnote-venvs\be679997-ac8f-4298-880a-500e4d41ee44
10:07:35.804 [info] Base interpreter: ~\AppData\Local\Python\pythoncore-3.13-64\python.exe
10:07:35.806 [info] Creating virtual environment at ~\AppData\Roaming\Code\User\globalStorage\deepnote.vscode-deepnote\deepnote-venvs\be679997-ac8f-4298-880a-500e4d41ee44
Setting up Deepnote toolkit environment...
10:08:06.179 [info] Installing deepnote-toolkit (1.1.0) and ipykernel in venv from PyPI
Installing deepnote-toolkit and ipykernel...
10:08:06.190 [info] Process Execution: ~\AppData\Roaming\Code\User\globalStorage\deepnote.vscode-deepnote\deepnote-venvs\be679997-ac8f-4298-880a-500e4d41ee44\Scripts\python.exe -m pip install --upgrade deepnote-toolkit[server]==1.1.0 ipykernel
Collecting deepnote-toolkit==1.1.0 (from deepnote-toolkit[server]==1.1.0)
Using cached deepnote_toolkit-1.1.0-py3-none-any.whl.metadata (10 kB)
Collecting ipykernel
Using cached ipykernel-7.1.0-py3-none-any.whl.metadata (4.5 kB)
Collecting clickhouse-sqlalchemy<0.4,>0 (from deepnote-toolkit==1.1.0->deepnote-toolkit[server]==1.1.0)
Using cached clickhouse_sqlalchemy-0.3.2-py3-none-any.whl
[SNIP]
Collecting clickhouse-driver>=0.1.2 (from clickhouse-sqlalchemy<0.4,>0->deepnote-toolkit==1.1.0->deepnote-toolkit[server]==1.1.0)
Using cached clickhouse-driver-0.2.9.tar.gz (357 kB)
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 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
[SNIP]
Building wheels for collected packages: clickhouse-driver
Building wheel for clickhouse-driver (pyproject.toml): started
Building wheel for clickhouse-driver (pyproject.toml): finished with status 'error'
Failed to build clickhouse-driver
error: subprocess-exited-with-error
× Building wheel for clickhouse-driver (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [110 lines of output]
C:\Users\dunn0172\AppData\Local\Temp\pip-build-env-6dyaz0a3\overlay\Lib\site-packages\setuptools\_distutils\dist.py:289: UserWarning: Unknown distribution option: 'test_suite'
warnings.warn(msg)
C:\Users\dunn0172\AppData\Local\Temp\pip-build-env-6dyaz0a3\overlay\Lib\site-packages\setuptools\dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
!!
********************************************************************************
Please consider removing the following classifiers in favor of a SPDX license expression:
License :: OSI Approved :: MIT License
See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
********************************************************************************
!!
self._finalize_license_expression()
running bdist_wheel
running build
running build_py
creating build\lib.win-amd64-cpython-313\clickhouse_driver
copying clickhouse_driver\block.py -> build\lib.win-amd64-cpython-313\clickhouse_driver
copying clickhouse_driver\blockstreamprofileinfo.py -> build\lib.win-amd64-cpython-313\clickhouse_driver
copying clickhouse_driver\client.py -> build\lib.win-amd64-cpython-313\clickhouse_driver
copying clickhouse_driver\clientinfo.py -> build\lib.win-amd64-cpython-313\clickhouse_driver
copying clickhouse_driver\connection.py -> build\lib.win-amd64-cpython-313\clickhouse_driver
copying clickhouse_driver\context.py -> build\lib.win-amd64-cpython-313\clickhouse_driver
copying clickhouse_driver\defines.py -> build\lib.win-amd64-cpython-313\clickhouse_driver
copying clickhouse_driver\errors.py -> build\lib.win-amd64-cpython-313\clickhouse_driver
copying clickhouse_driver\log.py -> build\lib.win-amd64-cpython-313\clickhouse_driver
copying clickhouse_driver\opentelemetry.py -> build\lib.win-amd64-cpython-313\clickhouse_driver
copying clickhouse_driver\progress.py -> build\lib.win-amd64-cpython-313\clickhouse_driver
copying clickhouse_driver\protocol.py -> build\lib.win-amd64-cpython-313\clickhouse_driver
copying clickhouse_driver\queryprocessingstage.py -> build\lib.win-amd64-cpython-313\clickhouse_driver
copying clickhouse_driver\reader.py -> build\lib.win-amd64-cpython-313\clickhouse_driver
copying clickhouse_driver\readhelpers.py -> build\lib.win-amd64-cpython-313\clickhouse_driver
copying clickhouse_driver\result.py -> build\lib.win-amd64-cpython-313\clickhouse_driver
copying clickhouse_driver\writer.py -> build\lib.win-amd64-cpython-313\clickhouse_driver
copying clickhouse_driver\__init__.py -> build\lib.win-amd64-cpython-313\clickhouse_driver
creating build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\arraycolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\base.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\boolcolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\datecolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\datetimecolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\decimalcolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\enumcolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\exceptions.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\floatcolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\intcolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\intervalcolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\ipcolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\jsoncolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\lowcardinalitycolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\mapcolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\nestedcolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\nothingcolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\nullablecolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\nullcolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\service.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\simpleaggregatefunctioncolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\stringcolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\tuplecolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\util.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\uuidcolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
copying clickhouse_driver\columns\__init__.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns
creating build\lib.win-amd64-cpython-313\clickhouse_driver\compression
copying clickhouse_driver\compression\base.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\compression
copying clickhouse_driver\compression\lz4.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\compression
copying clickhouse_driver\compression\lz4hc.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\compression
copying clickhouse_driver\compression\zstd.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\compression
copying clickhouse_driver\compression\__init__.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\compression
creating build\lib.win-amd64-cpython-313\clickhouse_driver\dbapi
copying clickhouse_driver\dbapi\connection.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\dbapi
copying clickhouse_driver\dbapi\cursor.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\dbapi
copying clickhouse_driver\dbapi\errors.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\dbapi
copying clickhouse_driver\dbapi\extras.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\dbapi
copying clickhouse_driver\dbapi\__init__.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\dbapi
creating build\lib.win-amd64-cpython-313\clickhouse_driver\numpy
copying clickhouse_driver\numpy\block.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\numpy
copying clickhouse_driver\numpy\helpers.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\numpy
copying clickhouse_driver\numpy\result.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\numpy
copying clickhouse_driver\numpy\__init__.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\numpy
creating build\lib.win-amd64-cpython-313\clickhouse_driver\settings
copying clickhouse_driver\settings\available.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\settings
copying clickhouse_driver\settings\types.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\settings
copying clickhouse_driver\settings\writer.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\settings
copying clickhouse_driver\settings\__init__.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\settings
creating build\lib.win-amd64-cpython-313\clickhouse_driver\streams
copying clickhouse_driver\streams\compressed.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\streams
copying clickhouse_driver\streams\native.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\streams
copying clickhouse_driver\streams\__init__.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\streams
creating build\lib.win-amd64-cpython-313\clickhouse_driver\util
copying clickhouse_driver\util\compat.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\util
copying clickhouse_driver\util\escape.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\util
copying clickhouse_driver\util\helpers.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\util
copying clickhouse_driver\util\__init__.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\util
creating build\lib.win-amd64-cpython-313\clickhouse_driver\columns\numpy
copying clickhouse_driver\columns\numpy\base.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns\numpy
copying clickhouse_driver\columns\numpy\boolcolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns\numpy
copying clickhouse_driver\columns\numpy\datecolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns\numpy
copying clickhouse_driver\columns\numpy\datetimecolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns\numpy
copying clickhouse_driver\columns\numpy\floatcolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns\numpy
copying clickhouse_driver\columns\numpy\intcolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns\numpy
copying clickhouse_driver\columns\numpy\lowcardinalitycolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns\numpy
copying clickhouse_driver\columns\numpy\service.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns\numpy
copying clickhouse_driver\columns\numpy\stringcolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns\numpy
copying clickhouse_driver\columns\numpy\tuplecolumn.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns\numpy
copying clickhouse_driver\columns\numpy\__init__.py -> build\lib.win-amd64-cpython-313\clickhouse_driver\columns\numpy
running build_ext
building 'clickhouse_driver.bufferedreader' extension
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/
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for clickhouse-driver
error: failed-wheel-build-for-install
× Failed to build installable wheels for some pyproject.toml based projects
╰─> clickhouse-driver
10:09:21.363 [info] Process Execution: ~\AppData\Roaming\Code\User\globalStorage\deepnote.vscode-deepnote\deepnote-venvs\be679997-ac8f-4298-880a-500e4d41ee44\Scripts\python.exe -c "import deepnote_toolkit; print(deepnote_toolkit.__version__)"
10:09:21.443 [info] isToolkitInstalled result:
10:09:21.443 [info] deepnote-toolkit installed successfully in venv
10:09:21.447 [info] Installing kernel spec 'deepnote-be679997-ac8f-4298-880a-500e4d41ee44' for venv at ~\AppData\Roaming\Code\User\globalStorage\deepnote.vscode-deepnote\deepnote-venvs\be679997-ac8f-4298-880a-500e4d41ee44...
10:09:21.456 [info] Process Execution: ~\AppData\Roaming\Code\User\globalStorage\deepnote.vscode-deepnote\deepnote-venvs\be679997-ac8f-4298-880a-500e4d41ee44\Scripts\python.exe -m ipykernel install --prefix ~\AppData\Roaming\Code\User\globalStorage\deepnote.vscode-deepnote\deepnote-venvs\be679997-ac8f-4298-880a-500e4d41ee44 --name deepnote-be679997-ac8f-4298-880a-500e4d41ee44 --display-name "Deepnote (be679997-ac8f-4298-880a-500e4d41ee44)"
10:09:21.516 [info] Kernel spec installed successfully to ~\AppData\Roaming\Code\User\globalStorage\deepnote.vscode-deepnote\deepnote-venvs\be679997-ac8f-4298-880a-500e4d41ee44\share\jupyter\kernels\deepnote-be679997-ac8f-4298-880a-500e4d41ee44
✓ Deepnote toolkit ready
[SNIP]
10:10:20.274 [info] Consecutive port check for base 8894: next=8895, inUseSet=false, available=true
10:10:20.274 [info] Allocated consecutive ports for ~\Documents\MyProject\example.deepnote-be679997-ac8f-4298-880a-500e4d41ee44: jupyter=8894, lsp=8895 (excluded: none)
10:10:20.274 [info] Starting deepnote-toolkit server on jupyter port 8894 and lsp port 8895 for ~\Documents\MyProject\example.deepnote-be679997-ac8f-4298-880a-500e4d41ee44 with environmentId be679997-ac8f-4298-880a-500e4d41ee44
Starting Deepnote server on jupyter port 8894 and lsp port 8895...
10:10:20.293 [info] Process Execution: ~\AppData\Roaming\Code\User\globalStorage\deepnote.vscode-deepnote\deepnote-venvs\be679997-ac8f-4298-880a-500e4d41ee44\Scripts\python.exe -m deepnote_toolkit server --jupyter-port 8894 --ls-port 8895
> cwd: ~\Documents\MyProject
10:10:20.298 [info] Created lock file for PID 21076 with session ID e63f51a2-37bd-4647-9148-82d4168a184d
10:10:20.410 [warn] Deepnote server stderr (~\Documents\MyProject\example.deepnote-be679997-ac8f-4298-880a-500e4d41ee44): ~\AppData\Roaming\Code\User\globalStorage\deepnote.vscode-deepnote\deepnote-venvs\be679997-ac8f-4298-880a-500e4d41ee44\Scripts\python.exe: No module named deepnote_toolkit
c:\Users\dunn0172\AppData\Roaming\Code\User\globalStorage\deepnote.vscode-deepnote\deepnote-venvs\be679997-ac8f-4298-880a-500e4d41ee44\Scripts\python.exe: No module named deepnote_toolkit
10:10:32.551 [info] onDidChangeActiveNotebookEditor: undefined
10:12:20.687 [info] Stopping Deepnote server for ~\Documents\MyProject\example.deepnote...
Deepnote server stopped for ~\Documents\MyProject\example.deepnote
10:12:20.699 [info] Deleted lock file for PID 21076
10:12:20.700 [error] Failed to switch environment [_j [DeepnoteServerTimeoutError]: Deepnote server failed to start within 120 seconds
at OR.startServerForEnvironment (~\.vscode\extensions\deepnote.vscode-deepnote-1.1.3\dist\extension.node.js:710:12514)
at runNextTicks (node:internal/process/task_queues:65:5)
at process.processTimers (node:internal/timers:520:9)
at async OR.startServer (~\.vscode\extensions\deepnote.vscode-deepnote-1.1.3\dist\extension.node.js:710:9385)
at async pk.ensureKernelSelectedWithConfiguration (~\.vscode\extensions\deepnote.vscode-deepnote-1.1.3\dist\extension.node.js:727:9047)
at async pk.rebuildController (~\.vscode\extensions\deepnote.vscode-deepnote-1.1.3\dist\extension.node.js:727:7055)
at async ~\.vscode\extensions\deepnote.vscode-deepnote-1.1.3\dist\extension.node.js:732:9184] {
serverUrl: 'http://localhost:8894',
timeoutMs: 120000,
lastError: 'c:\\Users\\<username>\\AppData\\Roaming\\Code\\User\\globalStorage\\deepnote.vscode-deepnote\\deepnote-venvs\\be679997-ac8f-4298-880a-500e4d41ee44\\Scripts\\python.exe: No module named deepnote_toolkit\r\n',
userMessage: 'Deepnote server failed to start within 120 seconds',
technicalDetails: 'Server URL: http://localhost:8894\n' +
'Timeout: 120000ms\n' +
'Last connection error: c:\\Users\\<username>\\AppData\\Roaming\\Code\\User\\globalStorage\\deepnote.vscode-deepnote\\deepnote-venvs\\be679997-ac8f-4298-880a-500e4d41ee44\\Scripts\\python.exe: No module named deepnote_toolkit\r\n' +
'\n' +
'The server process may still be starting or may have crashed silently',
troubleshootingSteps: [
'The server may be slow to start - try waiting a bit longer and reloading',
'Check the Output panel for server startup logs',
'Ensure no firewall is blocking localhost connections',
'Check that port is not being blocked by security software',
'Verify Python and deepnote-toolkit are correctly installed',
'Try closing other resource-intensive applications',
'Reload the VS Code window (Cmd/Ctrl+Shift+P → "Reload Window")',
'If the issue persists, report it with the error details'
]
}Coding Language and Runtime Version
Python 3.13.9
Language Extension Version (if applicable)
Python 2025.16.0
Anaconda Version (if applicable)
No response
Running Jupyter locally or remotely?
Local