R Under development (unstable) (2025-03-09 r87914 ucrt) -- "Unsuffered Consequences"
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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(laminr)
> 
> test_check("laminr")
Using Python: C:/Users/CRAN/AppData/Local/r-reticulate/r-reticulate/pyenv/pyenv-win/versions/3.11.9/python.exe
Creating virtual environment "laminr-test-20250310120005" ... 
+ "C:/Users/CRAN/AppData/Local/r-reticulate/r-reticulate/pyenv/pyenv-win/versions/3.11.9/python.exe" -m venv "C:\Users\CRAN\Documents/.virtualenvs/laminr-test-20250310120005"
Done!
Installing packages: pip, wheel, setuptools
+ "C:\Users\CRAN\Documents/.virtualenvs/laminr-test-20250310120005/Scripts/python.exe" -m pip install --upgrade pip wheel setuptools
Requirement already satisfied: pip in c:\users\cran\docume~1\virtua~1\laminr~4\lib\site-packages (24.0)
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Installing collected packages: wheel, setuptools, pip
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    Uninstalling setuptools-65.5.0:
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  Attempting uninstall: pip
    Found existing installation: pip 24.0
    Uninstalling pip-24.0:
      Successfully uninstalled pip-24.0
Successfully installed pip-25.0.1 setuptools-76.0.0 wheel-0.45.1
Virtual environment 'laminr-test-20250310120005' successfully created.
Using virtual environment "laminr-test-20250310120005" ...
+ "C:\Users\CRAN\Documents/.virtualenvs/laminr-test-20250310120005/Scripts/python.exe" -m pip install --upgrade --no-user "lamindb>=1.2" ipython bionty
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Collecting httpcore==1.* (from httpx<0.29,>=0.26->supabase<=2.11.0,>=2.8.1->lamindb_setup==1.3.0->lamindb_setup[aws]==1.3.0->lamindb>=1.2)
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Collecting h11<0.15,>=0.13 (from httpcore==1.*->httpx<0.29,>=0.26->supabase<=2.11.0,>=2.8.1->lamindb_setup==1.3.0->lamindb_setup[aws]==1.3.0->lamindb>=1.2)
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Collecting deprecation<3.0.0,>=2.1.0 (from postgrest<0.20,>=0.19->supabase<=2.11.0,>=2.8.1->lamindb_setup==1.3.0->lamindb_setup[aws]==1.3.0->lamindb>=1.2)
  Using cached deprecation-2.1.0-py2.py3-none-any.whl.metadata (4.6 kB)
Collecting websockets<15,>=11 (from realtime<3.0.0,>=2.0.0->supabase<=2.11.0,>=2.8.1->lamindb_setup==1.3.0->lamindb_setup[aws]==1.3.0->lamindb>=1.2)
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Collecting markdown-it-py>=2.2.0 (from rich>=10.7->rich-click>=1.7->lamin_cli==1.1.0->lamindb>=1.2)
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Collecting strenum<0.5.0,>=0.4.15 (from supafunc<0.10,>=0.9->supabase<=2.11.0,>=2.8.1->lamindb_setup==1.3.0->lamindb_setup[aws]==1.3.0->lamindb>=1.2)
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Collecting h2<5,>=3 (from httpx[http2]<0.29,>=0.26->gotrue<3.0.0,>=2.11.0->supabase<=2.11.0,>=2.8.1->lamindb_setup==1.3.0->lamindb_setup[aws]==1.3.0->lamindb>=1.2)
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Collecting mdurl~=0.1 (from markdown-it-py>=2.2.0->rich>=10.7->rich-click>=1.7->lamin_cli==1.1.0->lamindb>=1.2)
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INFO: pip is looking at multiple versions of s3transfer to determine which version is compatible with other requirements. This could take a while.
Collecting s3transfer<0.12.0,>=0.11.0 (from boto3<1.37.2,>=1.37.0->aiobotocore[boto3]<3.0.0,>=2.5.4; extra == "aws"->lamindb_setup[aws]==1.3.0->lamindb>=1.2)
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Collecting sniffio>=1.1 (from anyio->httpx<0.29,>=0.26->supabase<=2.11.0,>=2.8.1->lamindb_setup==1.3.0->lamindb_setup[aws]==1.3.0->lamindb>=1.2)
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Installing collected packages: wcwidth, strenum, pytz, pure-eval, lamin_utils, appdirs, wrapt, websockets, urllib3, tzdata, typing_extensions, traitlets, sqlparse, sniffio, six, pyyaml, python-dotenv, pygments, pyarrow, psycopg2-binary, psutil, propcache, prompt_toolkit, parso, packaging, numpy, networkx, natsort, mypy-extensions, multidict, mdurl, jmespath, idna, hyperframe, hpack, h11, graphviz, fsspec, frozenlist, filelock, fastobo, executing, decorator, colorama, charset-normalizer, chardet, certifi, attrs, asttokens, asgiref, array-api-compat, annotated-types, aioitertools, aiohappyeyeballs, yarl, universal_pathlib, typing_inspect, typeguard, stack_data, scipy, requests, python-dateutil, pydantic-core, matplotlib-inline, markdown-it-py, jedi, ipython-pygments-lexers, httpcore, h5py, h2, django, deprecation, click, anyio, aiosignal, rich, pydantic, pronto, pandas, ipython, httpx, dj_database_url, botocore, aiohttp, s3transfer, rich-click, realtime, pydantic-settings, pandera, anndata, aiobotocore, supafunc, storage3, s3fs, postgrest, lamin_cli, gotrue, boto3, supabase, lamindb_setup, lamindb, bionty
Successfully installed aiobotocore-2.21.1 aiohappyeyeballs-2.5.0 aiohttp-3.11.13 aioitertools-0.12.0 aiosignal-1.3.2 anndata-0.11.3 annotated-types-0.7.0 anyio-4.8.0 appdirs-1.4.4 array-api-compat-1.11.1 asgiref-3.8.1 asttokens-3.0.0 attrs-25.1.0 bionty-1.1.1 boto3-1.37.1 botocore-1.37.1 certifi-2025.1.31 chardet-5.2.0 charset-normalizer-3.4.1 click-8.1.8 colorama-0.4.6 decorator-5.2.1 deprecation-2.1.0 dj_database_url-2.3.0 django-5.1.7 executing-2.2.0 fastobo-0.13.0 filelock-3.17.0 frozenlist-1.5.0 fsspec-2025.2.0 gotrue-2.11.4 graphviz-0.20.3 h11-0.14.0 h2-4.2.0 h5py-3.13.0 hpack-4.1.0 httpcore-1.0.7 httpx-0.28.1 hyperframe-6.1.0 idna-3.10 ipython-9.0.2 ipython-pygments-lexers-1.1.1 jedi-0.19.2 jmespath-1.0.1 lamin_cli-1.1.0 lamin_utils-0.13.10 lamindb-1.2.0 lamindb_setup-1.3.0 markdown-it-py-3.0.0 matplotlib-inline-0.1.7 mdurl-0.1.2 multidict-6.1.0 mypy-extensions-1.0.0 natsort-8.4.0 networkx-3.4.2 numpy-2.2.3 packaging-24.2 pandas-2.2.3 pandera-0.23.1 parso-0.8.4 postgrest-0.19.3 prompt_toolkit-3.0.50 pronto-2.7.0 propcache-0.3.0 psutil-7.0.0 psycopg2-binary-2.9.10 pure-eval-0.2.3 pyarrow-19.0.1 pydantic-2.10.6 pydantic-core-2.27.2 pydantic-settings-2.8.1 pygments-2.19.1 python-dateutil-2.9.0.post0 python-dotenv-1.0.1 pytz-2025.1 pyyaml-6.0.2 realtime-2.4.1 requests-2.32.3 rich-13.9.4 rich-click-1.8.8 s3fs-2025.2.0 s3transfer-0.11.3 scipy-1.14.1 six-1.17.0 sniffio-1.3.1 sqlparse-0.5.3 stack_data-0.6.3 storage3-0.11.3 strenum-0.4.15 supabase-2.11.0 supafunc-0.9.3 traitlets-5.14.3 typeguard-4.4.2 typing_extensions-4.12.2 typing_inspect-0.9.0 tzdata-2025.1 universal_pathlib-0.2.6 urllib3-1.26.20 wcwidth-0.2.13 websockets-14.2 wrapt-1.17.2 yarl-1.18.3
✖ No current instance
\u2192 initialized lamindb: anonymous/laminr-test-20250310120005
→ connected lamindb: anonymous/laminr-test-20250310120005
! no run & transform got linked, call `ln.track()` & re-run
! no run & transform got linked, call `ln.track()` & re-run
Using Python: C:/Users/CRAN/AppData/Local/r-reticulate/r-reticulate/pyenv/pyenv-win/versions/3.11.9/python.exe
Creating virtual environment "laminr-test-20250310120005-install" ... 
+ "C:/Users/CRAN/AppData/Local/r-reticulate/r-reticulate/pyenv/pyenv-win/versions/3.11.9/python.exe" -m venv "C:\Users\CRAN\Documents/.virtualenvs/laminr-test-20250310120005-install"
Done!
Installing packages: pip, wheel, setuptools
+ "C:\Users\CRAN\Documents/.virtualenvs/laminr-test-20250310120005-install/Scripts/python.exe" -m pip install --upgrade pip wheel setuptools
Requirement already satisfied: pip in c:\users\cran\docume~1\virtua~1\la2ff3~1\lib\site-packages (24.0)
Collecting pip
  Using cached pip-25.0.1-py3-none-any.whl.metadata (3.7 kB)
Collecting wheel
  Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Requirement already satisfied: setuptools in c:\users\cran\docume~1\virtua~1\la2ff3~1\lib\site-packages (65.5.0)
Collecting setuptools
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Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 65.5.0
    Uninstalling setuptools-65.5.0:
      Successfully uninstalled setuptools-65.5.0
  Attempting uninstall: pip
    Found existing installation: pip 24.0
    Uninstalling pip-24.0:
      Successfully uninstalled pip-24.0
Successfully installed pip-25.0.1 setuptools-76.0.0 wheel-0.45.1
Virtual environment 'laminr-test-20250310120005-install' successfully created.
Using virtual environment "laminr-test-20250310120005-install" ...
+ "C:\Users\CRAN\Documents/.virtualenvs/laminr-test-20250310120005-install/Scripts/python.exe" -m pip install --upgrade --no-user "lamindb>=1.2" ipython
Collecting lamindb>=1.2
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Collecting ipython
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Collecting pandas>=2.0.0 (from lamindb>=1.2)
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Collecting anndata<=0.11.3,>=0.8.0 (from lamindb>=1.2)
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Collecting fsspec (from lamindb>=1.2)
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Collecting graphviz (from lamindb>=1.2)
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Collecting rich-click>=1.7 (from lamin_cli==1.1.0->lamindb>=1.2)
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Collecting django<5.2,>=5 (from lamindb_setup==1.3.0->lamindb_setup[aws]==1.3.0->lamindb>=1.2)
  Using cached Django-5.1.7-py3-none-any.whl.metadata (4.1 kB)
Collecting dj_database_url<3.0.0,>=1.3.0 (from lamindb_setup==1.3.0->lamindb_setup[aws]==1.3.0->lamindb>=1.2)
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Collecting pydantic-settings (from lamindb_setup==1.3.0->lamindb_setup[aws]==1.3.0->lamindb>=1.2)
  Using cached pydantic_settings-2.8.1-py3-none-any.whl.metadata (3.5 kB)
Collecting appdirs<2.0.0 (from lamindb_setup==1.3.0->lamindb_setup[aws]==1.3.0->lamindb>=1.2)
  Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
Collecting requests (from lamindb_setup==1.3.0->lamindb_setup[aws]==1.3.0->lamindb>=1.2)
  Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
Collecting universal_pathlib==0.2.6 (from lamindb_setup==1.3.0->lamindb_setup[aws]==1.3.0->lamindb>=1.2)
  Using cached universal_pathlib-0.2.6-py3-none-any.whl.metadata (25 kB)
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Collecting s3transfer<0.12.0,>=0.11.0 (from boto3<1.37.2,>=1.37.0->aiobotocore[boto3]<3.0.0,>=2.5.4; extra == "aws"->lamindb_setup[aws]==1.3.0->lamindb>=1.2)
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Installing collected packages: wcwidth, strenum, pytz, pure-eval, lamin_utils, appdirs, wrapt, websockets, urllib3, tzdata, typing_extensions, traitlets, sqlparse, sniffio, six, pyyaml, python-dotenv, pygments, pyarrow, psycopg2-binary, psutil, propcache, prompt_toolkit, parso, packaging, numpy, natsort, mypy-extensions, multidict, mdurl, jmespath, idna, hyperframe, hpack, h11, graphviz, fsspec, frozenlist, executing, decorator, colorama, charset-normalizer, certifi, attrs, asttokens, asgiref, array-api-compat, annotated-types, aioitertools, aiohappyeyeballs, yarl, universal_pathlib, typing_inspect, typeguard, stack_data, scipy, requests, python-dateutil, pydantic-core, matplotlib-inline, markdown-it-py, jedi, ipython-pygments-lexers, httpcore, h5py, h2, django, deprecation, click, anyio, aiosignal, rich, pydantic, pandas, ipython, httpx, dj_database_url, botocore, aiohttp, s3transfer, rich-click, realtime, pydantic-settings, pandera, anndata, aiobotocore, supafunc, storage3, s3fs, postgrest, lamin_cli, gotrue, boto3, supabase, lamindb_setup, lamindb
Successfully installed aiobotocore-2.21.1 aiohappyeyeballs-2.5.0 aiohttp-3.11.13 aioitertools-0.12.0 aiosignal-1.3.2 anndata-0.11.3 annotated-types-0.7.0 anyio-4.8.0 appdirs-1.4.4 array-api-compat-1.11.1 asgiref-3.8.1 asttokens-3.0.0 attrs-25.1.0 boto3-1.37.1 botocore-1.37.1 certifi-2025.1.31 charset-normalizer-3.4.1 click-8.1.8 colorama-0.4.6 decorator-5.2.1 deprecation-2.1.0 dj_database_url-2.3.0 django-5.1.7 executing-2.2.0 frozenlist-1.5.0 fsspec-2025.2.0 gotrue-2.11.4 graphviz-0.20.3 h11-0.14.0 h2-4.2.0 h5py-3.13.0 hpack-4.1.0 httpcore-1.0.7 httpx-0.28.1 hyperframe-6.1.0 idna-3.10 ipython-9.0.2 ipython-pygments-lexers-1.1.1 jedi-0.19.2 jmespath-1.0.1 lamin_cli-1.1.0 lamin_utils-0.13.10 lamindb-1.2.0 lamindb_setup-1.3.0 markdown-it-py-3.0.0 matplotlib-inline-0.1.7 mdurl-0.1.2 multidict-6.1.0 mypy-extensions-1.0.0 natsort-8.4.0 numpy-2.2.3 packaging-24.2 pandas-2.2.3 pandera-0.23.1 parso-0.8.4 postgrest-0.19.3 prompt_toolkit-3.0.50 propcache-0.3.0 psutil-7.0.0 psycopg2-binary-2.9.10 pure-eval-0.2.3 pyarrow-19.0.1 pydantic-2.10.6 pydantic-core-2.27.2 pydantic-settings-2.8.1 pygments-2.19.1 python-dateutil-2.9.0.post0 python-dotenv-1.0.1 pytz-2025.1 pyyaml-6.0.2 realtime-2.4.1 requests-2.32.3 rich-13.9.4 rich-click-1.8.8 s3fs-2025.2.0 s3transfer-0.11.3 scipy-1.14.1 six-1.17.0 sniffio-1.3.1 sqlparse-0.5.3 stack_data-0.6.3 storage3-0.11.3 strenum-0.4.15 supabase-2.11.0 supafunc-0.9.3 traitlets-5.14.3 typeguard-4.4.2 typing_extensions-4.12.2 typing_inspect-0.9.0 tzdata-2025.1 universal_pathlib-0.2.6 urllib3-1.26.20 wcwidth-0.2.13 websockets-14.2 wrapt-1.17.2 yarl-1.18.3
Using virtual environment "laminr-test-20250310120005-install" ...
+ "C:\Users\CRAN\Documents/.virtualenvs/laminr-test-20250310120005-install/Scripts/python.exe" -m pip install --upgrade --no-user "lamindb>=1.2" ipython bionty wetlab
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Using cached bionty-1.1.1-py3-none-any.whl (92 kB)
Using cached wetlab-1.1.1-py2.py3-none-any.whl (22 kB)
Using cached filelock-3.17.0-py3-none-any.whl (16 kB)
Using cached pronto-2.7.0-py3-none-any.whl (63 kB)
Using cached chardet-5.2.0-py3-none-any.whl (199 kB)
Using cached fastobo-0.13.0-cp311-cp311-win_amd64.whl (2.2 MB)
Using cached networkx-3.4.2-py3-none-any.whl (1.7 MB)
Installing collected packages: networkx, filelock, fastobo, chardet, pronto, bionty, wetlab
Successfully installed bionty-1.1.1 chardet-5.2.0 fastobo-0.13.0 filelock-3.17.0 networkx-3.4.2 pronto-2.7.0 wetlab-1.1.1
Virtual environment "laminr-test-20250310120005-install" removed.
! no run & transform got linked, call `ln.track()` & re-run
[ FAIL 0 | WARN 5 | SKIP 2 | PASS 67 ]

�� Skipped tests (2) �����������������������������������������������������������
• check_requires("Testing imports", "clinicore", language = "Python", (1):
  'test-import.R:42:3'
• check_requires("Testing imports", "wetlab", language = "Python", (1):
  'test-import.R:27:3'

[ FAIL 0 | WARN 5 | SKIP 2 | PASS 67 ]
! calling anonymously, will miss private instances
• deleting instance anonymous/laminr-test-20250310120005
! Did not have permission to delete SQLite file: D:\temp\2025_03_10_11_55_17_1106\RtmpuoGfgr\laminr-test-20250310120005\e529a2f4a2015439b8ae37d2e492a11a.lndb
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "C:\Users\CRAN\DOCUME~1\VIRTUA~1\LAMINR~4\Scripts\lamin.exe\__main__.py", line 7, in <module>
  File "C:\Users\CRAN\DOCUME~1\VIRTUA~1\LAMINR~4\Lib\site-packages\rich_click\rich_command.py", line 378, in __call__
    return super().__call__(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\CRAN\DOCUME~1\VIRTUA~1\LAMINR~4\Lib\site-packages\click\core.py", line 1161, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\CRAN\DOCUME~1\VIRTUA~1\LAMINR~4\Lib\site-packages\rich_click\rich_command.py", line 166, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "C:\Users\CRAN\DOCUME~1\VIRTUA~1\LAMINR~4\Lib\site-packages\click\core.py", line 1697, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\CRAN\DOCUME~1\VIRTUA~1\LAMINR~4\Lib\site-packages\click\core.py", line 1443, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\CRAN\DOCUME~1\VIRTUA~1\LAMINR~4\Lib\site-packages\click\core.py", line 788, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\CRAN\DOCUME~1\VIRTUA~1\LAMINR~4\Lib\site-packages\lamin_cli\__main__.py", line 237, in delete
    return delete(instance, force=force)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\CRAN\DOCUME~1\VIRTUA~1\LAMINR~4\Lib\site-packages\lamindb_setup\_delete.py", line 140, in delete
    isettings.storage.root.rmdir()
  File "C:\Users\CRAN\AppData\Local\R-RETI~1\R-RETI~1\pyenv\PYENV-~1\versions\311~1.9\Lib\pathlib.py", line 1156, in rmdir
    os.rmdir(self)
OSError: [WinError 145] Das Verzeichnis ist nicht leer: 'D:\\temp\\2025_03_10_11_55_17_1106\\RtmpuoGfgr\\laminr-test-20250310120005'
✖ `instance` is "NULL", `lamin connect` will not be run
Virtual environment "laminr-test-20250310120005" removed.
Warning messages:
1: In check_forbidden_install("Python packages") :
  cannot install Python packages during R CMD check
2: In check_forbidden_install("Python packages") :
  cannot install Python packages during R CMD check
3: In check_forbidden_install("Python Virtual Environments") :
  cannot install Python Virtual Environments during R CMD check
> 
> proc.time()
   user  system elapsed 
   8.43   10.92  291.79