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theislab / anndata2ri

Convert between AnnData and SingleCellExperiment
https://icb-anndata2ri.readthedocs-hosted.com/
GNU General Public License v3.0
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Issue with ExperimentHub when trying to run test cases #160

Open stkgo opened 6 months ago

stkgo commented 6 months ago

Example of the errors:

WARNING  rpy2.rinterface_lib.callbacks:callbacks.py:124 R[write to console]: Cannot connect to ExperimentHub server, using 'localHub=TRUE' instead

WARNING  rpy2.rinterface_lib.callbacks:callbacks.py:124 R[write to console]: Using 'localHub=TRUE'
  If offline, please also see BiocManager vignette section on offline use

WARNING  rpy2.rinterface_lib.callbacks:callbacks.py:124 R[write to console]: Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) :
  Invalid Cache: sqlite file
  Hub has not been added to cache
  Run again with 'localHub=FALSE'

Relevant tests:

=========================== short test summary info ============================
FAILED tests/test_rpy2py.py::test_convert_manual[manual-allen] - rpy2.rinterf...
FAILED tests/test_rpy2py.py::test_convert_manual[local-allen] - rpy2.rinterfa...
FAILED tests/test_rpy2py.py::test_convert_manual[activate-allen] - rpy2.rinte...
================== 3 failed, 92 passed, 13 warnings in 13.89s ==================

The experimenthub cache files don't seem to be working properly.