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theislab / zellkonverter

Conversion between scRNA-seq objects
https://theislab.github.io/zellkonverter/
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bump up anndata dependency version to 0.7.4 #21

Closed kevinrue closed 4 years ago

kevinrue commented 4 years ago

Currently, https://github.com/kevinrue/velociraptor fails R CMD check with error 

Quitting from lines 64-67 (userguide.Rmd) 
Error: processing vignette 'userguide.Rmd' failed with diagnostics:
ImportError: cannot import name 'concat' from 'anndata' (/github/home/.cache/basilisk/1.1.9/velociraptor-0.99.0/env/lib/python3.7/site-packages/anndata/__init__.py)

See https://github.com/kevinrue/velociraptor/runs/1043289251

Running conda install anndata==0.7.4 in the basilisk/conda environment allowed R CMD check to pass successfully.

Which seems to make sense as https://anndata.readthedocs.io/en/latest/#id1 mentions a new function anndata.concat()

kevinrue commented 4 years ago

I can confirm that this PR fixes the velociraptor R CMD check issue (locally, macOS).

lazappi commented 4 years ago

Sorry I have been slow to look at this, I was on leave until today 🏝. Shouldn't cause any problems so will merge and push to Bioconductor.