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ebi-gene-expression-group / monocle-scripts

Command line scripts wrapping functions in monocle3
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Error in monocle create #15

Open a-solovyev12 opened 3 years ago

a-solovyev12 commented 3 years ago

Hello,

We are running into problem when calling monocle3 create on a standard 10X-like directory. The following error is produced: 

Error in checkSlotAssignment(object, name, value) : 
  'reducedDims' is not a slot in class "SingleCellExperiment"
Calls: do.call ... .valid.Vector.length -> as -> asMethod -> slot<- -> checkSlotAssignment
Execution halted

Package versions: 

monocle3-cli              0.0.9                     r36_1    bioconda
r-monocle3                0.1.3                     r36_0    bioconda

The same behaviour is observed with r-monocle3=0.2.0.

This issue was already mentioned here: https://github.com/cole-trapnell-lab/monocle3/issues/246 and as a result the version of bioconductor-singlecellexperiment was pinned in this PR: https://github.com/bioconda/bioconda-recipes/pull/20002.

However, I noticed that this pin was removed in the further updates to the recipe. Was there a particular reason for that? Re-introducing the pin in a local environment does not solve the issue, either. How do you think this could be fixed?

Thanks, Andrey