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plger / scDblFinder

Methods for detecting doublets in single-cell sequencing data
https://plger.github.io/scDblFinder/
GNU General Public License v3.0
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Deprecated "dgcMatrix" #63

Closed ATpoint closed 1 year ago

ATpoint commented 1 year ago

Hi Pierre-Luc,

fyi, the Matrix package >= 1.5.0 has deprecated the as(., "dgCMatrix") syntax, now erroring if that is used. It now must be as(., "CsparseMatrix"). I would therefore suggest to update the respective lines in the source and require Matrix to be >= 1.5.0 in the DESCRIPTION.

I do not have a MRE at hand now, but once you update Matrix you get something like:

> bp  <- BiocParallel::MulticoreParam(mc_workers, RNGseed=1234)
> sce <- scDblFinder::scDblFinder(sce, clusters="cluster", samples="zt", BPPARAM=bp)
Error: BiocParallel errors
  2 remote errors, element index: 1, 2
  0 unevaluated and other errors
  first remote error:
Error in value[[3L]](cond): An error occured while processing sample 'zt1':
Error: as(<dgeMatrix>, "dgCMatrix") is deprecated since Matrix 1.5-0; do as(., "CsparseMatrix") instead

best, -Alex

plger commented 1 year ago

Hi Alex, thanks for pointing this out. I pushed the change, and since this is quite critical I've also altered the stable Bioc 3.16 release. (Haven't changed the explicit Matrix dependency yet, since CsparseMatrix did work in previous Matrix versions) Best, Pierre-Luc

ATpoint commented 1 year ago

Great, thanks for the prompt reply!