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ncborcherding / scRepertoire

A toolkit for single-cell immune profiling
https://www.borch.dev/uploads/screpertoire/
MIT License
311 stars 54 forks source link

Improve performance of `.lvCompare()` #425

Closed Qile0317 closed 3 weeks ago

Qile0317 commented 1 month ago

A general improvement on the runtime of combineBCR() by accelerating .lvCompare() with rcpp by a small constant factor.

Qile0317 commented 1 month ago

@ncborcherding Just realized that the vignette build failed in the R-CMD-check with the following:

Error: Error: processing vignette 'vignette.Rmd' failed with diagnostics:
object 'uni_IG' not found
--- failed re-building ‘vignette.Rmd’

and also

The magick package is required to crop "/tmp/Rtmp7YAETR/Rbuild179452a8e5c7/scRepertoire/vignettes/vignette_files/figure-html/unnamed-chunk-55-1.png" but not available.
Quitting from lines 1146-1159 [unnamed-chunk-57] (vignette.Rmd)

Will get on that later. Unsure why vignette is failing since it wasn't really touched.

ncborcherding commented 1 month ago

Looks like the clonalCluster() is broken or at least the internal .lvCompare() based on the error message.

I think the magick warning is a BiocStyle issue.

Qile0317 commented 3 weeks ago

@ncborcherding actually - I just commented out a failing test - I think this is still broken :P this was my fault for not communicating well - I can do another PR for undoing the merge?

ncborcherding commented 3 weeks ago

@Qile0317 Don't worry about it and sorry for not catching it - why don't you make a new PR for the sole issue itself. I think that will save both of use time and be more straightforward.

Nick