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satijalab / azimuth

A Shiny web app for mapping datasets using Seurat v4
https://satijalab.org/azimuth
GNU General Public License v3.0
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Persistant warning: compareStrings no longer part of Biostrings #236

Open bkohrn opened 2 weeks ago

bkohrn commented 2 weeks ago

I recently updated my R installation to R 4.4.1, and resetup all my packages, then went to do setup for a workshop that wanted me to install Azimuth. I got the installation to work, but then on loading, got a warning

> library(Azimuth)
Registered S3 method overwritten by 'SeuratDisk':
  method            from  
  as.sparse.H5Group Seurat

No methods found in package 'Biostrings' for request: 'compareStrings' when loading 'CNEr'
Attaching shinyBS

Further investigation showed that compareStrings is no longer part of Biostrings:

> Biostrings::compareStrings()
Error: unable to find an inherited method for function 'compareStrings' for signature 'pattern = "missing", subject = "missing"'
In addition: Warning message:
In .call_fun_in_pwalign("compareStrings", ...) :
  compareStrings() has moved to the
  pwalign package. Please call
  pwalign::compareStrings() to get rid
  of this warning.

The function still seems to work as expected, it just pops up a warning every time it is run.