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alanocallaghan / scater

Clone of the Bioconductor repository for the scater package.
https://bioconductor.org/packages/devel/bioc/html/scater.html
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Strange warning #199

Closed RiboRings closed 1 year ago

RiboRings commented 1 year ago

Hi!

This warning kind of looks out of place. It doesn’t go away when useNames = TRUE. In scater 1.28, mia 1.8 and R 4.3.

library(mia)
data("GlobalPatterns", package = "mia")

GlobalPatterns <- runMDS(GlobalPatterns,
                         FUN = vegan::vegdist,
                         method = "bray",
                         name = "bray",
                         assay.type = "counts",
                         useNames = TRUE)

# Warning message:
#   useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = TRUE.
alanocallaghan commented 1 year ago

See https://github.com/LTLA/scuttle/issues/22

alanocallaghan commented 1 year ago

This is fixed now