Error in `dimnames<-.data.frame` when using "flag_remove" function

[hannierpulido]

Hello,

Description:
I encountered the following error while executing the "flag_remove" function:

xcmsObj2 <- flag_remove(xcmsObj, ref.class = "meoh") 
# or
xcmsObj2 <- flag_remove(xcmsObj)

Error Message:

Error in `dimnames<-.data.frame`(`*tmp*`, value = list(n)) : 
  invalid 'dimnames' given for data frame

Context:

• The "xcmsObj@phenoData@data" object is a dataframe with a "class" column containing levels: c("blank", "meoh", "sample").
• The "xcmsObj@phenoData@varMetadata" object is also a dataframe:

> xcmsObj@phenoData@varMetadata
  labelDescription
1   sampleMetadata
2            class
3   injectionOrder
4             mode

• The xcmsObj is of class "XCMSnExp"

R and msPurity Versions:

• R version 4.2.2 (2022-10-31 ucrt)
• msPurity version 1.24.0

Any insights or suggestions to resolve this issue would be greatly appreciated.

Thank you.