data.table 1.12 incompatibility?

[johnstonmj]

I recently re-installed sleuth in a conda environment, re-ran a previously functioning sleuth script, and encountered this error in sleuth_prep:

Error in `[.data.table`(counts_test, , .(total = sum(est_counts)), by = "sample") : 
  column or expression 1 of 'by' or 'keyby' is type closure. Do not quote column names. Usage: DT[,sum(colC),by=list(colA,month(colB))]

Which seems to stem from Line 372 of sleuth.R

I note that my latest conda environment runs r-data.table = 1.12

Is it possible that the latest data.table no longer accepts "sample" as it is quoted in sleuth.R?

[ZimmerA]

I am currently running into the same issue. Did you ever solve this?