Don't suggest aggr.ref=TRUE if it was already set.

LTLA · LTLA · commit 40ff41ae2387 · 2026-01-05T21:05:14.000+11:00
diff --git a/R/trainSingleR.R b/R/trainSingleR.R
@@ -256,7 +256,7 @@ trainSingleR <- function(
             if (de.method == "classic") {
                 hints <- c(hints, "'de.method = \"t\"' or \"wilcox\"")
             }
-            if (ncol(curref) >= 1000) {
+            if (ncol(curref) >= 1000 && !aggr.ref) {
                 what <- paste("large", what)
                 hints <- c(hints, "'aggr.ref = TRUE' for speed")
             }

Original file line number	Diff line number	Diff line change
`@@ -256,7 +256,7 @@ trainSingleR <- function(`
`256`	`256`	`if (de.method == "classic") {`
`257`	`257`	`hints <- c(hints, "'de.method = \"t\"' or \"wilcox\"")`
`258`	`258`	`}`
`259`		`- if (ncol(curref) >= 1000) {`
	`259`	`+ if (ncol(curref) >= 1000 && !aggr.ref) {`
`260`	`260`	`what <- paste("large", what)`
`261`	`261`	`hints <- c(hints, "'aggr.ref = TRUE' for speed")`
`262`	`262`	`}`