@@ -78,14 +78,15 @@ exportMethods(runParams)

 exportMethods(sampleLabel)

 import(Rcpp)

 import(RcppEigen)

-import(data.table, except = melt)

+import(SummarizedExperiment)

+import(data.table, except = c(melt, shift))

 import(foreach)

 import(ggplot2)

 import(grDevices)

 import(graphics)

 import(grid)

 import(gridExtra, except = c(combine))

-import(stats)

+import(stats, except = c(start, end))

 importFrom(MAST,FromMatrix)

 importFrom(MAST,summary)

 importFrom(MAST,zlm)

@@ -521,7 +521,7 @@ celda_C <- function(counts,

 #' @examples

 #' celdaCSim <- simulateCells(model = "celda_C", K = 10)

 #' simCounts <- celdaCSim$counts

-#' @import stats

+#' @rawNamespace import(stats, except = c(start, end))

 #' @export

 simulateCellscelda_C <- function(model,

     S = 5,

@@ -26,7 +26,7 @@

 #' clusterDiffexpRes = differentialExpression(celdaCGSim$counts,

 #'     celdaCGMod, c1 = c(1, 2))

 #' @export

-#' @rawNamespace import(data.table, except = melt)

+#' @rawNamespace import(data.table, except = c(melt, shift))

 #' @importFrom MAST FromMatrix

 #' @importFrom MAST zlm

 #' @importFrom MAST summary

@@ -34,6 +34,7 @@

 #' @importFrom SummarizedExperiment assay

 #' @importFrom SummarizedExperiment colData

 #' @importFrom SummarizedExperiment assayNames

+#' @import SummarizedExperiment

 differentialExpression <- function(counts,

     celdaMod,

     c1,

@@ -80,7 +81,7 @@ differentialExpression <- function(counts,

     # explicitly load library SummarizedExperiment due to MAST package

     # dependency error

-    requireNamespace(SummarizedExperiment)

+    # requireNamespace(SummarizedExperiment)

     sca <- suppressMessages(MAST::FromMatrix(log_normalized_mat, cdat))

     cdr2 <- colSums(SummarizedExperiment::assay(sca) > 0)