Run checks

Import SummarizedExperiment to avoid warnings

DESCRIPTION

@@ -35,7 +35,8 @@ Imports:
     matrixStats,
     ggplot2,
     scales,
-    BiocParallel
+    BiocParallel,
+    SummarizedExperiment
 Suggests:
     testthat,
     scran,
@@ -48,8 +49,8 @@ Suggests:
     BiocStyle,
     covr,
     S4Vectors,
-    SummarizedExperiment,
-    cowplot
+    cowplot,
+    limSolve
 biocViews: SingleCell, RNASeq, Transcriptomics, GeneExpression, Sequencing,
     Software
 URL: https://github.com/Oshlack/splatter

R/scDD-estimate.R

@@ -20,10 +20,12 @@
 #' @return SCDDParams object containing the estimated parameters.
 #'
 #' @examples
+#' \dontrun{
 #' data("sc_example_counts")
 #' conditions <- sample(1:2, ncol(sc_example_counts), replace = TRUE)
 #' params <- scDDEstimate(sc_example_counts, conditions)
 #' params
+#' }
 #' @importFrom BiocParallel SerialParam
 #' @export
 scDDEstimate <- function(counts, conditions, params = newSCDDParams(),

man/scDDEstimate.Rd

@@ -41,8 +41,10 @@ simulate. The output is then converted to a SCDDParams object. See
 \code{\link[scDD]{preprocess}} and \code{\link[scDD]{scDD}} for details.
 }
 \examples{
+\dontrun{
 data("sc_example_counts")
 conditions <- sample(1:2, ncol(sc_example_counts), replace = TRUE)
 params <- scDDEstimate(sc_example_counts, conditions)
 params
 }
+}