use BiocBaseUtils::checkInstalled

waldronlab · Dec 20, 2024 · 794b963 · 794b963
1 parent 7d6b9c4
commit 794b963
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Showing 4 changed files with 5 additions and 8 deletions.
diff --git a/R/MultiAssayExperiment-helpers.R b/R/MultiAssayExperiment-helpers.R
@@ -352,8 +352,7 @@ setMethod("mergeReplicates", "ANY",
     if (is(object, "SummarizedExperiment") || is(object, "RaggedExperiment"))
         object <- assay(object, i = i)
 
-    if (!requireNamespace("reshape2", quietly = TRUE))
-        stop("Package 'reshape2' is required for 'longFormat()' conversion")
+    BiocBaseUtils::checkInstalled("reshape2")
 
     res <- reshape2::melt(
         object, varnames = c("rowname", "colname"), value.name = "value"

diff --git a/R/MultiAssayExperimentToMAF.R b/R/MultiAssayExperimentToMAF.R
@@ -32,8 +32,7 @@
 MultiAssayExperimentToMAF <-
     function(x, synAssay = "maf_syn", nonSynAssay = "maf_nonSyn")
 {
-    if (!requireNamespace("maftools", quietly = TRUE))
-        stop("Install the 'maftools' package to convert to MAF")
+    BiocBaseUtils::checkInstalled("maftools")
 
     ns <- nonSynAssay %in% names(x)
     sy <- synAssay %in% names(x)

diff --git a/R/saveHDF5MultiAssayExperiment.R b/R/saveHDF5MultiAssayExperiment.R
@@ -3,8 +3,8 @@
 
 .load_HDF5Array_package <- function()
 {
-    if (!requireNamespace("HDF5Array", quietly=TRUE))
-        stop("Please install the 'HDF5Array' package to use this function")
+    BiocBaseUtils::checkInstalled("HDF5Array")
+    requireNamespace("HDF5Array", quietly = TRUE)
 }
 
 .isSingleString <- S4Vectors::isSingleString

diff --git a/R/upsetSamples.R b/R/upsetSamples.R
@@ -42,8 +42,7 @@ upsetSamples <- function(
     MultiAssayExperiment, nsets = NULL, sets = names(MultiAssayExperiment),
     nintersects = NA_integer_, order.by = "freq", check.names = FALSE, ...
 ) {
-    if (!requireNamespace("UpSetR", quietly = TRUE))
-        stop("Please install the 'UpSetR' package to use 'upsetSamples()'")
+    BiocBaseUtils::checkInstalled("UpSetR")
     mae <- MultiAssayExperiment
     datf <- do.call(
         function(...) { data.frame(..., check.names = check.names) },