From 794b963a79ed6f6022c99ec868a4b2ba081aee9f Mon Sep 17 00:00:00 2001 From: LiNk-NY Date: Fri, 20 Dec 2024 17:03:07 -0500 Subject: [PATCH] use BiocBaseUtils::checkInstalled --- R/MultiAssayExperiment-helpers.R | 3 +-- R/MultiAssayExperimentToMAF.R | 3 +-- R/saveHDF5MultiAssayExperiment.R | 4 ++-- R/upsetSamples.R | 3 +-- 4 files changed, 5 insertions(+), 8 deletions(-) diff --git a/R/MultiAssayExperiment-helpers.R b/R/MultiAssayExperiment-helpers.R index beb4db9..e5392a4 100644 --- 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 index 6645fbc..fdd0a28 100644 --- 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 index 4bd9eb2..498d8b2 100644 --- 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 index b596ed2..f4a5812 100644 --- 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) },