diff --git a/DESCRIPTION b/DESCRIPTION index bb4f60c2..eb1fc5db 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -52,7 +52,8 @@ Imports: teal.logger (>= 0.1.3.9013), teal.reporter (>= 0.2.0), teal.widgets (>= 0.4.0), - tern (>= 0.7.10) + tern (>= 0.7.10), + utils Suggests: BiocStyle, covr, diff --git a/NAMESPACE b/NAMESPACE index cccf61a1..b526f3bd 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -73,3 +73,4 @@ import(teal.data) importFrom(S4Vectors,DataFrame) importFrom(S4Vectors,setListElement) importFrom(lifecycle,deprecate_soft) +importFrom(utils,str) diff --git a/R/barplot.R b/R/barplot.R index c204e596..d58482fa 100644 --- a/R/barplot.R +++ b/R/barplot.R @@ -201,7 +201,7 @@ srv_g_barplot <- function(id, if (.test) { table_r <- reactive({ - str(layer_data(plot_r())) + utils::str(layer_data(plot_r())) }) output$table <- renderPrint(table_r()) } diff --git a/R/boxplot.R b/R/boxplot.R index b275be4c..b8b39e3b 100644 --- a/R/boxplot.R +++ b/R/boxplot.R @@ -195,7 +195,7 @@ srv_g_boxplot <- function(id, if (.test) { table_r <- reactive({ - str(layer_data(plot_r())) + utils::str(layer_data(plot_r())) }) output$table <- renderPrint(table_r()) } diff --git a/R/package.R b/R/package.R index e21acf41..035989a3 100644 --- a/R/package.R +++ b/R/package.R @@ -10,4 +10,5 @@ #' @import teal teal.data #' @importFrom S4Vectors setListElement DataFrame #' @importFrom lifecycle deprecate_soft +#' @importFrom utils str NULL diff --git a/tests/testthat/test-pca.R b/tests/testthat/test-pca.R index 8fe6205b..0c2115a7 100644 --- a/tests/testthat/test-pca.R +++ b/tests/testthat/test-pca.R @@ -97,7 +97,7 @@ test_that("pca module works as expected in the test app", { ) # Now update experiment name, assay name, cluster & matrix option on correlation tab. - app$set_inputs(!!ns("experiment-name") := "hd2") + app$set_inputs(!!ns("experiment-name") := "hd2", timeout_ = 30000) app$set_inputs(!!ns("assay-name") := "voom") app$set_inputs(!!ns("cluster_columns") := TRUE) app$set_inputs(!!ns("show_matrix") := FALSE) @@ -117,7 +117,7 @@ test_that("pca module works as expected in the test app", { app$set_inputs(!!ns("var_pct") := FALSE) app$set_inputs(!!ns("label") := FALSE) - app$wait_for_idle() + app$wait_for_idle(timeout = 30000) res <- app$get_value(output = ns("test_pca")) expect_snapshot( cat(res)