Fix BiocCheck warnings (#28)

* fix some warnings

* fixing the tests to match the reworked parameter set

* added value section to remove warnings

* version bump and news

---------

Co-authored-by: Federico Marini <[email protected]>

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: iSEEpathways
 Title: iSEE extension for panels related to pathway analysis
-Version: 0.99.1
-Date: 2023-09-19
+Version: 0.99.2
+Date: 2023-09-21
 Authors@R: 
     c(person("Kevin", "Rue-Albrecht", email = "[email protected]",
              role = c("aut", "cre"),
@@ -45,6 +45,7 @@ Imports:
     S4Vectors,
     shiny,
     shinyWidgets,
+    stats,
     SummarizedExperiment
 Suggests:
     airway,

NEWS.md

@@ -1,3 +1,17 @@
+# iSEEpathways 0.99.2
+
+MINOR UPDATES
+
+* Added missing depedency to DESCRIPTION file (Bioconductor WARNING).
+* Moved `set.seed()` out of functions (Bioconductor WARNING).
+* Added `\value` section to man pages (Bioconductor WARNING).
+
+# iSEEpathways 0.99.1
+
+MINOR UPDATES
+
+* Added BiocViews (Bioconductor NOTE).
+
 # iSEEpathways 0.99.0
 
 NEW FEATURES

R/AllGenerics.R

@@ -2,12 +2,12 @@
 #'
 #' An overview of the generics for accessing common pieces of information in pathway analysis results.
 #'
-#' @section Definitions:
-#' \itemize{
-#' \item `pathwayType(x)` returns a character scalar indicating the type of pathways analysed.
-#' \item `pathwaysList(x)` returns the named list of pathways used in the analysis, or `NULL`.
-#' \item `featuresStats(x)` returns the named numeric vector of feature-level statistics used in the analysis, or `NULL`.
-#' }
+#' @return
+#' `pathwayType(x)` returns a character scalar indicating the type of pathways analysed.
+#'
+#' `pathwaysList(x)` returns the named list of pathways used in the analysis, or `NULL`.
+#'
+#' `featuresStats(x)` returns the named numeric vector of feature-level statistics used in the analysis, or `NULL`.
 #'
 #' @docType methods
 #' @aliases featuresStats pathwayType pathwaysList

R/FgseaEnrichmentPlot-class.R

@@ -12,6 +12,8 @@
 #' Defaults to an empty list, i.e., no brush or lasso.
 #' }
 #'
+#' @return `FgseaEnrichmentPlot()` returns an object of class `FgseaEnrichmentPlot`.
+#'
 #' In addition, this class inherits all slots from its parent [Panel-class] class.
 #'
 #' @docType methods
@@ -179,11 +181,11 @@ setMethod(".generateOutput", "FgseaEnrichmentPlot", function (x, se, all_memory,
   all_cmds <- list()
   # Doing this first so all_active is available in the environment
   iSEE:::.populate_selection_environment(x, plot_env)
-  all_cmds$pre_cmds = paste0(c(
+  all_cmds$pre_cmds <- paste0(c(
     sprintf('.pathways <- pathwaysList(pathwaysResults(se, %s))', dQuote(result_name, FALSE)),
     sprintf('.stats <- featuresStats(pathwaysResults(se, %s))', dQuote(result_name, FALSE))
   ), collapse = "\n")
-  plot_cmds <- sprintf('fgsea_plot <- fgsea::plotEnrichment(.pathways[[%s]], .stats) + labs(title=%s)', 
+  plot_cmds <- sprintf('fgsea_plot <- fgsea::plotEnrichment(.pathways[[%s]], .stats) + labs(title=%s)',
                        dQuote(pathway_id, FALSE), dQuote(pathway_id, FALSE))
   if (!is.null(.multiSelectionActive(x))) {
     brush_src <- sprintf("all_active[['%s']]", plot_name)

R/PathwaysTable-class.R

@@ -3,6 +3,8 @@
 #' The `PathwaysTable` is a \linkS4class{Panel} where each row represents a set of features (i.e., rows).
 #' Selections in this panel can be transmitted to other row-oriented panels.
 #'
+#' @return `PathwaysTable()` returns an object of class `PathwaysTable`.
+#'
 #' @section Slot overview:
 #' The following slots control the test procedure:
 #' \itemize{

R/iSEEfgseaResults-class.R

@@ -5,7 +5,7 @@
 #' @section Slot overview:
 #' This class inherits all its slots directly from its parent class `DataFrame`.
 #'
-#' @section Supported methods:
+#' @return
 #' In the following code snippets, \code{x} is an instance of a [`iSEEpathwaysResults-class`] class.
 #' Refer to the documentation for each method for more details on the remaining arguments.
 #'
@@ -55,6 +55,8 @@ setValidity2("iSEEpathwaysResults", function(.Object) {
 #' The `iSEEfgseaResults` class is used to provide an common interface to pathway analysis results produced by the \pkg{fgsea} package.
 #' It provides methods to access the set of features in each pathway.
 #'
+#' @return `iSEEfgseaResults()` returns an object of class `iSEEfgseaResults`.
+#'
 #' @section Slot overview:
 #' This class inherits all its slots directly from its parent class `iSEEpathwaysResults`.
 #'

R/observers_zoom.R

@@ -1,28 +1,30 @@
 #' Double-click observer
-#' 
+#'
 #' Double-clicking anywhere in the panel clears an existing brush.
-#' 
+#'
 #' @details
 #' Adapted from `iSEE:::.create_zoom_observer()`.
-#' 
+#'
 #' @param plot_name String containing the name of the panel.
 #' @param input The Shiny input object from the server function.
 #' @param session The Shiny session object from the server function.
 #' @param pObjects An environment containing global parameters generated in the \code{\link{iSEE}} app.
 #' @param rObjects A reactive list of values generated in the \code{\link{iSEE}} app.
-#' 
+#'
+#' @return Invisible `NULL`, after setting observers.
+#'
 #' @rdname INTERNAL_create_double_click_observer
 #'
 #' @importFrom iSEE .requestUpdate
 .create_double_click_observer <- function(plot_name, input, session, pObjects, rObjects) {
   dblclick_field <- paste0(plot_name, "_", iSEE:::.zoomClick)
-  
+
   # nocov start
   observeEvent(input[[dblclick_field]], {
     existing_brush <- slot(pObjects$memory[[plot_name]], iSEE:::.brushData)
     # Zooming destroys all active brushes or lassos.
     slot(pObjects$memory[[plot_name]], iSEE:::.brushData) <- list()
-    
+
     # While re-creating the plot clears the brush, it doesn't
     # re-trigger the observer as the observer ignores NULLs.
     # So we have to manually retrigger the downstream effects.
@@ -33,6 +35,6 @@
     }
   }, ignoreInit=TRUE)
   # nocov end
-  
+
   invisible(NULL)
 }

R/utils-simulate.R

@@ -22,7 +22,6 @@
 #' @param n_features integer scalar, number of features to simulate.
 #' @param n_samples integer scalar, number of samples to simulate.
 #' @param pathway_sizes integer vector, possible sizes of pathway to sample from.
-#' @param seed a single value, passed to [set.seed()].
 #'
 #' @return A list of three elements:
 #' \describe{
@@ -40,22 +39,20 @@
 #' @importFrom SummarizedExperiment SummarizedExperiment
 #'
 #' @examples
+#' set.seed(1)
 #' simulated_data <- simulateExampleData()
 #' head(lengths(simulated_data$pathwaysList))
 #' head(simulated_data$featuresStat)
-simulateExampleData <- function(n_pathways = 5E3, n_features = 15E3, n_samples = 8, pathway_sizes = 15:500, seed = 1) {
+simulateExampleData <- function(n_pathways = 5E3, n_features = 15E3, n_samples = 8, pathway_sizes = 15:500) {
   # identifiers
   feature_ids <- paste0("feature_", seq_len(n_features))
   pathway_ids <- paste0("pathway_", seq_len(n_pathways))
   sample_ids <- paste0("sample_", seq_len(n_samples))
   # pathways
-  set.seed(seed)
   pathway_lengths <- sample(pathway_sizes, length(pathway_ids), replace = TRUE)
   names(pathway_lengths) <- pathway_ids
-  set.seed(seed)
   pathways_list <- lapply(pathway_ids, function(x) { sample(feature_ids, pathway_lengths[[x]]) })
   names(pathways_list) <- pathway_ids
-  set.seed(seed)
   # features
   feature_stats <- rnorm(length(feature_ids))
   names(feature_stats) <- feature_ids

tests/testthat/setup-fgsea.R

@@ -1,6 +1,7 @@
 stopifnot(requireNamespace("fgsea"))
 
-setup_data <- simulateExampleData(n_pathways = 5, n_features = 100, pathway_sizes = 10:20, seed = 1)
+set.seed(1)
+setup_data <- simulateExampleData(n_pathways = 5, n_features = 100, pathway_sizes = 10:20)
 
 fgsea_result <- fgsea::fgsea(
   pathways = setup_data$pathwaysList,

vignettes/iSEEpathways.Rmd

@@ -98,6 +98,7 @@ library("iSEE")
 
 # Example data ----
 
+set.seed(1)
 simulated_data <- simulateExampleData()
 
 pathways_list <- simulated_data[["pathwaysList"]]