218: fix bioc devel problems

DESCRIPTION

@@ -31,7 +31,7 @@ Description: Provides classes and functions for quality control,
     number of reads is supported. The standard normalization methods
     including cpm, rpkm and tpm can be used, and 'DESeq2` as well as voom
     differential expression analyses are available.
-License: Apache License 2.0 | file LICENSE
+License: Apache License 2.0
 URL: https://github.com/insightsengineering/hermes/
 BugReports: https://github.com/insightsengineering/hermes/issues
 Depends:
@@ -89,9 +89,8 @@ biocViews: RNASeq, DifferentialExpression, Normalization, Preprocessing,
     QualityControl
 Encoding: UTF-8
 Language: en-US
-LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0.9000
 Collate:
     'GeneSpec-class.R'
     'HermesData-validate.R'

NAMESPACE

@@ -118,17 +118,17 @@ import(ggplot2)
 import(methods)
 importClassesFrom(biomaRt,Mart)
 importFrom(Biobase,samples)
-importFrom(BiocGenerics,`annotation<-`)
-importFrom(BiocGenerics,`counts<-`)
+importFrom(BiocGenerics,"annotation<-")
+importFrom(BiocGenerics,"counts<-")
 importFrom(BiocGenerics,annotation)
 importFrom(BiocGenerics,counts)
 importFrom(BiocGenerics,normalize)
 importFrom(ComplexHeatmap,add_heatmap)
 importFrom(R6,is.R6)
 importFrom(Rdpack,append_to_Rd_list)
-importFrom(S4Vectors,`metadata<-`)
-importFrom(S4Vectors,`rename`)
+importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,isEmpty)
+importFrom(S4Vectors,rename)
 importFrom(circlize,add_transparency)
 importFrom(dplyr,mutate)
 importFrom(forcats,as_factor)

R/HermesData-methods.R

@@ -81,7 +81,7 @@ NULL
 #' @param value (`list`)\cr the list to replace the current metadata with.
 #'
 #' @return The metadata which is a list.
-#' @importFrom S4Vectors `metadata<-`
+#' @importFrom S4Vectors metadata<-
 #' @importMethodsFrom S4Vectors metadata
 #' @exportMethod metadata
 #' @export `metadata<-`
@@ -146,7 +146,7 @@ setMethod(
 #'   that additional annotations beyond the required ones may be supplied and
 #'   will be stored.
 #'
-#' @importFrom BiocGenerics `annotation<-`
+#' @importFrom BiocGenerics annotation<-
 #' @rdname annotation
 #' @export
 setReplaceMethod(
@@ -188,6 +188,7 @@ setReplaceMethod(
 #'
 #' @param object (`AnyHermesData`)\cr object to access the counts from.
 #' @param value (`matrix`)\cr what should the counts assay be replaced with.
+#' @param ... not used.
 #'
 #' @return The counts assay.
 #'
@@ -202,7 +203,7 @@ setReplaceMethod(
 setMethod(
   f = "counts",
   signature = "AnyHermesData",
-  definition = function(object) {
+  definition = function(object, ...) {
     assay(object)
   }
 )
@@ -214,7 +215,7 @@ setMethod(
 #'   are not identical to the `dimnames` on the `AnyHermesData` object;
 #'   it does not influence actual assignment of `dimnames` to the assay
 #'   (they're always stored as-is).
-#' @importFrom BiocGenerics `counts<-`
+#' @importFrom BiocGenerics counts<-
 #' @export
 #'
 #' @examples
@@ -223,7 +224,7 @@ setMethod(
 setReplaceMethod(
   f = "counts",
   signature = signature(object = "AnyHermesData", value = "matrix"),
-  definition = function(object, value, withDimnames = TRUE) {
+  definition = function(object, ..., withDimnames = TRUE, value) {
     assay(object, withDimnames = withDimnames) <- value
     validObject(object)
     object
@@ -581,7 +582,7 @@ h_map_pos <- function(names, map) {
 #'
 #' @return The [`SummarizedExperiment::SummarizedExperiment`] object with renamed contents.
 #'
-#' @importFrom S4Vectors `rename`
+#' @importFrom S4Vectors rename
 #' @export
 #' @examples
 #' x <- summarized_experiment