Fix gha after moving data.table to import (#117)

* add fread to imports in NAMESPACE
* fix datatable load in examples
* bump pre bioconductor release

---------

Co-authored-by: Christian Mertes <mertes@in.tum.de>

Author: AtaJadidAhari

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: FRASER
 Type: Package
 Title: Find RAre Splicing Events in RNA-Seq Data
-Version: 2.5.5
+Version: 2.4.6
 Date: 2025-10-24
 Authors@R: c(
     person("Christian", "Mertes", role=c("aut", "cre"), 
@@ -34,7 +34,7 @@ biocViews:
 License: file LICENSE
 URL: https://github.com/gagneurlab/FRASER
 BugReports: https://github.com/gagneurlab/FRASER/issues
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Encoding: UTF-8
 VignetteBuilder: knitr
 Depends:

R/FraserDataSet-class.R

@@ -271,13 +271,13 @@ setMethod("show", "FraserDataSet", function(object) {
 #'   fraser <- FraserDataSet()
 #'   
 #'   # example sample annoation
-#'   sampleTable <- fread(system.file("extdata",
+#'   sampleTable <- data.table::fread(system.file("extdata",
 #'           "sampleTable_countTable.tsv", package="FRASER", mustWork=TRUE))
 #'  
 #'   # get raw counts 
-#'   junctionCts   <- fread(system.file("extdata", 
+#'   junctionCts   <- data.table::fread(system.file("extdata",
 #'           "raw_junction_counts.tsv.gz", package="FRASER", mustWork=TRUE))
-#'   spliceSiteCts <- fread(system.file("extdata", 
+#'   spliceSiteCts <- data.table::fread(system.file("extdata",
 #'           "raw_site_counts.tsv.gz", package="FRASER", mustWork=TRUE))
 #'   
 #'   # create FRASER object

R/mergeExternalData.R

@@ -23,7 +23,7 @@
 #' @return Merged \code{FraserDataSet} object.
 #' 
 #' @examples
-#' anno <- fread(system.file("extdata", "externalCounts", 
+#' anno <- data.table::fread(system.file("extdata", "externalCounts",
 #'         "annotation.tsv.gz", package="FRASER"))
 #' ctsFiles <- list.files(full.names = TRUE, pattern="counts",
 #'         system.file("extdata", "externalCounts", package="FRASER"))

R/plotMethods.R

@@ -278,7 +278,7 @@
 #' plotVolcano(fds, "sample1", "jaccard", aggregate=TRUE, subsetName="testSet")
 #' 
 #' # dive into gene/sample level results
-#' res <- as.data.table(results(fds))
+#' res <- data.table::as.data.table(results(fds))
 #' res
 #' plotExpression(fds, result=res[1])
 #' plotQQ(fds, result=res[1])
@@ -319,7 +319,7 @@
 #'     orgDb <- org.Hs.eg.db
 #'  
 #'     res <- results(fds, padjCutoff=NA, deltaPsiCutoff=NA)
-#'     res_dt <- as.data.table(res)
+#'     res_dt <- data.table::as.data.table(res)
 #'     res_dt <- res_dt[sampleID == "sample2",]
 #'     
 #'     # plot full range of gene containing outlier junction

man/FraserDataSet.Rd

@@ -311,6 +311,7 @@ If a \textbf{NA} is assigned, no P-values will be calculated. An example sample
 table is given within the package:
 
 <<sampleData Table, echo=TRUE>>=
+library(data.table)
 sampleTable <- fread(system.file(
     "extdata", "sampleTable.tsv", package="FRASER", mustWork=TRUE))
 head(sampleTable)