Respect application overrides when saving SE base from the RSE method.

ArtifactDB · May 21, 2024 · d038c27 · d038c27
1 parent f48c749
commit d038c27
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Showing 3 changed files with 14 additions and 3 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: alabaster.se
 Title: Load and Save SummarizedExperiments from File
-Version: 1.5.0
-Date: 2024-02-21
+Version: 1.5.1
+Date: 2024-05-20
 Authors@R: person("Aaron", "Lun", role=c("aut", "cre"), email="[email protected]")
 License: MIT + file LICENSE
 Description: 

diff --git a/R/saveRangedSummarizedExperiment.R b/R/saveRangedSummarizedExperiment.R
@@ -38,7 +38,11 @@ NULL
 #' @importFrom SummarizedExperiment rowRanges
 #' @importFrom S4Vectors mcols<-
 setMethod("saveObject", "RangedSummarizedExperiment", function(x, path, ...) {
-    callNextMethod()
+    # Can't use callNextMethod() as we want to dispatch on application
+    # overrides; to avoid potential infinite recursion from the override
+    # calling back to saveObject, we explicitly cast to the base class.
+    base <- as(x, "SummarizedExperiment")
+    altSaveObject(base, path, ...)
 
     if (!emptyRowRanges(x)) {
         rr <- rowRanges(x)

diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
@@ -0,0 +1,7 @@
+\name{alabaster.se News}
+\title{alabaster.se News}
+\encoding{UTF-8}
+
+\section{Version 1.6.0}{\itemize{
+\item Respect application-level overrides when saving the SummarizedExperiment base from the RangedSummarizedExperiment's \code{saveObject} method.
+}}