From 42f23afe470276ac8ae5def8ddf3c69abe5c0fbf Mon Sep 17 00:00:00 2001
From: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: Thu, 17 Oct 2024 09:38:22 -0400
Subject: [PATCH] fixing issues related to saveRDS

---
 DESCRIPTION       | 2 +-
 R/BSmooth.R       | 2 +-
 R/BSseq-class.R   | 2 +-
 R/collapseBSseq.R | 2 +-
 R/read.bismark.R  | 2 +-
 inst/NEWS.Rd      | 5 +++++
 6 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 8148456..32f7b8c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: bsseq
-Version: 1.41.0
+Version: 1.41.1
 Encoding: UTF-8
 Title: Analyze, manage and store whole-genome methylation data
 Description: A collection of tools for analyzing and visualizing whole-genome
diff --git a/R/BSmooth.R b/R/BSmooth.R
index 3faf492..79b4f9b 100644
--- a/R/BSmooth.R
+++ b/R/BSmooth.R
@@ -327,7 +327,7 @@ BSmooth <- function(BSseq,
         dir <- dirname(h5_path)
         x <- BSseq
         x@assays <- HDF5Array::shorten_assay2h5_links(x@assays)
-        saveRDS(x, file = file.path(dir, "se.rds"))
+        base::saveRDS(x, file = file.path(dir, "se.rds"))
     }
     BSseq
 }
diff --git a/R/BSseq-class.R b/R/BSseq-class.R
index 585b196..ad85723 100644
--- a/R/BSseq-class.R
+++ b/R/BSseq-class.R
@@ -319,7 +319,7 @@ strandCollapse <- function(BSseq, shift = TRUE, BPPARAM = bpparam(),
         #       HDF5Array::saveHDF5SummarizedExperiment().
         x <- bsseq
         x@assays <- HDF5Array::shorten_assay2h5_links(x@assays)
-        saveRDS(x, file = file.path(dir, "se.rds"))
+        base::saveRDS(x, file = file.path(dir, "se.rds"))
     }
     bsseq
 }
diff --git a/R/collapseBSseq.R b/R/collapseBSseq.R
index c508048..c0ad5b3 100644
--- a/R/collapseBSseq.R
+++ b/R/collapseBSseq.R
@@ -145,7 +145,7 @@ collapseBSseq <- function(BSseq, group, BPPARAM = bpparam(),
         #       HDF5Array::saveHDF5SummarizedExperiment().
         x <- bsseq
         x@assays <- HDF5Array::shorten_assay2h5_links(x@assays)
-        saveRDS(x, file = file.path(dir, "se.rds"))
+        base::saveRDS(x, file = file.path(dir, "se.rds"))
     }
     bsseq
 }
diff --git a/R/read.bismark.R b/R/read.bismark.R
index ae93f94..f486e09 100644
--- a/R/read.bismark.R
+++ b/R/read.bismark.R
@@ -538,7 +538,7 @@ read.bismark <- function(files,
         #       HDF5Array::saveHDF5SummarizedExperiment().
         x <- bsseq
         x@assays <- HDF5Array::shorten_assay2h5_links(x@assays)
-        saveRDS(x, file = file.path(dir, "se.rds"))
+        base::saveRDS(x, file = file.path(dir, "se.rds"))
     }
     bsseq
 }
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index 3fc3775..6e13fad 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -1,6 +1,11 @@
 \name{bsseqnews}
 \title{bsseq news}
 \encoding{UTF-8}
+\section{Version 1.41.x}{
+  \itemize{
+    \item Changing saveRDS to base::saveRDS following upstream changes.
+  }
+}
 \section{Version 1.39.x}{
   \itemize{
     \item{Changing the default value of k in \code{BSmooth.tstat} from