Browse code

SummarizedExperiment 1.35.4

The saveRDS() method for SummarizedExperiment now suggests using
base::saveRDS() as an alternative to saveHDF5SummarizedExperiment()
when the object to serialize contains out-of-memory data. Only for
users who know what they are doing!

Hervé Pagès authored on 09/10/2024 02:29:33
Showing 2 changed files

... ...
@@ -8,7 +8,7 @@ biocViews: Genetics, Infrastructure, Sequencing, Annotation, Coverage,
8 8
 	GenomeAnnotation
9 9
 URL: https://bioconductor.org/packages/SummarizedExperiment
10 10
 BugReports: https://github.com/Bioconductor/SummarizedExperiment/issues
11
-Version: 1.35.3
11
+Version: 1.35.4
12 12
 License: Artistic-2.0
13 13
 Encoding: UTF-8
14 14
 Authors@R: c(
... ...
@@ -1048,11 +1048,15 @@ setMethod("saveRDS", "SummarizedExperiment",
1048 1048
              compress=TRUE, refhook=NULL)
1049 1049
     {
1050 1050
         if (containsOutOfMemoryData(object))
1051
-            stop(wmsg(class(object), " object contains out-of-memory ",
1051
+            stop(wmsg("This ", class(object), " object contains out-of-memory ",
1052 1052
                       "data so cannot be serialized reliably. Please use ",
1053 1053
                       "saveHDF5SummarizedExperiment() from the HDF5Array ",
1054
-                      "package instead. Also see '?containsOutOfMemoryData' ",
1055
-                      "in the BiocGenerics package for some context."))
1054
+                      "package instead. Alternatively you can call ",
1055
+                      "base::saveRDS() on it but only if you know what ",
1056
+                      "you are doing."),
1057
+                "\n  ",
1058
+                 wmsg("See '?containsOutOfMemoryData' in the BiocGenerics ",
1059
+                      "package for more information."))
1056 1060
         invisible(callNextMethod())
1057 1061
     }
1058 1062
 )