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!
... | ... |
@@ -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 |
) |