[Bioc-devel] ExpData in SummarizedExperiment

[Laurent Gatto]

Dear Hervé, dear maintainers

We are bitten by the following issue related to SE and SCE:

Using version 1.38.0:

## BiocManager::install("Bioconductor/SummarizedExperiment",
##                      ref = "a320baea6278ba6d7e6c646f5576ea6e8b6cd732",
##                      force = TRUE) ## version 1.38.0

> suppressPackageStartupMessages(library("SummarizedExperiment"))
> suppressPackageStartupMessages(library("SingleCellExperiment"))
> packageVersion("SummarizedExperiment")
[1] ‘1.38.0’
> example("SummarizedExperiment", echo = FALSE)
> as(se0, "SingleCellExperiment") ## OK
class: SingleCellExperiment 
dim: 200 6 
metadata(0):
assays(1): counts
rownames: NULL
rowData names(0):
colnames(6): A B ... E F
colData names(1): Treatment
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):

But with the latest version:

## BiocManager::install("SummarizedExperiment",
##                      force = TRUE) ## version 1.38.1

> suppressPackageStartupMessages(library("SummarizedExperiment"))
> suppressPackageStartupMessages(library("SingleCellExperiment"))
> example("SummarizedExperiment", echo = FALSE)
> packageVersion("SummarizedExperiment")
[1] ‘1.38.1’
> as(se0, "SingleCellExperiment") ## Error
Error in validObject(.Object) : 
  invalid class “SingleCellExperiment” object: superclass "ExpData" not defined in the environment of the object's class

Which can be recovered with (which was removed from 1.38.1):

> setClassUnion("ExpData", c("matrix", "SummarizedExperiment"))
> as(se0, "SingleCellExperiment") ## Error
class: SingleCellExperiment 
dim: 200 6 
metadata(0):
assays(1): counts
rownames: NULL
rowData names(0):
colnames(6): A B ... E F
colData names(1): Treatment
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):

Is this a matter of patience that will fix itself with another update?

Best wishes,

Laurent