I think you're right. I'm going to work on identifying the exact list
but my first rough estimate indicates at least 85 packages affected.
DESeq2 is one of them e.g. with the current 1.48.0 binary (Windows or
Mac) one gets:
library(DESeq2)
countData <- matrix(1:100,ncol=4)
condition <- factor(c("A","A","B","B"))
dds <- DESeqDataSetFromMatrix(countData, DataFrame(condition), ~
condition)
# Error in validObject(.Object) :
# invalid class “DESeqDataSet” object: superclass "ExpData" not
defined in the environment of the object's class
Do you think you can take care of DESeq2? I'll work on bumping all other
affected packages.
Thanks and sorry again for the inconvenience,
H.
On 07/05/2025 07:48, Michael Love wrote:
Just to clarify: do all packages that define classes on top of
SummarizedExperiment need to bump their version number in release to
fix?
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
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