Hi Laurent, Mike,
The culprit is an unintentional commit to SummarizedExperiment that made
its way to BioC 3.21 and that I reverted last week in
SummarizedExperiment 1.38.1. See:
https://github.com/Bioconductor/SummarizedExperiment/commit/421e175e3615d643b694e0bcb3bc579c74b3ed71
Problem is that we now have an S4 caching issue: SingleCellExperiment
still has the old (and now stale) definition of the SummarizedExperiment
class (from SummarizedExperiment 1.38.0) in its cache. Yes, for some
reasons I never really understood packages cache the definitions of
classes that they don't own, which sounds like a bad idea and has caused
a lot of trouble and headaches already.
The immediate workaround is to reinstall SingleCellExperiment **from
source**. In the meantime I'll bump SingleCellExperiment version in
order to trigger build and propagation of new binaries.
Sorry for the inconvenience.
H.
On 06/05/2025 07:52, Michael Love wrote:
Yes, us too. Users are reporting DESeq2 1.48.0 for Bioconductor 3.21
is failing with something similar:
```
Error in validObject(.Object) :
invalid class “DESeqDataSet” object: superclass "ExpData" not defined
in the environment of the object's class
```
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Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
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