[Bioc-devel] ExpData in SummarizedExperiment

[Hervé Pagès]

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
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