On 06/05/2025 10:07, Hervé Pagès wrote:
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.
Ah... looks like Aaron already took care of that yesterday:
https://github.com/drisso/SingleCellExperiment/commit/06f6cedcf72716bc79c28c2e518437b4b5952f31
We build release twice a week only so the new SingleCellExperiment
(1.30.1) will only become available on Thursday.
Cheers,
H.
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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