[Bioc-devel] ExpData in SummarizedExperiment

[Hervé Pagès]

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

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