Ok so I found 81 software packages with broken binaries in release. See
list below.
I just bumped their version. The commit message says: "Version bump to
trigger rebuilding/propagation of Windows and Mac binaries". The version
bump was pushed to the RELEASE_3_21 branch of the packages at
git.
yes I'll bump DESeq2 in release now
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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)
conditi
Just to clarify: do all packages that define classes on top of
SummarizedExperiment need to bump their version number in release to
fix?
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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/421e175e3615d
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 t
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
```
__
Dear Hervé, dear maintainers
We are bitten by the following issue related to SE and SCE:
Using version 1.38.0:
## BiocManager::install("Bioconductor/SummarizedExperiment",
## ref = "a320baea6278ba6d7e6c646f5576ea6e8b6cd732",
## force = TRUE) ## version 1
