[Bioc-devel] Compatibility Issue: 'imputeMethods' Not Exported from MSnbase Affecting DEP Package

[Neumann, Steffen]

Hi Bijaya,

I recommend opening an issue in https://github.com/lgatto/MSnbase
and discuss best plan of action with Laurent.

Yours,
Steffen


On Wed, 2025-08-06 at 17:17 +0530, Bijaya wrote:
> Dear Bioconductor Support Team,
>
> I hope this message finds you well.
>
> I am currently using R version 4.5.1 with Bioconductor 3.21 on
> Windows, and
> I have installed the latest official release versions of the DEP
> (v1.30.0)
> and MSnbase (v2.34.1) packages into a custom library.
>
> However, when I run DEP functions involving imputation, I receive the
> following error:
>
> text
> Error: 'imputeMethods' is not an exported object from
> 'namespace:MSnbase'
>
> This issue appears to stem from MSnbase 2.34.1 removing or
> reorganizing
> functions that DEP relies on. I have confirmed my packages are valid
> via
> BiocManager::valid(), and reinstalling DEP has not resolved the
> problem.
>
> This breaks the imputation step in DEP workflows, which previously
> worked
> with earlier versions of MSnbase. Unfortunately, due to version
> constraints, I cannot downgrade MSnbase without downgrading the
> entire
> Bioconductor and R versions.
>
> Could you please advise if there is a planned fix or an update
> timeline for
> DEP to regain compatibility with the current MSnbase? Alternatively,
> are
> there recommended workarounds for continuing imputation workflows
> under the
> current package versions?
>
> Thank you very much for your support and guidance.
>
> Best regards,
> B.Nag
> ICGEB,New Delhi
>
>       [[alternative HTML version deleted]]
>
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--
IPB Halle                    Computational Plant Biochemistry (CPB)
Dr. Steffen Neumann          https://www.ipb-halle.de/
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