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

[Laurent Gatto]

DEP should import imputeMethods from MsCoreUtils rather than from MSnbase. It has been moves some time ago.

Laurent

________________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Bijaya <itsbijayaofficial23 using gmail.com>
Sent: 06 August 2025 13:47
To: support using bioconductor.org; bioc-devel using r-project.org; maintainer using bioconductor.org; hubs using bioconductor.org
Subject: [Bioc-devel] Compatibility Issue: 'imputeMethods' Not Exported from MSnbase Affecting DEP Package

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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

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