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
[Bioc-devel] Compatibility Issue: 'imputeMethods' Not Exported from MSnbase Affecting DEP Package
3 messages · Bijaya, Neumann, Steffen, Laurent Gatto
4 days later
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]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- IPB Halle Computational Plant Biochemistry (CPB) Dr. Steffen Neumann https://www.ipb-halle.de/ Weinberg 3 Tel. +49 (0) 345 5582 - 1770 06120 Halle Fax. +49 (0) 345 5582 - 1009 sneumann(at)IPB-Halle.DE
4 days later
DEP should import imputeMethods from MsCoreUtils rather than from MSnbase. It has been moves some time ago. Laurent
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Bijaya <itsbijayaofficial23 at gmail.com>
Sent: 06 August 2025 13:47
To: support at bioconductor.org; bioc-devel at r-project.org; maintainer at bioconductor.org; hubs at bioconductor.org
Subject: [Bioc-devel] Compatibility Issue: 'imputeMethods' Not Exported from MSnbase Affecting DEP Package
Sent: 06 August 2025 13:47
To: support at bioconductor.org; bioc-devel at r-project.org; maintainer at bioconductor.org; hubs at bioconductor.org
Subject: [Bioc-devel] Compatibility Issue: 'imputeMethods' Not Exported from MSnbase Affecting DEP Package
[You don't often get email from itsbijayaofficial23 at gmail.com. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] 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]] _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel