DEP should import imputeMethods from MsCoreUtils rather than from MSnbase. It has been moves some time ago.
Laurent ________________________________________ From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Bijaya <itsbijayaofficia...@gmail.com> Sent: 06 August 2025 13:47 To: supp...@bioconductor.org; bioc-devel@r-project.org; maintai...@bioconductor.org; h...@bioconductor.org Subject: [Bioc-devel] Compatibility Issue: 'imputeMethods' Not Exported from MSnbase Affecting DEP Package [You don't often get email from itsbijayaofficia...@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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
