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@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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
