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We discovered a bug in the ‘holm’ and ‘user’ corrections for the ‘stageWiseAdjustment’ function that was introduced when making changes for Bioconductor submission. The bug was present in version 0.99.08 until version 1.1.1. It is also present in the Bioconductor 3.6 release branch, hence it is preferable to install the package through Github.