[Bioc-devel] Error building package

Kern, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Mon Apr 19 15:21:24 CEST 2021

Even though you did not make any changes to your package,  a dependency you use has changed.  This currently requires attention by you (and any other package / package maintainer affected) to make appropriate changes in your package code and to push up to bioconductor.org

The changes comes from an update in CRAN package knitr version 1.33.  See https://github.com/yihui/knitr/issues/1864 regarding the change.

The ERROR is very informative and following its advice by updating the Suggest of the package DESCRIPTION should remedy.

If your vignette is based on the vignette engine knitr::rmarkdown, you have to declare the dependency on
 rmarkdown, e.g.,

Suggests: rmarkdown
VignetteBuilder: knitr

If your vignette is based on the vignette engine knitr::markdown, you have to declare the dependency on
 markdown, e.g.,

Suggests: markdown
VignetteBuilder: knitr

For quick reference, here is a useful help page on fixing bugs in release and devel for Bioconductor.

We are exploring other options for fixing this issue since it affects hundreds of Bioconductor package but currently if you would like to follow the above instructions it is greatly appreciated.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of alan murphy <alanmurph94 using hotmail.com>
Sent: Saturday, April 17, 2021 4:52 AM
To: ELENI ADAM <eadam002 using odu.edu>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Error building package

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