[Bioc-devel] knitr ERROR on Biocondcutor builders

Kern, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Thu Jun 17 19:59:52 CEST 2021

Hello developers,

Recent changes to knitr are producing an ERROR on the build reports for many packages (software,  experiment data, workflows).  This is a legitimate ERROR and as a maintainer you should address the issue in any offending package as soon as possible.   As an example, I fixed the Bioconductor maintained experiment data package GSE62944 this morning. The ERROR will read something like:

Error: processing vignette 'GSE62944.Rmd' failed with diagnostics:
The 'rmarkdown' package should be installed and declared as a dependency of the 'GSE62944' package (e.g., in the 'Suggests' field of DESCRIPTION), because the latter contains vignette(s) built with the 'rmarkdown' package. Please see https://github.com/yihui/knitr/issues/1864 for more information.

The ERROR message knitr produces is very explicit on how to fix and is very straightforward.  Please remember to always do a version bump when making changes to your package in addition to updating the Suggest field in the DESCRIPTION.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

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