[Bioc-devel] knitr ERROR on Biocondcutor builders
Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Thu Jun 17 19:59:52 CEST 2021
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.
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
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