[prev in list] [next in list] [prev in thread] [next in thread] 

List:       bioc-devel
Subject:    [Bioc-devel] knitr ERROR on Biocondcutor builders
From:       "Kern, Lori" <Lori.Shepherd () RoswellPark ! org>
Date:       2021-06-17 17:59:52
Message-ID: MN2PR12MB4094DDADD80362D22171D328F90E9 () MN2PR12MB4094 ! namprd12 ! prod ! outlook ! com
[Download RAW message or body]

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.


 Cheers.



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential information.  \
If you are not the intended recipient(s), or the employee or agent responsible for \
the delivery of this message to the intended recipient(s), you are hereby notified \
that any disclosure, copying, distribution, or use of this email message is \
prohibited.  If you have received this message in error, please notify the sender \
immediately by e-mail and delete this email message from your computer. Thank you.  \
[[alternative HTML version deleted]]

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


[prev in list] [next in list] [prev in thread] [next in thread]