How can I redirect R Markdown errors to a log file when running .Rmd scripts from a pipeline?

Question

I generate reports at the end of my Snakemake pipeline using a series of R markdown scripts. If one of these markdown files has an error and fails, the error is not saved to a log file making it impossible to investigate afterwards.

From my research I have not found a way to do this, but: is there a way to redirect errors in R markdown to a log file when running the markdown file in a pipeline? (My pipeline uses SnakeMake for the pipeline, but I assume this would apply to any pipeline).

question from:https://stackoverflow.com/questions/65850328/how-can-i-redirect-r-markdown-errors-to-a-log-file-when-running-rmd-scripts-fro

Answer 1

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