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Unfortunately, both R markdown and logger try to use the same globalCallingHandlers -- which is not supported. Honestly, I do not see a way to overcome this limitation, see #70 for more details (marking as duplicated issue).
I try to put errors in the log file from rmarkdown, but the compilation of the following rmarkdown fails :
title: "test logger"
output:
html_document
with the error
Error in globalCallingHandlers(error = function(m) { : should not be called with handlers on the stack.
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