R warn Option Ignored

Yihui Xie

2013-08-08 06:29:49 UTC

Internally warn is set to 1 so that warnings are always recorded. The
correct way to discard warnings is through the chunk option
warning=FALSE: http://yihui.name/knitr/options

Note you almost never need to setwd(); please read ?knit to know more
information about the working directory.

Regards,
Yihui
--
Yihui Xie <***@gmail.com>
Phone: 206-667-4385 Web: http://yihui.name
Fred Hutchinson Cancer Research Center, Seattle

Post by d***@gmail.com
One of the first code chunks in my file is
<<label = SETUP, echo=FALSE>>=
options(prompt = " ", continue = " ", width = 90, scipen = 9, warn = -1)
setwd("/nb/dario/projects/CAGE")
library(knitr)
opts_chunk$set(tidy = FALSE)
@
However, when I see my final PDF, I notice the warnings have been included.
e.g.
hyperTable <-
read.table("/nb/dario/resources/wgEncodeRegDnaseClustered.bed",
sep = '\t')
## Warning: cannot open file
'/nb/dario/resources/wgEncodeRegDnaseClustered.bed': No such
file or directory
## Error: cannot open the connection
I realise I have to fix the path, but why is warn = -1 ignored ? It's also
weird that it appears as both a warning and an error message.
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