knitr doesn't generate the figure correctly when knit_hooks$set is enabled in the shell script.

gistfile1.sh

#!/bin/sh

set -o errexit
set -o nounset
set -o noclobber

name=predis-sm

R --no-save --restore <<'EOF'
library(knitr)
opts_knit$set(error=TRUE)
opts_chunk$set(echo=FALSE, cache=TRUE)
if(1) {
knit_hooks$set(inline=function (x) {
  if (any(is.na(x))) return(paste("\\textbf{TODO}\\todo{Sexpr evaluated to NA}"))
  if (is.numeric(x))
        x = round(x, getOption("digits"))
    paste(as.character(x), collapse = ", ")
})
}
library(ggplot2)

update <- function(stem) {
  rnw <- paste(stem,"Rnw",sep='.')
#  if (file.info(rnw)$mtime > file.info(paste(stem,"tex",sep='.'))$mtime) {
    knit(rnw)
#  }
}
update("predis-sm")
EOF
[ -d gen ] || mkdir gen
pdflatex -shell-escape $name

predis-sm.Rnw

\documentclass{article}
\usepackage[backgroundcolor=yellow,shadow,textwidth=1in]{todonotes}

\begin{document}

<<cache=FALSE>>=
if (length(ls())) rm(list=ls())  # new section
opts_chunk$set(fig.path="figure/intro/")
@ 

\begin{figure}
<<fig.height=3>>=
plot(sin)
@ 
\caption{Empirical response}
\end{figure}

Much work remains \Sexpr{NA}, but I have already begun to use OpenMx

\end{document}

opts_knit$set(error=TRUE) should be opts_chunk$set(error=TRUE)