Error with R function using Knitr in Lyx

Question

I am getting an error when using the summary() function using Knitr in Lyx. The functions preceding it works.

<<>>=
library(faraway)
head(teengamb)
mdl <- lm(gamble ~ sex + status, data=teengamb) 
summary(mdl)
@

I am inputing this code through Insert Tex Code in Lyx. I just tested I can run summary(teengamb) but not summary(mdl). Both codes work in RStudio.

The error is "Undefined Control Sequence" with description "\end{verbatim} ..."

Answer 1

This problem has been solved in knitr after version 1.1. You do not need to change anything in LyX or R. For now, you can install the development version from:

install.packages('knitr', repos = 'http://www.rforge.net/')

Please ignore both answers below:

---

I have finally found out the reason for this error (this is the deepest bug I have ever seen). It is because the upquote package does not work if the T1 encoding is declared after it is loaded, e.g.

\documentclass{article}
\usepackage{upquote}
\usepackage[T1]{fontenc}
\usepackage[latin9]{inputenc}
\begin{document}
\begin{verbatim}
'
\end{verbatim}
\end{document}

But if we move upquote after fontenc, it works:

\documentclass{article}
\usepackage[T1]{fontenc}
\usepackage[latin9]{inputenc}
\usepackage{upquote}
\begin{document}
\begin{verbatim}
'
\end{verbatim}
\end{document}

Or just do not use the T1 encoding -- uncheck the checkbox before the font encoding in the preferences:

The reason that Ubuntu users were not able to reproduce the problem was because upquote.sty was from R's texmf tree instead of the one in TeXLive, and R's version of upquote works.

The other way to fix the problem is to add R's texmf tree to MikTeX under Windows.

Please ignore the answer below:

---

Since options(show.signif.stars = FALSE) worked, I'm posting it as one possible answer, but this is still a very weird problem to me. Setting show.signif.stars = FALSE removes the significance codes from the results below (which was from summary(mdl)):

Call:
lm(formula = gamble ~ sex + status, data = teengamb)

Residuals:
    Min      1Q  Median      3Q     Max 
-35.873 -15.755  -3.007  10.924 111.586 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept)  60.2233    15.1347   3.979 0.000255 ***
sex         -35.7094     9.4899  -3.763 0.000493 ***
status       -0.5855     0.2727  -2.147 0.037321 *  
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 27.99 on 44 degrees of freedom
Multiple R-squared: 0.2454, Adjusted R-squared: 0.2111 
F-statistic: 7.154 on 2 and 44 DF,  p-value: 0.002042 

The error came from the line Signif. codes, and I do not understand why any of these characters could possibly cause errors in LaTeX: all of them are ASCII and should work inside the verbatim environment.

From the comments above, neither @mrdwab nor me could reproduce the problem. I guess there must be something weird about the OP's LaTeX installation.