I'm using Lyx 2.1.2 and knitr (not sure how to determine the version) on Fedora 20. I'm running into a problem with the termination of knitr chunks when the chunk is embedded in a table cell. If I do not enter the final @ line for the chunk, I get an error and the document cannot be created. If I do enter the final @ line for the chunk, it works, but the @ mark appears literally in the table cell after the output from the R code.
I suspect that this is part of a general problem that I mentioned in another posting, is related to LaTex objects immediately following a knitr chunk.
This is an example Lyx document that demonstrates the problem:
\lyxformat 474
\begin_document
\begin_header
\textclass article
\use_default_options true
\begin_modules
knitr
\end_modules
\maintain_unincluded_children false
\language english
\language_package default
\inputencoding auto
\fontencoding global
\font_roman default
\font_sans default
\font_typewriter default
\font_math auto
\font_default_family default
\use_non_tex_fonts false
\font_sc false
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
\graphics default
\default_output_format default
\output_sync 0
\bibtex_command default
\index_command default
\paperfontsize default
\spacing single
\use_hyperref false
\papersize default
\use_geometry false
\use_package amsmath 1
\use_package amssymb 1
\use_package cancel 1
\use_package esint 1
\use_package mathdots 1
\use_package mathtools 1
\use_package mhchem 1
\use_package stackrel 1
\use_package stmaryrd 1
\use_package undertilde 1
\cite_engine basic
\cite_engine_type default
\biblio_style plain
\use_bibtopic false
\use_indices false
\paperorientation portrait
\suppress_date false
\justification true
\use_refstyle 1
\index Index
\shortcut idx
\color #008000
\end_index
\secnumdepth 3
\tocdepth 3
\paragraph_separation indent
\paragraph_indentation default
\quotes_language english
\papercolumns 1
\papersides 1
\paperpagestyle default
\tracking_changes false
\output_changes false
\html_math_output 0
\html_css_as_file 0
\html_be_strict false
\end_header
\begin_body
\begin_layout Standard
This is an example of a problem that arises when knitr chunks are embedded
in Lyx table cells.
Here is the table:
\end_layout
\begin_layout Standard
\begin_inset Tabular
<lyxtabular version="3" rows="2" columns="2">
<features rotate="0" tabularvalignment="middle">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<row>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
Text
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
Chunk
\end_layout
\end_inset
</cell>
</row>
<row>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
Arbitrary Text
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
\begin_inset Flex Chunk
status open
\begin_layout Plain Layout
<<example,echo=FALSE>>=
\end_layout
\begin_layout Plain Layout
print("Hello World")
\end_layout
\begin_layout Plain Layout
@
\end_layout
\end_inset
\end_layout
\end_inset
</cell>
</row>
</lyxtabular>
\end_inset
\end_layout
\end_body
\end_document
This is the Tex output from pdflatex:
\batchmode
\makeatletter
\def\input@path{{/home/loga/bugs/cell-chunk//}}
\makeatother
\documentclass[english]{article}\usepackage[]{graphicx}\usepackage[]{color}
%% maxwidth is the original width if it is less than linewidth
%% otherwise use linewidth (to make sure the graphics do not exceed the margin)
\makeatletter
\def\maxwidth{ %
\ifdim\Gin@nat@width>\linewidth
\linewidth
\else
\Gin@nat@width
\fi
}
\makeatother
\definecolor{fgcolor}{rgb}{0.345, 0.345, 0.345}
\newcommand{\hlnum}[1]{\textcolor[rgb]{0.686,0.059,0.569}{#1}}%
\newcommand{\hlstr}[1]{\textcolor[rgb]{0.192,0.494,0.8}{#1}}%
\newcommand{\hlcom}[1]{\textcolor[rgb]{0.678,0.584,0.686}{\textit{#1}}}%
\newcommand{\hlopt}[1]{\textcolor[rgb]{0,0,0}{#1}}%
\newcommand{\hlstd}[1]{\textcolor[rgb]{0.345,0.345,0.345}{#1}}%
\newcommand{\hlkwa}[1]{\textcolor[rgb]{0.161,0.373,0.58}{\textbf{#1}}}%
\newcommand{\hlkwb}[1]{\textcolor[rgb]{0.69,0.353,0.396}{#1}}%
\newcommand{\hlkwc}[1]{\textcolor[rgb]{0.333,0.667,0.333}{#1}}%
\newcommand{\hlkwd}[1]{\textcolor[rgb]{0.737,0.353,0.396}{\textbf{#1}}}%
\usepackage{framed}
\makeatletter
\newenvironment{kframe}{%
\def\at@end@of@kframe{}%
\ifinner\ifhmode%
\def\at@end@of@kframe{\end{minipage}}%
\begin{minipage}{\columnwidth}%
\fi\fi%
\def\FrameCommand##1{\hskip\@totalleftmargin \hskip-\fboxsep
\colorbox{shadecolor}{##1}\hskip-\fboxsep
% There is no \\@totalrightmargin, so:
\hskip-\linewidth \hskip-\@totalleftmargin \hskip\columnwidth}%
\MakeFramed {\advance\hsize-\width
\@totalleftmargin\z@ \linewidth\hsize
\@setminipage}}%
{\par\unskip\endMakeFramed%
\at@end@of@kframe}
\makeatother
\definecolor{shadecolor}{rgb}{.97, .97, .97}
\definecolor{messagecolor}{rgb}{0, 0, 0}
\definecolor{warningcolor}{rgb}{1, 0, 1}
\definecolor{errorcolor}{rgb}{1, 0, 0}
\newenvironment{knitrout}{}{} % an empty environment to be redefined in TeX
\usepackage{alltt}
\usepackage[T1]{fontenc}
\usepackage[latin9]{inputenc}
\makeatletter
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% LyX specific LaTeX commands.
%% Because html converters don't know tabularnewline
\providecommand{\tabularnewline}{\\}
\makeatother
\usepackage{babel}
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
\begin{document}
This is an example of a problem that arises when knitr chunks are
embedded in Lyx table cells. Here is the table:
\begin{tabular}{|c|c|}
\hline
Text &
Chunk\tabularnewline
\hline
\hline
Arbitrary Text &
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{verbatim}
## [1] "Hello World"
\end{verbatim}
\end{kframe}
\end{knitrout}
@\tabularnewline
\hline
\end{tabular}
\end{document}
Looking at the Tex output (four lines from the bottom) the @ mark is appearing outside the knitrout environment, yet within the Lyx file, the @ mark is inside the chunk and (at least in WYSIWYM terms) obviously not intended to appear in the document.
Is there a way around this or is it a bug that needs fixing? Of course, if there is any other data I can post that would help, just let me know.
Thanks!
This is due to the following LyX bug: http://www.lyx.org/trac/ticket/8875 (which will be fixed in LyX 2.2.0)
You already have one work around (adding a @). Another work around which you might prefer is to use LyX ERT (to learn more about the differences between ERT and LyX chunks, see Difference between ERT and LyX' custom knitr insets). To do this, delete the chunk inset, and put the cursor in the table cell where it was, and press "ctrl + l", (or Insert > TeX Code)
I cannot add empty lines inside the code, but there needs to be an empty line inside the ERT box at the top and the bottom. This ensures that knitr recognizes that it's a knitr chunk.
Note that exporting to Rnw can help in diagnosing these issues.