Im trying to include some R results in a TeX document using RStudio. I have managed to get RStudio to generate, what to me looks to be, a fine tex file but it fails to compile the pdf.
I get errors returned saying ! Undefined control sequence. ' which seems to be returned due to the first lines of str(data) calls and the lines showing significance levels:
"! Undefined control sequence.
<argument> '
data.frame': 1980 obs. of 5 variables:
l.39 'data.frame': 1980 obs. of 5 variables:
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined."
"! Undefined control sequence. <argument>
Signif. codes: 0 '
***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
l.95 ...**' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined."
Files with just the summary(data) for instance work fine
Looking around other mailing lists etc Ive seen that this could be because tex cannot find the Sweave package so have copied it to various locations (the same folder as the Rnw and tex files, and a directory without spaces in the path) and tried to rerun the file. Nothing seems to work.
Similarly, this doesnt work, but using summary(cars) instead of str(cars) does. This suggests to me that its something to do with the ' character.
\documentclass [a4paper]{article}
\usepackage{Sweave}
\title {Sweave Example 1}
\author {Friedrich Leisch}
\begin {document}
\maketitle
In this example we embed parts of the examples from the
\texttt {kruskal.test} help page into a \ LaTeX {} document :
<<>>=
data ( cars )
str(cars)
#
\end{document}
(adapted from the sweave manual)
Any ideas on what Im doing wrong?
Any suggestions would be much appreciated.
Add the [noae] package option to your \usepackage{Sweave} statement.
Related
When attempting to convert a jupyter notebook to pdf with the following command:
jupyter nbconvert --to pdf "Search and Other Content Finding Features.ipynb"
I'm getting an error message:
! Missing $ inserted.
<inserted text>
$
l.380 ... Other Content Finding Features_10_0.png}
?
! Emergency stop.
<inserted text>
$
l.380 ... Other Content Finding Features_10_0.png}
I've found some discussion of what that is here.
However, I can't find these characters in my code. Could there be another cause?
For me it was another, although related issue: underlines. I assume that the cause is that text in cells marked as Raw Text will be passed directly to LaTeX, where it can be interpreted as LaTeX code itself. Maybe the underlines in your figure's name?
At some point, I had a raw cell with three underlines ___ which were then making the conversion break. The temporary solution was to convert the cell to markdown, instead of raw (and not run it) to appear in the pdf.
To find the error, I used the following conversion (taken from this answer):
jupyter nbconvert thenotebook.ipynb --to latex
Another error, related, was caused by a link containing underlines:
[text](https://en.wikipedia.org/wiki/Python_(programming_language))
This was also in a Raw Text cell, which I converted to markdown to generate the pdf. The format (colors, links) are different, though.
Last note: My file's name also contains empty spaces, but that wasn't an issue at all!
A very common gotcha here might be the following:
Leading or trailing spaces are not allowed in the pandoc extension tex_math_dollars, which is used by nbconvert.
This means, that this won't work:
$ \epsilon \gt 0 $
And we see the error message:
! Missing $ inserted.
<inserted text>
$
l.364 \$ \epsilon
\gt 0 \$
?
! Emergency stop.
<inserted text>
$
l.364 \$ \epsilon
\gt 0 \$
No pages of output.
Transcript written on notebook.log.
The correct formula without spaces works fine:
$\epsilon \gt 0$
This seems to be a bug in Jupyter nbconvert.
The pandoc documentation suggests that for pandoc this is by design to allow to use dollar symbols without escape sequence:
Anything between two $ characters will be treated as TeX math. The
opening $ must have a non-space character immediately to its right,
while the closing $ must have a non-space character immediately to its
left, and must not be followed immediately by a digit. Thus, $20,000
and $30,000 won’t parse as math. If for some reason you need to
enclose text in literal $ characters, backslash-escape them and they
won’t be treated as math delimiters.
The problem in this case seems to have been caused by my notebook's filename. I don't fully understand what caused the problem, but the error message above includes a reference to some text:
... Other Content Finding Features_10_0.png}.
That text includes _ which can cause this error. I think what happens is that somewhere in the conversion script, if there are spaces in the filename, a file is generated with underscores as shown, and that then triggers the error. (This seems a little bit like a bug to me, or at least a weakness).
The fix that worked for me was simply to change the jupyter notebook's filename not to include any spaces. Then the conversion ran without a hitch.
For me it's caused by significant difference between LaTeX and MathJax. For example cases environment can be rendered outside math mode with MathJax, which is the default choice of jupyter notebook. However, it causes an error stating "missing $ insert" in LaTeX. The error message disappeared after correcting syntax in Markdown cells.
I want to make use of Maxima as the backend to solve some computations used in my LaTeX input file.
I did the following steps.
Step 1
Download and install Maxima.
Step 2
Create a batch file named cas.bat (for example) as follows.
rem cas.bat
echo off
set PATH=%PATH%;"C:\Program Files (x86)\Maxima-5.31.2\bin"
maxima --very-quiet -r %1 > solution.tex
Save the batch in the same directory in which your input file below exists. It is just for the sake of simplicity.
Step 3
Create the input file named main.tex (for example) as follows.
% main.tex
\documentclass[preview,border=12pt,12pt]{standalone}
\usepackage{amsmath}
\def\f(#1){(#1)^2-5*(#1)+6}
\begin{document}
\section{Problem}
Evaluate $\f(x)$ for $x=\frac 1 2$.
\section{Solution}
\immediate\write18{cas "x: 1/2;tex(\f(x));"}
\input{solution}
\end{document}
Step 4
Compile the input file with pdflatex -shell-escape main and you will get a nice output as follows.
!
Step 5
Done.
Questions
Apparently the output of Maxima is as follows. I don't know how to make it cleaner.
solution.tex
1
-
2
$${{15}\over{4}}$$
false
Now, my question are
how to remove such texts?
how to obtain just \frac{15}{4} without $$...$$?
(1) To suppress output, terminate input expressions with dollar sign (i.e. $) instead of semicolon (i.e. ;).
(2) To get just the TeX-ified expression sans the environment delimiters (i.e. $$), call tex1 instead of tex. Note that tex1 returns a string, which you have to print yourself (while tex prints it for you).
Combining these ideas with the stuff you showed, I think your program could look like this:
"x: 1/2$ print(tex1(\f(x)))$"
I think you might find the Maxima mailing list helpful. I'm pretty sure there have been several attempts to create a system such as the one you describe. You can also look at the documentation.
I couldn't find any way to completely clean up Maxima's output within Maxima itself. It always echoes the input line, and always writes some whitespace after the output. The following is an example of a perl script that accomplishes the cleanup.
#!/usr/bin/perl
use strict;
my $var = $ARGV[0];
my $expr = $ARGV[1];
sub do_maxima_to_tex {
my $m = shift;
my $c = "maxima --batch-string='exptdispflag:false; print(tex1($m))\$'";
my $e = `$c`;
my #x = split(/\(%i\d+\)/,$e); # output contains stuff like (%i1)
my $f = pop #x; # remove everything before the echo of the last input
while ($f=~/\A /) {$f=~s/\A .*\n//} # remove echo of input, which may be more than one line
$f =~ s/\\\n//g; # maxima breaks latex tokens in the middle at end of line; fix this
$f =~ s/\n/ /g; # if multiple lines, get it into one line
$f =~ s/\s+\Z//; # get rid of final whitespace
return $f;
}
my $e1 = do_maxima_to_tex("diff($expr,$var,1)");
my $e2 = do_maxima_to_tex("diff($expr,$var,2)");
print <<TEX;
The first derivative is \$$e1\$. Differentiating a second time,
we get \$$e2\$.
TEX
If you name this script a.pl, then doing
a.pl z 3*z^4
outputs this:
The first derivative is $12\,z^3$. Differentiating a second time,
we get $36\,z^2$.
For the OP's application, a script like this one could be what is invoked by the write18 in the latex file.
If you really want to use LaTeX then the maxiplot package is the answer. It provides a maxima environment inside of which you enter Maxima commands. When you process your LaTeX file a Maxima batch file is generated. Process this file with Maxima and process your LaTeX file again to typeset the equations generated by Maxima.
If you would rather have 2D math input with live typesetting then use TeXmacs. It is a cross-platform document authoring environment (a word processor on steroids if you like) that includes plugins for Maxima, Mathematica and many more scientific computing tools. If you need to or are not satisfied with the typesetting, you can export your document to LaTeX.
I know this is a very old post. Excellent answers for the question asked by OP. I was using --very-quiet -r options on the command line for a long time like OP, but in maxima version 5.43.2 they behave differently. See maxima command line v5.43 is behaving differently than v5.41. I am answering this question with a cross reference because when incorporating these answers in your solutions, make sure the changes in behavior of those command line flags are also incorporated.
I'm trying to convert a latex document to docx (damn you journals that do not accept latex or pdf submissions), but get an error referring to a line outside the range of the latex source file (the file is 385 lines). I have checked the only instances of \\ (within a table) and these seem unproblematic. The error also remains if the table is removed. The latex source compiles to pdf in MiKTeX.
The error occurs if I try to convert to other formats as well, so it is not an issue specific to docx conversion. It is hard to make a reproducible example since I dont know what part of the code that is causing the problem (since it is referring to a line number outside of the inputfile). Is the error message referring to the pandoc source?
Command:
pandoc -f latex article.tex -o article.docx
Error message:
pandoc.exe:
Error:
"source" (line 407, column 1):
unexpected "\\"
expecting white space, "%", new-line, "begin", letter, "*", "[", "}", "egroup",
"endgroup", "{", "bgroup", "begingroup", "-", "``", "`", "'", "~", "$$", "$", "^", "_",
"^^", "]", "#", "&", "\\" or "
end"
Any ideas on how to trouble shoot?
Don't know if this more suitable for Stackoverflow or http://tex.stackexchange.com, but there are more search hits for pandoc over here.
Edit:
I have now found out that the conversion works if the input file is moved to ./temp/input.tex, and I'm really confused. The associated files (.eps, .bib) was moved along with it, and files in both folders have been renamed so that no old temporary files are influencing the tex conversion. The original folder does not have any weird characters or white space. I'm even more confused and annoyed. However, at least I can get the converted file.
For your question about how to troubleshoot, try putting an \end{document} in places in your document. If your issue is an element that can reach its closure in latex, but fails to close in pandoc, you might be able to locate the unclosed element by truncating the document at other places.
The following doesn't give exactly your error, but I was able to binary-search and pare down a much longer failing document to this bug using this \end{document} idea.
\documentclass{article}
\usepackage{alltt}
\begin{document}
\begin{alltt}
main <- {sprintf("x = %5.3f",3.1415926)}
\end{alltt}
\end{document}
I've been using Doxygen successfully to generate PDF documentation for a sizable Fortran 90 project since v1.6. After a recent upgrade to Doxygen 1.8, pdflatex is choking with an error I can't understand. From refman.log:
.
.
.
<use classfate__source_a022bf629bdc1d3059ebd5fb86d13b4f4_icgraph.pdf>
Package pdftex.def Info: classfate__source_a022bf629bdc1d3059ebd5fb86d13b4f4_ic
graph.pdf used on input line 607.
(pdftex.def) Requested size: 350.0pt x 65.42921pt.
)
(./classm__aerosol.tex
! Undefined control sequence.
<recently read> \LT#LL#FM#cr
l.25 ...1833ffa6f2fae54ededb}{ia\-\_\-nsize}), \\*
? ?
Type <return> to proceed, S to scroll future error messages,
R to run without stopping, Q to run quietly,
I to insert something, E to edit your file,
1 or ... or 9 to ignore the next 1 to 9 tokens of input,
H for help, X to quit.
Looking at the first 25 lines of classm__aerosol.tex, nothing obviously matches the error message:
\hypertarget{classm__aerosol}{\section{m\-\_\-aerosol Module Reference}
\label{classm__aerosol}\index{m\-\_\-aerosol#{m\-\_\-aerosol}}
}
Contains general aerosol-\/related constants and routines.
\subsection*{Public Member Functions}
\begin{DoxyCompactItemize}
\item
subroutine \hyperlink{classm__aerosol_aa06c1f39c6bd34f22be92d21535f0320}{aerdis} (I\-A\-E\-R\-O, M\-A\-E\-R\-O, V\-O\-L, A\-R\-E\-A, M\-U, T\-G\-A\-S, R\-H\-O, A\-G\-A\-M\-M\-A, X\-L\-A\-E\-R, D\-M\-E\-A\-N, N\-A\-E\-R, X\-N\-D\-A\-E\-R, L\-S\-D\-A\-E\-R)
\begin{DoxyCompactList}\small\item\em Return aerosol mass given a volume, based on aerosol size distribution function. \end{DoxyCompactList}\item
real(kind=wp) function \hyperlink{classm__aerosol_a2dff4ff413057e8788fba7270a30c093}{lamsed} (V\-O\-L, H, M\-U\-G, R\-H\-O\-A\-E\-R, A\-G\-A\-M\-M\-A, A\-C\-H\-I, A\-F\-E\-O, K\-O, M\-A\-E\-R, F\-M\-A\-E\-R, F\-A\-E\-R\-S\-S, F\-S\-E\-D\-D\-K)
\begin{DoxyCompactList}\small\item\em Calculate aerosol removal constant and interpolation factor between steady-\/state and decaying aerosol correlations. \end{DoxyCompactList}\item
pure real(kind=wp) function \hyperlink{classm__aerosol_a6d0a04004f49c404c67e0aa69dd39ee1}{fdbend} (V\-E\-L, H\-S\-E\-D, T\-G, R\-H\-O\-G, M\-U\-G, R\-H\-O\-P\-A\-R, C\-A\-E\-R\-O, X\-D\-B\-E\-N\-D, N90\-J)
\begin{DoxyCompactList}\small\item\em Find total impaction efficiency for aerosol deposition considering 90-\/degree bends in a flow path. \end{DoxyCompactList}\end{DoxyCompactItemize}
\subsection*{Public Attributes}
\begin{DoxyCompactItemize}
\item
integer, parameter \hyperlink{classm__aerosol_a8f604b7ffe3c1833ffa6f2fae54ededb}{ia\-\_\-nsize} = 30
\item
integer, parameter \hyperlink{classm__aerosol_ae71813ecf0c7768af9d6292efb14774f}{ia\-\_\-nmass} = 10
\item
real(kind=wp), dimension(\hyperlink{classm__aerosol_a8f604b7ffe3c1833ffa6f2fae54ededb}{ia\-\_\-nsize}), \\*
Nothing obviously matches the recently read chunk "\LT#LL#FM#cr" and I don't know enough low-level TeX to translate that into something that might actually be in the source text.
Suspecting this might have been fixed in a later version of Doxygen than the one shipping with Linux Mint (v1.8.1.2), I built & installed v1.8.3.1 from source, updated my doxyfile, blew away the old documentation and regenerated it. I get the same baffling error.
There's nothing obvious in refman.log that would indicate missing or broken LaTeX packages and I'm completely at a loss as to what's causing this.
As this still gets a hit on Google when you search:
doxygen missing $ inserted
I would like to add something.
Do not use a PROJECT_NAME containing underscores (_)!
After a brief look into the doxygen's current documentation (I am using 1.8.4) it does not make that explicit.
this will be difficult to solve unless you provide a bit more information - possibly using \errorcontextlines=9999 as suggested in the comments on the question.
as a first short though, the name of the control sequence that can't be found (i.e. \LT#LL#FM#cr) is one defined by the longtable package (documentation, p. 15) - thus adding:
\usepackage{longtable}
to the preamble of the document might help.
If so, according to the doxygen documentation here, adding the following to your configuration file should do the trick:
EXTRA_PACKAGES=longtable
I use the listings package to insert source code. I would like to print all keywords uppercase in the output, regardless of the case in the input.
The manual states that
keywordstyle=[number][*]style
produces just what I want. However the following (almost) minimal example does not work.
if I set keywordstyle to "[1][]{\bfseries}" I end up with "[]" in front of every keyword
and "[*]{\bfseries}" gives me an asterisk in the start of the document.
I also tried "\MakeUppercase" and "{\MakeUppercase}" for keywordstyle which resulted in several errors, the first being:
! Incomplete \iffalse; all text was ignored after line 11
Minimal example:
\documentclass{article}
\usepackage{listings}
\lstdefinelanguage{KA_assembler}
{morekeywords={add,and,or,xor},
keywordstyle=[1][*]{\bfseries},
sensitive=false,
}
\lstset{language=KA_assembler}
\begin{document}
\begin{lstlisting}
and %r1, %r2
xor %r2, %r3
and %r4, %r5
\end{lstlisting}
\end{document}
I use Miktex for compilation of the tex files. So how do I force uppercase for Keywords?
In the manual, the brackets around the * look a bit different then the brackets around number. The reason is that the brackets around * are not meant to be used in the latex code, they just indicate that the presence of the * is optional. So try
keywordstyle=[1]*\bfseries
or
keywordstyle=*\bfseries
- it worked for me.