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:
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<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
Related
To say that I am a LaTeX amateur is an understatement, though by some miracle, I am managing to write my thesis in it. I am using RStudio to write and compile my thesis, due to all of my analysis being done in R and wanting the ability to insert dynamic plots etc.
As my thesis has increased in size, I wanted to break the chapters off into sub .Rnw files so that I could work on each chapter independently (with my need for R code within each chapter ruling out using .tex files). The only way I could get this to work, was using \Sexpr{knit_child('chapter.Rnw')}. I weave my files using knitr rather than Sweave as again, that is the only I can get it to compile correctly. Unfortunately, I've never managed to understand why!
Nevertheless, this is working very nicely, is much easier to manage and my plots and R code are compiling correctly, but my previously functioning \ref and \label commands no longer work. Well, they work within a chapter, but not between them.
I include my main document here and the latex commands that I think are relevant to my question. I have googled this all morning, but am getting nowhere alone.
\documentclass[12pt]{report} %What kind of document
\usepackage{titlesec} %can actually name chapters rather than having "Chapter 1" etc
\usepackage[backend=bibtex,style=authoryear-comp,sorting=nyt,maxcitenames=2,url=false]{biblatex}
\bibliography{library}
% ----------- KNITR SETUP ------------------------
<<setup, include=FALSE, cache=FALSE, echo=FALSE>>=
opts_chunk$set(fig.path='figures/plots-', fig.align='center', fig.show='hold', eval=TRUE, echo=TRUE)
options(replace.assign=TRUE,width=80)
# setwd("C:/Users/cainswor/Box Sync/Imperial/Reports/Thesis")
setwd("D:/BoxSync/BoxSync/Reports/Thesis")
data_loc <- "D:/BoxSync/BoxSync/Reports/Thesis/Data for Thesis"
Sys.setenv(TEXINPUTS=getwd(),
BIBINPUTS=getwd(),
BSTINPUTS=getwd())
x <- c("shiny","flowViz","nls2","plyr","RColorBrewer","abind","MASS","gplots","hexbin",
"data.table","fastmatch","stringr","hypergeo","rgl","mclust","knitr","dbscan")
lapply(x, require, character.only=T)
# Sweave2knitr('ThesisSecondDraft.Rnw')
#
\begin{document}
\Sexpr{knit_child('Th1_Introduction.Rnw')}
\part{The Experiment}
\Sexpr{knit_child('Th2_Characterisation.Rnw')}
\end{document}
Here is an example which work on my files.
In the main.Rnw document :
\documentclass{article}
\begin{document}
\SweaveOpts{concordance=TRUE}
Hello world
\SweaveInput{child_test.Rnw}
\end{document}
In the child_test.Rnw file
%!Rnw root = main.Rnw
\SweaveOpts{echo = TRUE, eval = TRUE}
\section{Analysis}
This is the analysis.
<<analysis, result = tex>>=
summary(cars)
#
This is the code I use for my bibliography
\usepackage[style=authoryear,sorting=ynt]{biblatex}
\addbibresource{bibliography.bib}
\printbibliography
This is an example of my bibliopgrahy:
#Article{Acosta2008,author = {Acosta, EG and Castilla, V and Damonte, EB}, title = {Functional entry of dengue virus into Aedes albopictusmosquito cells is dependent on clathrin-mediated endocytosis.}, journal = {J Gen Virol}, volume = {89}, number = {Pt 2}, pages = {474--484}, year = {2008}, abstract = {Entry of dengue virus 2 (DENV-2) into Aedes albopictus mosquito C6/36 cells was analysed using biochemical and molecular inhibitors, together with confocal and electron microscopy observations. Treatment with monodansylcadaverine, chlorpromazine, sucrose and ammonium chloride inhibited DENV-2 virus yield and protein expression, whereas nystatin, a blocker of caveolae-mediated endocytosis, did not have any effect. Using confocal microscopy, co-localization of DENV-2 E glycoprotein and the marker protein transferrin was observed at the periphery of the cytoplasm. To support the requirement of clathrin function for DENV-2 entry, overexpression of a dominant-negative mutant of Eps15 in C6/36 cells was shown to impair virus entry. The disruption of actin microfilaments by cytochalasin D also significantly affected DENV-2 replication. In contrast, microtubule disruption by colchicine treatment did not impair DENV-2 infectivity, suggesting that DENV-2 does not require transport from early to late endosomes for successful infection of mosquito cells. Furthermore, using transmission electron microscopy, DENV-2 particles of approximately 44-52 nm were found attached within electron-dense invaginations of the plasma membrane and in coated vesicles that resembled those of clathrin-coated pits and vesicles, respectively. Together, these results demonstrate for the first time that DENV-2 enters insect cells by receptor-mediated, clathrin-dependent endocytosis, requiring traffic through an acidic pH compartment for subsequent uncoating and completion of a productive infection.}, location = {}, keywords = {}}
I have tried several ways to load the bibliography stored in my bibliography.bib file with no results.
The error is:
Empty bibliography on input line
The bibliography is not empty, and the bibligraphy is on the same folder as the main '.tex' file
If your bibliography with the above content is bibliography.bib, and the following
\documentclass{article}
\usepackage[style=authoryear,sorting=ynt]{biblatex}
\addbibresource{bibliography.bib}
\begin{document}
Text ... citation: \cite{Acosta2008}.
\printbibliography
\end{document}
is main.tex in the same folder, then you should have no problem.
Make sure that you compile once, then you compile the bibliography with Biber, then you compile the tex one last time.
Confront your minimal code with mine but - mainly - check in the settings of your editor that Biber, not BibTex, is used to build the bibliography (example: TeXstudio).
I had the same problem. But it worked for me when I deleted the whole [] at usepackage.
So, for \usepackage[style=alphabetic]{biblatex}, I deleted the middle part so there only was \usepackage{biblatex}. I ran it and it worked. After that, I could use this one again \usepackage[style=alphabetic]{biblatex} and it worked too.
I use lua to make some complex job to prepare arguments for macros in Tex/LaTex.
Part I
Here is a stupid minimal example :
\newcommand{\test}{\luaexec{tex.print("11,12")}}% aim to create 11,12
\def\compare#1,#2.{\ifthenelse{#1<#2}{less}{more}}
\string\compare11,12. : \compare11,12.\\ %answer is less
\string\test : \test\\ % answer is 11,12
\string\compare : \compare\test. % generate an error
The last line creates an error. Obviously, Tex did not detect the "," included in \test.
How can I do so that \test is understood as 11 followed by , followed by 12 and not the string 11,12 and finally used as a correctly formed argument for \compare ?
There are several misunderstandings of how TeX works.
Your \compare macro wants to find something followed by a comma, then something followed by a period. However when you call
\compare\test
no comma is found, so TeX keeps looking for it until finding either the end of file or a \par (or a blank line as well). Note that TeX never expands macros when looking for the arguments to a macro.
You might do
\expandafter\compare\test.
provided that \test immediately expands to tokens in the required format, which however don't, because the expansion of \test is
\luaexec{tex.print("11,12")}
and the comma is hidden by the braces, so it doesn't count. But it wouldn't help nonetheless.
The problem is the same: when you do
\newcommand{\test}{\luaexec{tex.print("11,12")}}
the argument is not expanded. You might use “expanded definition” with \edef, but the problem is that \luaexec is not fully expandable.
If you do
\edef\test{\directlua{tex.sprint("11,12")}}
then
\expandafter\compare\test.
would work.
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 currently searching for an application or a script that does a correct word count for a LaTeX document.
Up till now, I have only encountered scripts that only work on a single file but what I want is a script that can safely ignore LaTeX keywords and also traverse linked files...ie follow \include and \input links to produce a correct word-count for the whole document.
With vim, I currently use ggVGg CTRL+G but obviously that shows the count for the current file and does not ignore LaTeX keywords.
Does anyone know of any script (or application) that can do this job?
I use texcount. The webpage has a Perl script to download (and a manual).
It will include tex files that are included (\input or \include) in the document (see -inc), supports macros, and has many other nice features.
When following included files you will get detail about each separate file as well as a total. For example here is the total output for a 12 page document of mine:
TOTAL COUNT
Files: 20
Words in text: 4188
Words in headers: 26
Words in float captions: 404
Number of headers: 12
Number of floats: 7
Number of math inlines: 85
Number of math displayed: 19
If you're only interested in the total, use the -total argument.
I went with icio's comment and did a word-count on the pdf itself by piping the output of pdftotext to wc:
pdftotext file.pdf - | wc - w
latex file.tex
dvips -o - file.dvi | ps2ascii | wc -w
should give you a fairly accurate word count.
To add to #aioobe,
If you use pdflatex, just do
pdftops file.pdf
ps2ascii file.ps|wc -w
I compared this count to the count in Microsoft Word in a 1599 word document (according to Word). pdftotext produced a text with 1700+ words. texcount did not include the references and produced 1088 words. ps2ascii returned 1603 words. 4 more than in Word.
I say that's a pretty good count. I am not sure where's the 4 word difference, though. :)
In Texmaker interface you can get the word count by right clicking in the PDF preview:
Overleaf has a word count feature:
Overleaf v2:
Overleaf v1:
I use the following VIM script:
function! WC()
let filename = expand("%")
let cmd = "detex " . filename . " | wc -w | perl -pe 'chomp; s/ +//;'"
let result = system(cmd)
echo result . " words"
endfunction
… but it doesn’t follow links. This would basically entail parsing the TeX file to get all linked files, wouldn’t it?
The advantage over the other answers is that it doesn’t have to produce an output file (PDF or PS) to compute the word count so it’s potentially (depending on usage) much more efficient.
Although icio’s comment is theoretically correct, I found that the above method gives quite accurate estimates for the number of words. For most texts, it’s well within the 5% margin that is used in many assignments.
If the use of a vim plugin suits you, the vimtex plugin has integrated the texcount tool quite nicely.
Here is an excerpt from their documentation:
:VimtexCountLetters Shows the number of letters/characters or words in
:VimtexCountWords the current project or in the selected region. The
count is created with `texcount` through a call on
the main project file similar to: >
texcount -nosub -sum [-letter] -merge -q -1 FILE
<
Note: Default arguments may be controlled with
|g:vimtex_texcount_custom_arg|.
Note: One may access the information through the
function `vimtex#misc#wordcount(opts)`, where
`opts` is a dictionary with the following
keys (defaults indicated): >
'range' : [1, line('$')]
'count_letters' : 0/1
'detailed' : 0
<
If `detailed` is 0, then it only returns the
total count. This makes it possible to use for
e.g. statusline functions. If the `opts` dict
is not passed, then the defaults are assumed.
*VimtexCountLetters!*
*VimtexCountWords!*
:VimtexCountLetters! Similar to |VimtexCountLetters|/|VimtexCountWords|, but
:VimtexCountWords! show separate reports for included files. I.e.
presents the result of: >
texcount -nosub -sum [-letter] -inc FILE
<
*VimtexImapsList*
*<plug>(vimtex-imaps-list)*
The nice part about this is how extensible it is. On top of counting the number of words in your current file, you can make a visual selection (say two or three paragraphs) and then only apply the command to your selection.
For a very basic article class document I just look at the number of matches for a regex to find words. I use Sublime Text, so this method may not work for you in a different editor, but I just hit Ctrl+F (Command+F on Mac) and then, with regex enabled, search for
(^|\s+|"|((h|f|te){)|\()\w+
which should ignore text declaring a floating environment or captions on figures as well as most kinds of basic equations and \usepackage declarations, while including quotations and parentheticals. It also counts footnotes and \emphasized text and will count \hyperref links as one word. It's not perfect, but it's typically accurate to within a few dozen words or so. You could refine it to work for you, but a script is probably a better solution, since LaTeX source code isn't a regular language. Just thought I'd throw this up here.