My question is similar to this one.
Doxygen is outputing a warning while trying to generate docs for HTML:
warning: reached end of file while inside a f$ block!
The command that should end the block seems to be missing!
I understand what this means, but I have lots of LaTeX in this particular document. Unfortunately, the line number of the error is just the last line in the file, and Doxygen doesn't output the the \f$ that opened the math mode.
Is there a way to get Doxygen to output this, rather than me having to scour the file for a missing or malformed \f$? Something that might produce more verbose errors?
Before I finished typing this question, I found the offending line by browsing the generated HTML and looking for a function in that file that didn't get documented. That at least gave me enough of a hint for where to start looking. Still it would be great if there was a more concrete answer to this.
When generating for Latex with Doxygen, it is indeed not obvious to spot errors. One solution is to get down into the latex generated folder, and try these steps:
Run generated makefile ($ make), and look for pdflatex compiler output,
If it fails, load the file refman.tex into some Latex IDE (say, Texstudio or equivalent) and try to compile from there.
If still unable to locate error, you can run manually pdflatex with option halt-on-error:
($ pdflatex -halt-on-error refman.tex). This way, it will stop immediately at the error location.
Related
I have the following reference identified in file A:
.. _my-label:
and I reference it in file B :
this is a reference to file A :ref:`my-label`
This generates a cross-reference as expected when outputting HTML. However, when outputting LaTeX, it does not and I have the classical warning:
LaTeX Warning: Hyper reference `my-label:my-label' on page XX undefined on input line YY.
Is there a LaTeX trick like double compilation or something similar that I am not doing correctly?
I encountered the same issue. HTML compiled without errors for me, but LaTeX compilation did throw the hyperref errors you described. It seems to me that, for some obscure reason, Sphinx does not create the labels that hyperref tries to reference.
I came up with the following solution: since I do not know how to include the missing labels, I will just make it so that LaTeX does not look for them anymore. In detail, I am doing this by overwriting the \hyperref command.
I included the following code in my conf.py file:
latex_elements = {
'preamble': r'''
\renewcommand{\hyperref}[2][]{#2}
'''
}
This includes the \renewcommand{... in the preamble of the LaTeX document created by Sphinx. It will overwrite the \hyperref command so that it won't try to insert a link, but just print the link text.
Obviously, with this solution, the reference that caused the errors will not appear as hyperlinks in your PDF document, but at least it is compiling without errors.
Note
What I described worked perfectly fine for my use case, however, it is described in the Hyperref manual that the \hyperref command can be invoked in two different ways (\hyperref{URL}{category}{name}{text} and \hyperref[label]{text}). I am only overwriting the second one, as that seems to be the one that Sphinx is using for cross references. However, not accounting for the first one when overwriting the command might lead to issues in some cases.
Just created a markdown cell in Jupyter using some equations, and some of them using \mathscr to have like "math" fonts. When I run the kernel containing the equations everything is ok, however when I click the option to Download as PDF via LaTex, I'm getting the error below:
! Undefined control sequence.
l.300 [\mathscr
{L}({\bf{y}}|\beta, \sigma^2, {\bf{X}}) = (2\pi\sigma^2)^{-...
?
! Emergency stop.
l.300 [\mathscr
{L}({\bf{y}}|\beta, \sigma^2, {\bf{X}}) = (2\pi\sigma^2)^{-...
If I remove the \mathscr part everything can be exported with no issues (excepting some convertion problems for special characters), however, I wanted to know ho to solve it. I've been reading and it looks like the nbconvert configuration file can be modified to solve this, but I couldn't find the mentioned file and the exact way to modify it
Thanks for your help
I think the problem is with absent \usepackage{mathrsfs} directive in an intermediate .tex-file.
So you have a several ways to overcome it.
If you face with this problem occasianaly you could the following:
download the .tex-file instead pdf;
manually insert to \usepackage{mathrsfs} to it.
before the first \usepackage for example;
run something like
xelatex file.tex to finally convert to pdf.
If you will do it often, you could try to edit appropriate jinja-template.
At first, find the place where nbconvert was installed. For example with pip: pip show nbconvert. Imagine the path is /home/i/.local/lib/python3.5/site-packages
Then the template would be at /home/i/.local/lib/python3.5/site-packages/nbconvert/templates/latex/base.tplx.
And again: just add \usepackage{mathrsfs} right after ((* block packages *)).
Voila -- the problem should gone.
At the end you have the third option -- you can create your own template from scratch and use it with nbconvert. I don't think it's very convenient way to solve your problem. You could read more in the documentation: http://nbconvert.readthedocs.io/en/latest/customizing.html
I am trying to get lua2dox running but it's not generating the examples.
What I do is download the zip file and download doxygen 1.8.8. I'll then place the doxygen.exe file into the extracted content od lua2dox and simply call
> doxygen.exe
in my command line. The docs/ directory is getting created but it does not look like the example docs as it is shown e.g. here.
The generated documentation has just the list of files - and that's it.
I've checked the Doxygen file but I can't find anything that seems to be wrong.
What I am not sure about is if lua2dox_filter.bat is actually getting used by doxygen. As I run it, I do not see some output from this script, not even if I add some echo but maybe it's just doxygen itself suppressing it.
Two things: The only modification I had to make was to lua2dox_filter.bat. In order to run Lua it has to prompt lua5.1 instead of just lua as it is in the script.
Also the Doxyfile didn't point to the examples/lua directory so I hat to set it:
INPUT = examples/lua/
Answer: Don't use Doxygen 1.8.8.
I didn't test it with later versions but it worked with Doxygen v1.8.2. Apparently things broke later on for lua2dox.
I added a line "\cite{test}" as a test to my working Latex document. When I compiled the bibtex "!bibtex name_of_my_file, I got the expected error:
Warning--I didn't find a database entry for "test"
Then, I removed the line and compiled the bibtex again, hoping to have a working Latex file again. However, the same error occurs, even with a fresh shell. I cannot understand the behaviour. What is the logic? How can I get my Latex document working again?
[Updated Info]
The problem dissapeared as unexpectedly as it emerged. I have no idea why but it works now. Do you know the reason for the odd behaviour?
I think you are tripping over the multi-pass nature of LaTex plus Bibtex. If you look at Step 3 in this discussion, you'll see the following:
The first run (through latex)
generates an auxiliary file,
paper.aux, containing information
about citations (and other types of
references), the bibliography style
used, and the name of the bibtex
database. The second run (through
bibtex) uses the information in the
auxiliary file, along with the data
contained in the bibtex database, to
create a file paper.bbl. This file
contains a thebibliography environment
with \bibitem entries formatted
according to the bibliography style
specified.
So, what I think is happening is that your name_of_my_file.aux file still contains your placeholder \cite{test}. If you remove the auxiliary file, you should be able to start over with:
latex name_of_my_file
bibtex name_of_my_file
latex name_of_my_file
latex name_of_my_file
[Update based on additional info]: The problem was that you had a .aux file with your \cite{} still embedded. The second time that you ran latex, you overrode the old file with the new. That's why the complete set of steps includes an initial latex call, a bibtex call and two follow-up latex calls. Think of it as a multi-pass compiler and it might be more intuitive.
You could have a look at latexmk, which will take care of the fix point compilation for you.
Anyway, you should be able to build the document (pdflatex blah.tex), even if you're missing a bibliography item. The corresponding references will just appear as question marks in the PDF.
Rerun latex to regenerate the aux file.
Have a look at this discussion for pointers to a bit more information. Basically, you may have taken your citation out of the .tex file, but it still exists in one of the derived files (aux, bbl, whatever...)
Check if your bib file has the extension .bib and not .tex.
If it is .tex, just change it to .bib and that should do it.
Once I changed it accidentally to tex, by adding some references, and saving it with the "save as" option, without specifying the bib extension. That's how it can happen all of a sudden.
delete all your .aux and temporal files, re run with latex and then bibtex and then latex twice.
As suggested here, latexmk is a handy way to continually compile your document whenever the source changes. But often when you're working on a document you'll end up with errors and then latex will panic and wait for user input before continuing. That can get very annoying, especially recently when I hacked up something to compile latex directly from an etherpad document, which saves continuously as you type.
Is there a setting for latex or latexmk to make it just abort with an error message if it can't compile? Or, if necessary, how would I set up some kind of Expect script to auto-dismiss LaTeX's complaints?
(I had thought pdflatex's option -halt-on-error would do the trick but apparently not.)
Bonus question: Skim on Mac OSX is a nice pdf viewer that autorefreshes when the pdf changes (unlike Preview), except that whenever there's a latex error it makes you reconfirm that you want autorefreshing. Texniscope doesn't have this problem, but I had to ditch Texniscope for other reasons. Is there a way to make Skim always autorefresh, or is there another viewer that gets this right?
ADDED: Mini-tutorial on latexmk based on the answer to this question:
Get latexmk here: http://www.phys.psu.edu/~collins/software/latexmk-jcc/
Add the following to your ~/.latexmkrc file:
$pdflatex = 'pdflatex -interaction=nonstopmode';
(For OS X with Skim)
$pdf_previewer = "open -a /Applications/Skim.app";
While editing your source file, foo.tex, run the following in a terminal:
latexmk -pvc -pdf foo.tex
Use Skim or another realtime pdf viewer to view foo.pdf. For Skim, just look at the “Sync” tab in Skim’s preferences and set it up for your editor.
Voila! Hitting save on foo.tex will now cause foo.pdf to refresh without touching a thing.
With MikTeX, pdflatex has this command-line option:
-interaction=MODE Set the interaction mode; MODE must be one
of: batchmode, nonstopmode, scrollmode,
errorstopmode.
Edit suggested by #9999years:
Those values are equivalent to a set of LaTeX \commands that provide the same functionality.
From TeX usage tips:
The modes make TeX behave in the following way:
errorstopmode stops on all errors, whether they are about errors in the
source code or non-existent files.
scrollmode doesn't stop on errors in the source but requests input when a
more serious error like like a missing file occurs.
In the somewhat misnamed nonstopmode, TeX does not request input after
serious errors but stops altogether.
batchmode prevents all output in addition to that (intended for use in
automated scripts). In all cases, all errors are written to the log file
(yourtexfile.log).
You can also put \nonstopmode or \batchmode at the very beginning of your tex file; then it'll work with any TeX version, not just pdflatex. For more info on these and related commands see the very good reference on (raw) TeX commands by David Bausum. Especially the command from the debugging family could be of interest here.
Another possible hack is simply to use:
yes x | latexmk source.tex
You could always create an alias for 'yes x | latexmk' if you're going to use this option lots. The main advantage of this that I can see above the other suggestions is that it is very quick for when you occasionally want latexmk to behave like this.
Mehmet
There is also a \batchmode command may do the work.