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
Related
I'm trying to write a scientific article and the associated supplementary materials entirely in RStudio with rmarkdown.
It seems clear that book down is the way to go to cross-reference between files (https://stackoverflow.com/a/38884378/576684), but I also would like to be able to reference figures produced in one pdf in the other pdf.
Although my latex has got quite rusty with time, I imagine it could be achieved as follows:
compile the article tex and SuppMat tex a first time using rmarkdown::render()
compile these tex files from the command line in order to keep the corresponding .aux file with their references (missing references won't be resolved at this time)
recompile the 2 tex files from the command line another time where all references should now be resolved
Is it a reasonable way to do it? am I overlooking something simpler?
In any case, it requires:
a different numbering of figures in each pdf file (covered by https://stackoverflow.com/a/51337664/576684)
to prevent rmarkdown from trashing the .aux files (it seems that pandoc doesn't allow this, hence the need to create the aux file using standalone latex)
to tell latex to use the additional .aux file if it is found (probably using header-includes: in the YAML header). how can I achieve that?
Thank you very much for your help!
It turns out that the xr package is one way to go: https://texblog.org/2016/08/23/adding-references-from-an-external-file/
so this works from R:
rmarkdown::render("myarticle_ms.Rmd",
bookdown::pdf_book(base_format=rticles::plos_article),
clean=FALSE)
rmarkdown::render("myarticle_SM.Rmd",
bookdown::pdf_book(base_format=rticles::plos_article),
clean=FALSE)
tinytex::pdflatex("myarticle_ms.tex", clean=FALSE)
tinytex::pdflatex("myarticle_SM.tex", clean=FALSE)
tinytex::pdflatex("myarticle_ms.tex")
tinytex::pdflatex("myarticle_SM.tex")
with the following in the YAML header of myarticle_ms.Rmd (and the corresponding one the SuppMat file header):
header-includes:
\usepackage{xr} \externaldocument{myarticle_SM}
Hope it makes life easier for a few others :)
I'm producing a set of documents in LaTeX, and I would like to provide a single, global bibliography page for the whole set. This is because each document is page-limited: I don't want to take up space with references at the bottom of each one.
This means in each case, I would like to cite in the text, but not produce a reference at the end. I am using bibtex/natbib to handle the referencing.
Simplest example:
\documentclass[]{article}
\bibliographystyle{/usr/share/texmf/bibtex/bst/natbib/plainnat.bst}
\usepackage{natbib}
\begin{document}
In \citet*{MEF2010} I described the method.
\bibliography{bibliography.bib}
\end{document}
How can I do this? Essentially I just want it to cite correctly:
In Bloggs, Blagg and Blog (2010) I described the method.
But not add a references section at the end. Any ideas?
Thanks,
David
Instead of using \bibliography{bibliography.bib} you can try \nobibliography{bibliography.bib}.
You still need to enter the path so it can make the cross-references.
It happens due to missing packages. If you want to resolve the problem then enable the automatic installation packet. After that,First, you run the BibTeX file and generate the Pdf file (instead of pdfLatex file) and then pdfLatex to Pdf
When I generate a .pdf file from a .tex file using pdflatex, only the "Contents" title is shown with no actual TOC. If I run pdflatex my.tex once more, it generates the TOC just fine. I can reproduce this simply by removing the .toc file. What I think is happening is that my .toc file is being generated too late -- so how can I make the TOC work first time? Should I be generating the TOC beforehand without using pdflatex?
This is normal. LaTeX document need several compilations to reach a stable state. Use rubber -d my to compile the right number of times (rubber comes as a package on many linux distros).
I might be mistaken, but I think, that this is the default behaviour. I assume, you also won't find correct cross references (footnotes, end notes, literature) after the first run of pdflatex.
The point is, that LaTeX needs the extra rounds to resolve the references pointing inside the document, to get numbering and page numbers right.
I experienced the same problem with the editor Latexian. What solved the problem was changing the preferences. I changed "Number of typesetter runs at end" to 3, instead of the default 1. Then I added the "Refresh" button to the toolbar and tried refreshing and it worked.
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.