I get a fatal error compiling one of my documents -- "FATAL - Caught signal: SEGV Likely your .bib has a very bad entry which causes libbtparse to crash:" -- and I'm not sure what's causing it.
All my googling indicates that there is a corrupt entry in my bib file, but I can't find it. Furthermore, my bib file is created by zotero and all my other documents use the same bib file and compile just fine.
I have tried cleaning out errors in the bib file by validating it and correcting errors (there were a few "date" fields with something other than a date), changing the relative path to my bib file to an absolute path, and duplicating my bib file to the same folder as the tex document (also correcting the path to \addbibresource{}).
from the doc preamble:
\usepackage[backend=biber, style=authoryear, citestyle=authoryear, bibencoding=utf8]{biblatex}
\addbibresource{path/to/file.bib}
Anyone know how to solve this?
Well, it turns out there was a problematic bibtex entry. It's really strange that other documents continued to compile -- perhaps it's only relevant if you cite the particular reference with a problematic entry.
I ended up manually debugging the bib file in a manner that I found on another forum. Splitting the files in half and compiling until the problem entry is isolated. My bib file is a few thousand entries, so it took a while, but problem solved, at least.
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.
I'm trying to compile a LaTex file online with sharelatex. It works fine, but on top of my generated references the first seems to be broken. It only shows " [1] ." . All other 25 references seem to be fine. It is also awkward that the [1] reference doesn't even appear in the document anywhere.
I'm not sure, but I think this warning might be connected, since it is the only one I get:
/usr/local/texlive/2017/texmf-dist/tex/latex/biblatex/blx-bibtex.def Package biblatex Warning: Using fall-back BibTeX(8) backend: functionality may be reduced/unavailable.
The bibilography is generated with \printbibliography
I found a solution after looking on the right forum:
https://tex.stackexchange.com/questions/365060/warning-using-fall-back-bibtex8-backendbiblatex-functionality-may-be-redu
I had to use
\usepackage[backend=bibtex,style=numeric,sortcites,natbib=true,sorting=none]{biblatex}
instead of
%\usepackage[backend=bibtex, style=numeric]{biblatex}
I still don't really get why it works now. The warning is still displayed, but the problem with the first reference is gone. When i try to use biber with \usepackage[backend=biber, style=numeric]{biblatex} it simply doesn't output any table of references.
edit:
It seems what I thought fixed it here didn't, but just hid the broken reference in between fine ones. I made a mistake in the .bib file, one closing bracket } to much. I didn't notice it before because I didn't know how to assassinate the broken reference with its counterpart in the .bib file.
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 :)
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.
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.