🔥🔥📚🔥🔥 Whyyyyyyyyyy?!?!?

arXiv’s magic LaTeX elves know when you’re uploading a PDF made by LyX and make you upload the LaTeX source. This is a pain. But here is how to deal with it…

Steps to happiness (or non-anger)

  1. In LyX, have a document that compiles and looks right already.
  2. File > Export > LaTeX (pdflatex) this will spit out a bunch of .tex files in your document directory (one if you just have one file, more if you have use subdocuments (\input in LaTeX-lingo).
  3. Open the main (or only) .tex file: a. remove everything before \documentclass, especially \batchmode that seems to suppress output from the arXiv TeX compiler and \def\input@path etc which will be the wrong directory. b. if you used sub-documents, make sure the file names are correct in each \input, LyX seems to attach the directory names and some other nonsense to the front of the names. c. make sure the path in \bibliography is correct, again LyX gives the absolute path, which arXiv doesn’t have. d. if you are using multiple input files, rename your main file to ms.tex, as this will get processed first.
  4. Copy your figures/ directory, any .bib files etc to the places they are referenced in the .tex file you just edited.
  5. Try to compile your paper (running pdflatex, biber/bibtex etc) and hopefully get a working PDF out of it.
  6. Once you have a working PDF, zip up the files, this sould include a. the .bbl file see here b. any journal-specific .cls document classes c. any journal-specific .sty syle files d. any journal-specific .bst bibliography styles
  7. Try to upload this zipped folder using the submission site.
  8. Once you’ve uploaded try to process the file, if AutoTeX doesn’t work, go back to “add files”, fiddle with the LaTeX and reupload a new zip.

I switched back to bibtex from biblatex/biber as I was getting errors but I can’t confirm that was why.