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My LaTeX thesis is organised in a main file where I \input individual chapters. Until recently I was able to open the Main.pdf, navigate to the chapter I'm working on, and Jump to Source would open the appropriate chapter tex file.

Previously there was a bug, where if I had a compilation error, the texworks pdf viewer would go blank, and I would have to close and reopen it manually after correcting the error and recompiling the Thesis. But it would work fine after that.

Since a couple of days ago, following a compilation error, the texworks viewer has lost all ability to "see" the chapter file. If I "Jump to source" on any other part of the thesis, it opens the right file, but if I'm in the particular chapter where the error occured, it says: Cannot read file "": No file name specified. Furthermore, "autofollow focus" from the editor does not work anymore either.

  • Reverting to an earlier version of the document before the compilation error occured does not fix the issue, so the problem is not in the tex code.
  • Removing all auxiliary / unnecessary files, including synctex.gz, and compiling from scratch does not fix the issue so the problem isn't a corrupt synctex file.
  • Removing texworks, purging the ~/.TeXworks and ~/.config/TUG folders and reinstalling from scratch does not fix the issue, so the problem isn't my particular configuration (unless there are hidden configs and tempfiles in the system that I'm not aware of)

I have now had this problem on two machines, and I had to format one of them to see if I can resolve it. I wonder if maybe there's been a recent update of texworks that broke something? Has anyone else had this problem?

Apologies, I know tex.stackexchange isn't a bug tracker, but there really is no obvious place to ask or report this and this is decimating my workflow on the run-up to submission :|

EDIT: My TeXworks version is TeXworks 0.5r1350 (Debian) from the Linux Mint 17 repositories. I will try a newer version from the texworks ppa and update if this fixes the issue.
UPDATE: The issue continues on the latest version (0.6.1), and also with a version of the code from git before the compilation error was introduced.
FURTHER UPDATE: I have narrowed down the problem to the second run of pdflatex. My compilation is as follows:

pdflatex   # Synchronisation works but citations are broken
biber      
pdflatex   # Synchronisation works
pdflatex   # Sunchronisation breaks

This is the process I'd used for months. I'm not sure why it broke in the last week. I'm also not sure at the moment whether my citations are properly synchronised after the second run (which is what the third run used to be for).

The console output between #2 and #3 with the exception of renaming of a couple of ids, seems otherwise identical except that #2 displays the message:

Package rerunfilecheck Warning: File `Oxford_Thesis.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.

LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

whereas #3 doesn't.

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For anyone else landing on this question with he same problem, the issue was that my compilation script used pdflatex->biber->pdflatex->pdflatex.

This used to be the expected thing to do in order to get appropriate crossreferences. It appears that suddenly (following an update?) the correct procedure is to only use pdflatex->biber->pdflatex. Crossreferences seem to be ok after the second pdflatex call. A third pdflatex call breaks synctex.

If this happens, clear out all .aux files and compile again with pdflatex->biber->pdflatex.

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