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I'm writing a very long internship report in which I cited a lot of authors. I'm using TeX Maker and JabRef. I'm using subfiles for every chapter. I'm nearly finished and already translated the entire master document several times before, to get the PDF output, without any problems. The whole thing is basically finished and went to proofreading to my supervisor already. So the only thing I changed recently were spelling mistakes and such.

After fixing that, I went to run PDFLaTeX, Makeindex, bibtex, and PDFLaTex (like always) for the entire thing again and now it tells me the process exited with errors, but instead of real errors I only get "warnings" about citations being undefined in the log, and no PDF output. Usually when citations are undefined it still gives me an output and with just question marks, where the citation is supposed to be. This time it doesn't give me an output at all. Even if I run bibtex on the eintre thing several times and then run PDFLaTeX again it doesn't find them (what usually fixed the problem for me).

Curiously all the undefined citations are in one particular subfile. If I take the subfile out and just translate the rest with the other subfiles to PDF everything works just fine and it finds all the citations in the the other subfiles. As soon as I enter the "problematic" subfile again, it gives me the "Process exited with errors" but no errors just warnings and the problematic subfile just doesn't get included in the PDF.

I already tried:

  • Creating a new bibliography file with JabRef
  • Recreating the problematic subfile by copying the contents in a new file and rewriting + checking all the citation commands in case some } were mising. (triple checked EVERYTHING)
  • (Of course) googling the issue and trying fixes of people with similar problems.(I couldn't find a similar issue)
  • uninstalling and re-installing TeXMaker and JabRef
  • trying to run it on a different PC.

I am at my witts end, close to a breakdown. I KNOW all the citation-commands are fine as I have run the entire thing before and everything was fine I didn't change anything in the commands or the preamble, just spelling. It worked just fine before and all of a sudden my entire theory subfile won't be translated to PDF, because it can't find the citations for that part while it CAN find the citation for the other subfiles, which are in the SAME bibliography file (So i know a faulty bibliography can't be the issue). Please help me Im DESPARATE. I am sorry for my rambling I am not sure how to describe this very curious issue. I don't even know where to start looking. If it were a faulty command or preamble, I would have encountered issues before, which I never did and I didn't change any of that either.

I'm using

\bibliographystyle{apalike}
\usepackage{breakcites}
\usepackage{etoolbox}
\makeatletter
\patchcmd{\@citex}{,}{;}{}{}
\makeatother

and of course

\bibliography{Report_Literatur}

I cite with

\cite{bibtexkey}

I hope this is enough information I don't really know what else to provide since I don't know what the issue could be. If you need more information feel free to ask, I really need your help =((

UPDATE: This is the content of the .blg file

The style file: apalike.bst
I found no \bibdata command---while reading file 00_Masterdokument_Report.aux
Warning--I didn't find a database entry for "McCabe2008"
[And more of such I just cut it short]
(There was 1 error message)

Intrestingly the listed database entries that can't be found are only a hand full of all the entries in the literature file and all the missing ones are those that are cited in one certain subfile.

The .log file is immensely long. Posted are aprroximately the last 300 lines of the log file, everyting regarding the bibliograpghy issues (I hope).

) (03_Summary_abstract_Report.tex) [2] (00_Masterdokument_Report.toc)
\tf@toc=\write6
\openout6 = `00_Masterdokument_Report.toc'.
pdfTeX warning (ext4): destination with the same identifier (name{page.1}) has 
been already used, duplicate ignored
<to be read again> 
                   \relax 
l.114 \listoffigures
                     [1] (00_Masterdokument_Report.lof)
\tf@lof=\write7
\openout7 = `00_Masterdokument_Report.lof'.
 [2]
(00_Masterdokument_Report.lot)
\tf@lot=\write8
\openout8 = `00_Masterdokument_Report.lot'.
No file 00_Masterdokument_Report.nls.
(05_Theory_Report.tex [3]
chapter 1.
LaTeX Warning: Citation `McCabe2008' on page 4 undefined on input line 10.
LaTeX Warning: Citation `Singh2015' on page 4 undefined on input line 12.
LaTeX Warning: Citation `Singh2015' on page 4 undefined on input line 14.
LaTeX Warning: Citation `Reape2013' on page 4 undefined on input line 14.
LaTeX Warning: Citation `Singh2015' on page 4 undefined on input line 15.
LaTeX Warning: Citation `McCabe2008' on page 4 undefined on input line 15.
[4]
LaTeX Warning: Citation `McCabe2008' on page 5 undefined on input line 17.
LaTeX Warning: Citation `Reape2013' on page 5 undefined on input line 17.
LaTeX Warning: Citation `McCabe2008' on page 5 undefined on input line 19.
<Images/Bild2_Roothairs_Alive_PCD.jpg, id=51, 1294.8375pt x 1725.44624pt>
File: Images/Bild2_Roothairs_Alive_PCD.jpg Graphic file (type jpg)
<use Images/Bild2_Roothairs_Alive_PCD.jpg>
Package pdftex.def Info: Images/Bild2_Roothairs_Alive_PCD.jpg  used on input line 23.
(pdftex.def)             Requested size: 213.50066pt x 284.52756pt.
<Images/Bild1_Roothairs_necrosis.jpg, id=52, 920.68968pt x 1156.32pt>
File: Images/Bild1_Roothairs_necrosis.jpg Graphic file (type jpg)
<use Images/Bild1_Roothairs_necrosis.jpg>
Package pdftex.def Info: Images/Bild1_Roothairs_necrosis.jpg  used on input line 24.
(pdftex.def)             Requested size: 226.54732pt x 284.52756pt.
LaTeX Warning: Citation `Joanna2012' on page 5 undefined on input line 29.
LaTeX Warning: Citation `McCabeJuly2008' on page 5 undefined on input line 30.
[5 <./Images/Bild2_Roothairs_Alive_PCD.jpg> <./Images/Bild1_Roothairs_necrosis.jpg>]
LaTeX Warning: Citation `Bagirova2007' on page 6 undefined on input line 34.
LaTeX Warning: Citation `Heath2000' on page 6 undefined on input line 35.
LaTeX Warning: Citation `Heath2000' on page 6 undefined on input line 35.
LaTeX Warning: Citation `Heath2000' on page 6 undefined on input line 36.
LaTeX Warning: Citation `Heath2000' on page 6 undefined on input line 37.
LaTeX Warning: Citation `Bashir2013' on page 6 undefined on input line 38.
LaTeX Warning: Citation `Bagirova2007' on page 6 undefined on input line 38.
LaTeX Warning: Citation `Heath2000' on page 6 undefined on input line 40.
LaTeX Warning: Citation `Heath2000' on page 6 undefined on input line 40.
LaTeX Warning: Citation `Bashir2013' on page 6 undefined on input line 40.
[6]
LaTeX Warning: Citation `Bashir2013' on page 7 undefined on input line 42.
LaTeX Warning: Citation `Lee2009' on page 7 undefined on input line 42.
LaTeX Warning: Citation `Bonas1998' on page 7 undefined on input line 44.
LaTeX Warning: Citation `Robinson1988' on page 7 undefined on input line 44.
LaTeX Warning: Citation `Bonas1998' on page 7 undefined on input line 44.
LaTeX Warning: Citation `Bashir2013' on page 7 undefined on input line 44.
LaTeX Warning: Citation `Heath2000' on page 7 undefined on input line 45.
LaTeX Warning: Citation `Bashir2013' on page 7 undefined on input line 45.
LaTeX Warning: Citation `Heath2000' on page 7 undefined on input line 47.
LaTeX Warning: Citation `Bashir2013' on page 7 undefined on input line 49.
LaTeX Warning: Citation `Heath2000' on page 7 undefined on input line 49.
Underfull \vbox (badness 10000) has occurred while \output is active []
 [7]
LaTeX Font Info:    Font shape `T1/lmss/bx/it' in size <17.28> not available
(Font)              Font shape `T1/lmss/bx/sl' tried instead on input line 54.
LaTeX Warning: Citation `Meinke1998' on page 8 undefined on input line 57.
LaTeX Warning: Citation `Meinke1998' on page 8 undefined on input line 60.
[8]
LaTeX Warning: Citation `Murphy1995' on page 9 undefined on input line 63.
LaTeX Warning: Citation `Loudet2002' on page 9 undefined on input line 63.
LaTeX Warning: Citation `Murphy1995' on page 9 undefined on input line 63.
LaTeX Warning: Citation `Lourdes1999' on page 9 undefined on input line 63.
LaTeX Warning: Citation `Loudet2002' on page 9 undefined on input line 63.
LaTeX Warning: Citation `Meinke1998' on page 9 undefined on input line 67.
LaTeX Warning: Citation `Meinke1998' on page 9 undefined on input line 68.
LaTeX Warning: Citation `Meinke1998' on page 9 undefined on input line 70.
LaTeX Warning: Citation `Meinke1998' on page 9 undefined on input line 72.
[9] [10]
LaTeX Warning: Citation `Coates2010' on page 11 undefined on input line 80.
LaTeX Warning: Citation `Gaeumann1919' on page 11 undefined on input line 80.
LaTeX Warning: Citation `Goeker2004' on page 11 undefined on input line 80.
LaTeX Warning: Citation `Coates2010' on page 11 undefined on input line 81.
LaTeX Warning: Citation `Uchida1980' on page 11 undefined on input line 82.
LaTeX Warning: Reference `fig: Hypha+Haustoria' on page 11 undefined on input line 85.
LaTeX Warning: Citation `Mauch1993' on page 11 undefined on input line 85.
LaTeX Warning: Citation `Mauch1993' on page 11 undefined on input line 86.
[11]
<Images/incompatible_Interaction_Peronosp.jpg, id=93, 616.10175pt x 326.4195pt>
File: Images/incompatible_Interaction_Peronosp.jpg Graphic file (type jpg)
<use Images/incompatible_Interaction_Peronosp.jpg>
Package pdftex.def Info: Images/incompatible_Interaction_Peronosp.jpg  used on input line 91.
(pdftex.def)             Requested size: 469.47372pt x 312.99057pt.
LaTeX Warning: Citation `Coates2010' on page 12 undefined on input line 96.
LaTeX Warning: Citation `VanDamme2005' on page 12 undefined on input line 96.
LaTeX Warning: Citation `Coates2010' on page 12 undefined on input line 96.
[12 <./Images/incompatible_Interaction_Peronosp.jpg>]
LaTeX Font Info:    Font shape `T1/lmss/bx/it' in size <14.4> not available
(Font)              Font shape `T1/lmss/bx/sl' tried instead on input line 98.
LaTeX Warning: Reference `fig: Lifecycle' on page 13 undefined on input line 99.
LaTeX Warning: Citation `Coates2010' on page 13 undefined on input line 99.
LaTeX Warning: Citation `Mauch1993' on page 13 undefined on input line 99.
LaTeX Warning: Citation `Coates2010' on page 13 undefined on input line 100.
!pdfTeX error: pdflatex (file ./Images/Lifecycle_HA.jpeg): reading JPEG image failed (no JPEG header found)
 ==> Fatal error occurred, no output PDF file produced!

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  • 3
    Could you show us the contents of the log file? It has the same name as your LaTeX file but it ends in .log, so if your LaTeX file is called mydocument.tex then the log file is called mydocument.log. You can find it in the same folder as the LaTeX file. The errors are usually at the end. Alternatively, if this file does not contain any error messages, then you can check the .blg file, the bibliography log file that is created by BibTeX and that contains any errors specific for the bibliography.
    – Marijn
    Aug 8, 2020 at 18:39
  • Thank you for your reply! I just checked, neither a .log file nor a .blg file are created somehow. I am really puzzuled they should be in there they are usually created automatically when you compile, right? Maybe that is the issue? Can I fix this? Help =(
    – Juliane
    Aug 8, 2020 at 21:53
  • The problem with issues like this is that they are hard to diagnose. We don't know a whole lot about your code and the issue could also be caused by your editor or folder setup. Is there any chance you could ask someone who knows a thing or two about TeX to look at your PC in person? We can only say very general things without having seen any more. The first step is certainly to look at the .log and .blg files. Those files must be present somewhere if you ran LaTeX and BibTeX, respectively. If you can't find them, try to 'unhide' the file extensions ...
    – moewe
    Aug 9, 2020 at 6:40
  • 1
    For the log file the end is probably the most important, so post the last 100 lines or so from that file.
    – Marijn
    Aug 9, 2020 at 13:06
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    And the contents of the problematic subfile may also be relevant, if it is large and/or confidential then you could try removing some content and checking if the problem still appears, and post the stripped down version here.
    – Marijn
    Aug 9, 2020 at 13:11

1 Answer 1

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Apparently the issue was a follow up cause from a fatal error. A picture I newly inserted while editing (file ./Images/Lifecycle_HA.jpeg) created a fatal error, according to the .log. The picture file must have been damaged and thus it mucked up everything else. Removing the picture fixed everything. I could still open the original picture on my PC but to be save, I took a screenshot of it and inserted that screenshot into the LaTeX subfile. Now everything works in a reliable manner.

If you encounter a similar issue, make sure to not only look at the mucked up citations but also check every picture! =)

Huge thanks to Marijn and moewe for putting so much time and effort into helping me and finding the culprit. I am immensely grateful!

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    More than "check every picture", I think the moral is "look at the end of the log file".
    – Teepeemm
    Aug 9, 2020 at 16:33
  • Yes definetely! I just oversaw it because I was so focussed in finding the issue with the citations. I never expected a picture to be the issue in first place. =)
    – Juliane
    Aug 10, 2020 at 15:35

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