I wrote my thesis with Sweave (R+LaTeX). Everything went fine until I bought a new computer. I copied the Sweave file (.Rnw) with all figures and tables, as well as with the bibliography (.bib).

When I compile the file on my new computer, everything is fine, text, figures, tables and layout.... BUT:

  • every in-text reference is a question mark, although the bibliography at the end of the document is 100% (number, title etc).

  • every cross-reference for the figures and tables is a double question mark, although the figures and tables are 100% (number, title etc).

Any idea of what is wrong?

Thanks, Elsa





Additional information:

The error I get when running bibtex is:

> This is BibTeX, Version 0.99d (MiKTeX 2.9.6840 64-bit) The top-level
> auxiliary file: Draft_PhDThesis_dec2017.aux The style file: acm.bst I
> found no \bibdata command---while reading file
> Draft_PhDThesis_dec2017.aux Warning--I didn't find a database entry
> for "Wulf" Warning--I didn't find a database entry for "Haeckel"
> Warning--I didn't find a database entry for "bioce" Warning--I didn't
> find a database entry for "Strauss" ... (There was 1 error message)

When I look at the .aux file I notice that there is no \bibdata{...} which I believe is created by \bibliography{...}. Not sure what is wrong.

I don't think the problem only lies with the bibtex and the bibliography because the cross-referencing of figures and tables is also not working properly. Unless there are two independent problems, but I don't think so.

The problem definitely lies with the installation because it works fine when I run it on my old laptop... I have not managed to find out what was wrong... if someone can someday shed some light, thanks!

  • 1
    Did you compiled with bibtex? Also, have you tried to compile twice after bibtex with pdflatex? – koleygr Oct 7 '18 at 21:55
  • I assume I am compiling with bibtex. All the reference information is in a .bib file (TemporalPartitioning2.bib), which is called with \bibliography{TemporalPartitioning2}. I compiled the document multiple times. However, I don't know if that has anything to do with my issue, but I get the error message that sweave.sty is not found... – Elsa Bussiere Oct 11 '18 at 8:09
  • Hi @ElsaBussiere, please check this: tex.stackexchange.com/q/153193/120578 – koleygr Oct 11 '18 at 8:17
  • Thanks, I resolved this problem following the instructions on the link you gave me. However, the question marks are still there... – Elsa Bussiere Oct 11 '18 at 9:37
  • Please compile by using pdflatex mainFile then bibtex mainFile and again twice pdflatex mainFile... where "mainFile" is the name of your main file without extensions – koleygr Oct 11 '18 at 9:47

I eventually solved the problem. In R studio, I clicked: Tools > Global Options > Sweave > Latex editing and compilation

And there, the box 'clean auxiliary output after compile' was ticked. I unticked it and it now works fine.

Thanks, Elsa

This is a screenshot of the window in which I could change the auxiliary output settings

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