Hi,
I'm encountering the very same problem. I've tried the solution mentioned at
http://promberger.info/linux/2009/03/18 ... -document/ , but unfortunately, that solution does not work for me. [The remainder of this post is a slightly more accurate version of a post I made there that is presently, 2011-02-09, awaiting moderation before it will show up.]
I do have a workable solution, but it is very inconvenient. Fortunately, I only need to generate a PDF with hyperref included when I share a document with other people, so I can live with my workaround. However, I would love to get it fixed if anyone has any suggestions. Moreover, given that my workaround is somewhat convoluted, it might actually help a more knowledgeable LaTeX person better diagnose the problem. Plus, perhaps someone else might find this workaround helpful.
This workaround is both necessary and functional for MiKTeX on WinXP SP3 and for Texlive 2009 on Ubuntu 10.04 LTS (Texlive 2009 as distributed by Ubuntu, not downloaded from the TUG website) as of 2011-02-09.
The workaround is as follows:
1. Comment out the \usepackage{hyperref} line.
2. Comment out anything that depends on hyperref (in my case, the \hypersetup entry and several \pdfbookmark entries).
3. Run pdflatex mydoc.tex; run bibtex mydoc.bib; run pdflatex mydoc.tex two more times. This generates a clean PDF, without any PDF bookmarks or hypertext links.
4. Uncomment (i.e., re-enable) my \usepackage{hyperref} and \hypersetup{} lines, as well as in my case several \pdfbookmark lines. In other words, in this step 4, undo the commenting done in step 2.
5. Run, ONLY ONCE, pdflatex mydoc.tex.
At this point, I have a clean PDF, with hypertext links, but NONE of my bookmarks show up. So, continue with the following steps:
6. Step 5 will have generated a mydoc.out file. KEEP THIS .out file, but DELETE all other intermediate files generated. In my case, this means deleting all files with the following extensions, which I do as follows: rm -f *.dvi *.aux *.bbl *.blg *.log *.fff *.ttt (note that not all of these necessarily get generated, most notable *.dvi; this is simply a line that I have in a Makefile).
7. REPEAT steps 1-5.
At this point, I have a correctly formated PDF file, having used both apacite and hyperref together, and my PDF correctly creates links from footnote numbers to the corresponding footnotes, links from in-text citations to the corresponding reference entries in the bibliography, and nested bookmarks for all my \section, \subsection, \subsubsetion, etc. and \pdfbookmark entries.
It's quite nice, after all is said and done. However, it is a major pain, in particular step 7, that is, having to repeate ALL PREVIOUS STEPS just because steps 1-5 are needed to generate a .out file. Fortunately, if I don't add, change, or delete any bookmarks or sections/subsection/etc., I can just keep the .out file around and I only have to run steps 1-5 once. This isn't beneficial that often, though, because (obviously) document structure (i.e., sections) and bookmarks can change a lot. So, I just don't generate a hyperref-enabled version that often -- only when I absolutely must.
I hope this is helpful to someone and, ideally, I hope it helps someone help me get the problem fixed.
Cheers,
Doug
) It worked in previous versions and I don't know what I've changed to get this broken :-s. If someone could clarify my errors i would be very thankful.