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the Glossary's index number is 3, which should be 75,
so people could not navigate "Glossary" by clicking the title showed in
Table of Content, or index link which is beside the content in Evince.

Which version of the Ref Manual is this supposed to be?
By Evince do you mean the Gnome document viewer?
http://www.gnome.org/projects/evince/
If so, are you trying to view a .pdf downloaded from python.org?
If so, did you try viewing it with acrobat or some other .pdf viewer?
This would indicate whether the fault is with the Evince or Python's
.pdf generation or index support.
The screenshot shows two other major problems with the TOC.
Data model should not be indented; it is not part of lexical analysis.
Three chapters between Data Model and Compound Statements are missing.

hi, sorry for didn't present very clear.
> Which version of the Ref Manual is this supposed to be?
the newest python documentations, Release 2.6, October 2, 2008
> By Evince do you mean the Gnome document viewer?
> http://www.gnome.org/projects/evince/
Yes
> If so, are you trying to view a .pdf downloaded from python.org?
Yes, from the official site. download the docs from
http://docs.python.org/ftp/python/doc/2.6/python-docs-pdf-a4.tar.bz2
> If so, did you try viewing it with acrobat or some other .pdf viewer?
Yes, the same. I tested in acrobat. both has this problem. 
> This would indicate whether the fault is with the Evince or Python's
> .pdf generation or index support.
I guess the problem is index support.
> The screenshot shows two other major problems with the TOC.
> Data model should not be indented; it is not part of lexical analysis.
> Three chapters between Data Model and Compound Statements are missing.
exactly, the index may be messed up.

In addition to the same issue: library.pdf, downloaded from
http://docs.python.org/ftp/python/doc/2.6/python-docs-pdf-a4.tar.bz2:
Glossary points to chapter 1, 
"About these documents" chapter 2,
History and License chapter 3,
Copyright chapter 4.
The Index points correctly to the "Symbol Index", but misplaces the
"Module Index": the "Module Index" is a subchapter of the "Copyright".

distutils.pdf shows the wrong behaviour quite nicely. See attached png file

any feedback here?

We are all volunteers here, and I see three replies.
This may or may not be trivial to fix, and may take some time.
Python docs are written in rst format and translated by Sphinx to
various formats. The main translation is to html, as viewed on the
site. Translation to .pdf is indirect via translation to latex and then
from latex to .pdf. Since the .html index appears flawless, and since a
different .pdf has problems, I suspect that the .pdf index problem is in
one of the two translation steps. Hence the change of component.
In the meanwhile, either ignore the index or use the html version.

> We are all volunteers here, and I see three replies.
> This may or may not be trivial to fix, and may take some time.
> Python docs are written in rst format and translated by Sphinx to
> various formats. The main translation is to html, as viewed on the
> site. Translation to .pdf is indirect via translation to latex and then
> from latex to .pdf. Since the .html index appears flawless, and since a
> different .pdf has problems, I suspect that the .pdf index problem is in
> one of the two translation steps. Hence the change of component.
> In the meanwhile, either ignore the index or use the html version.
Thanks a lot for you reply. I just intend to raise somebody's attention
to this 
problem in order to improve reader's experience.
It might or might not be a trivial to fix though.

This problem also applies to Python 3.0rc1. 
Georg, could you please comment on ray's and tjreedy's question. Thanks

I'm not ignoring this issue; I think it's a trivial fix once I find out
where :)

ah, thanks goodness, what a fortune that you are not ignoring this problem.
I expect the fix could be happen in the near future. :)

OK, I have the problem. The hyperref package must not be included before
fncychap, in fact, it should be included last.
I'll fix this as soon as I've found the most adaptable way to do it. :)

Woohoo, you are awesome, thanks a lot!

Should be fixed now in r66955. Thanks for your patience!

Hi Georg,
I tried to rebuilt the documentation from scratch (2.6 as well as
3.0rc1) and make fails with the command " \tableofcontents", which is
part of the generated *.tex file. I will include the typescript output
of the make command. The error message in 'typescript' is line 77. The
checked ot revision of sphinx is: 'Checked out revision 66957.'

Interesting: I reran the build of PDFs under Windows (XP) and it works
like a charm! Everything is there, the TOC, the Index and the Contents.
I have no idea why Ubuntus pdflatex decided to go on strike. Thanks a
lot for all your work!

Thanks for your big efforts!

Winfried, can you try again with the newest trunk?

Georg, 
sphinx r66972 works perfectly. Thanks again!