Hi

        I am writing a rather long tex document which is divided into sub-documents
with a single master.tex. I am using pdflatex and thumpdf to generate a PDF
file.

        Until a few hours ago, all the chapters were visible at top level in the
left pane (in acroread). I do not know what I have done, but now last m
chapters appear (in bookmarks) below the hierarchical level of the n-m th
chapter (where n is the total number of chapters). There is nothing wrong
with the references or chapter numbers in the document per se. In fact, if
one printed out the document, there would not appear to be anything wrong
with it. However, the bookmarks are screwed up when viewed in a PDF viewer
(both acroread and xpdf).

        One thing that I can remember is that when I first used xpdf to view the
document and the bookmarks all appeared awry (this is when the problems
seemed to start), and returning to acroread (and rerunning pdflatex and
thumbpdf) has not helped matters. Though I find it hard to believe that
just a PDF viewer can by itself spoil the bookmarks (or any other part of a
PDF document).

        My system - Debian Sarge running teTeX (latest version -  I compiled it
myself). xpdf version - 3.00-7. 

        How do I fix the bookmarks ?

Thanks,

MS

Madhusudan Singh <spammers-go-here@yahoo.com> wrote:

>         Until a few hours ago, all the chapters were visible at top level in the
> left pane (in acroread). I do not know what I have done, but now last m
> chapters appear (in bookmarks) below the hierarchical level of the n-m th
> chapter (where n is the total number of chapters).
> [...] 
>         How do I fix the bookmarks ?

* It is a good idea to use a version control system (cvs, ...)
  Then you can compare the current state with a state where all
  was ok.
* When writing long complex documents, then you will probably
  have backups. Then you can find out the differences between
 a running version and a version with broken bookmarks.
* Method of "minimal example" can be used to strip down the whole
  file until the error/problem is isolated.

Yours sincerely
  Heiko <oberdiek@uni-freiburg.de>

Madhusudan Singh wrote:
>         Until a few hours ago, all the chapters were visible at top level in the
> left pane (in acroread). I do not know what I have done, but now last m
> chapters appear (in bookmarks) below the hierarchical level of the n-m th
> chapter (where n is the total number of chapters). There is nothing wrong
> with the references or chapter numbers in the document per se. In fact, if
> one printed out the document, there would not appear to be anything wrong
> with it. However, the bookmarks are screwed up when viewed in a PDF viewer
> (both acroread and xpdf).

I have no idea if this could be the problem in this particular case, but
I have heard of similar problems being caused by a messed-up .aux file
-- specifically, the .aux file gets broken in such a way that it causes
the .aux file from the next run to be similarly broken, and so even
though the problem in the source file is fixed, the problem persists.  

The solution, if this is the problem, is to delete all of the
"intermediate" files like the .aux file, and re-run pdflatex.  Hopefully
that will solve the problem, but if not it has at least eliminated one
possibility.

- Brooks


-- 
The "bmoses-nospam" address is valid; no unmunging needed.

On Monday 31 May 2004 15:37, Brooks Moses (bmoses-nospam@cits1.stanford.edu) 
held forth in comp.text.tex (<40BB898D.FA92B89D@cits1.stanford.edu>):

> Madhusudan Singh wrote:
>>         Until a few hours ago, all the chapters were visible at top level
>>         in the
>> left pane (in acroread). I do not know what I have done, but now last m
>> chapters appear (in bookmarks) below the hierarchical level of the n-m th
>> chapter (where n is the total number of chapters). There is nothing wrong
>> with the references or chapter numbers in the document per se. In fact,
>> if one printed out the document, there would not appear to be anything
>> wrong with it. However, the bookmarks are screwed up when viewed in a PDF
>> viewer (both acroread and xpdf).
> 
> I have no idea if this could be the problem in this particular case, but
> I have heard of similar problems being caused by a messed-up .aux file
> -- specifically, the .aux file gets broken in such a way that it causes
> the .aux file from the next run to be similarly broken, and so even
> though the problem in the source file is fixed, the problem persists.
> 
> The solution, if this is the problem, is to delete all of the
> "intermediate" files like the .aux file, and re-run pdflatex.  Hopefully
> that will solve the problem, but if not it has at least eliminated one
> possibility.
> 
> - Brooks
> 
> 

No, it just eliminated one possibility. I did that. Removed *all* non .tex
files. (includes, .loa, .lot, .aux, .bbl, .ind, .ilg, etc.) and recompiled.
No go.

On Sat, 29 May 2004 05:23:30 -0400, Madhusudan Singh
<spammers-go-here@yahoo.com> wrote:

>Hi
>
>        I am writing a rather long tex document which is divided into sub-documents
>with a single master.tex. I am using pdflatex and thumpdf to generate a PDF
>file.
>
>        Until a few hours ago, all the chapters were visible at top level in the
>left pane (in acroread). I do not know what I have done, but now last m
>chapters appear (in bookmarks) below the hierarchical level of the n-m th
>chapter (where n is the total number of chapters). There is nothing wrong
>with the references or chapter numbers in the document per se. In fact, if
>one printed out the document, there would not appear to be anything wrong
>with it. However, the bookmarks are screwed up when viewed in a PDF viewer
>(both acroread and xpdf).
>
>        One thing that I can remember is that when I first used xpdf to view the
>document and the bookmarks all appeared awry (this is when the problems
>seemed to start), and returning to acroread (and rerunning pdflatex and
>thumbpdf) has not helped matters. Though I find it hard to believe that
>just a PDF viewer can by itself spoil the bookmarks (or any other part of a
>PDF document).
>
>        My system - Debian Sarge running teTeX (latest version -  I compiled it
>myself). xpdf version - 3.00-7. 
>
>        How do I fix the bookmarks ?
>
>Thanks,
>
>MS


I agree with Heiko that getting a minimal example will probably be the
best way to go about this.  If you don't have too many chapters,
replace their contents one at a time with plain text (no commands).
I'd start with the chapter that includes the rest as subheadings, or
maybe the one after it.  If you get a *minimal* example that has the
problem, post it here and hopefully someone will spot the error.

Also, thumbpdf has a list of known problems.  The only one that sounds
vaguely like yours is that 'pdfpagetransition' in hyperref is
incompatible.  You should take a look at that section (if you haven't
already done so).  

David

David Walthall wrote:

> 
> I agree with Heiko that getting a minimal example will probably be the
> best way to go about this.  If you don't have too many chapters,

I have a lot of chapters and most of them are very lengthy :(

> replace their contents one at a time with plain text (no commands).
> I'd start with the chapter that includes the rest as subheadings, or
> maybe the one after it.  If you get a *minimal* example that has the
> problem, post it here and hopefully someone will spot the error.
> 
> Also, thumbpdf has a list of known problems.  The only one that sounds
> vaguely like yours is that 'pdfpagetransition' in hyperref is
> incompatible.  You should take a look at that section (if you haven't
> already done so).
> 

I have used the same version of hyperref consistently (same TeX
installation). Could it be the side effect of adding some other packages (I
have used a few new \usepackage{}'s lately) ?

David Walthall <david.nospam.walthall@stanford.edu> wrote:

> Also, thumbpdf has a list of known problems.

Which?

> The only one that sounds
> vaguely like yours is that 'pdfpagetransition' in hyperref is
> incompatible.

Example?
And pdfpagetransition does not have anything to do with bookmarks.

Yours sincerely
  Heiko <oberdiek@uni-freiburg.de>

On Wed, 02 Jun 2004 12:03:54 +0200, Heiko Oberdiek
<oberdiek@uni-freiburg.de> wrote:

>David Walthall <david.nospam.walthall@stanford.edu> wrote:
>
>> Also, thumbpdf has a list of known problems.
>
>Which?

http://www.ctan.org/tex-archive/support/thumbpdf/
Specifically section "I. Known Problems" of readme.txt

>> The only one that sounds
>> vaguely like yours is that 'pdfpagetransition' in hyperref is
>> incompatible.
>
>Example?
>And pdfpagetransition does not have anything to do with bookmarks.

Ah, thank you.  I was merely suggesting that the known incompatibility
between that option in hyperref and thumbpdf could cause an issue.
Without a (minimal) listing of your tex file, it is I did not know
which options you were using.

David

David Walthall wrote:

> On Wed, 02 Jun 2004 12:03:54 +0200, Heiko Oberdiek
> <oberdiek@uni-freiburg.de> wrote:
> 
>>David Walthall <david.nospam.walthall@stanford.edu> wrote:
>>
>>> Also, thumbpdf has a list of known problems.
>>
>>Which?
> 
> http://www.ctan.org/tex-archive/support/thumbpdf/
> Specifically section "I. Known Problems" of readme.txt
> 
>>> The only one that sounds
>>> vaguely like yours is that 'pdfpagetransition' in hyperref is
>>> incompatible.
>>
>>Example?
>>And pdfpagetransition does not have anything to do with bookmarks.
> 
> Ah, thank you.  I was merely suggesting that the known incompatibility
> between that option in hyperref and thumbpdf could cause an issue.
> Without a (minimal) listing of your tex file, it is I did not know
> which options you were using.
> 
> David

I am using :

\documentclass[12pt]{report}
\usepackage{times}
\usepackage{rac}
\usepackage{dbl12}
\usepackage[pdftex]{graphicx}
\usepackage{subfigure}
\usepackage{dcolumn}
\usepackage{thumbpdf}
\usepackage{amsmath}
\usepackage{amscd}
\usepackage{makeidx}
\makeindex
\usepackage{listings}
\usepackage{wasysym}
\usepackage{caption}
\usepackage{hyperref}

David Walthall wrote:

> On Wed, 02 Jun 2004 12:03:54 +0200, Heiko Oberdiek
> <oberdiek@uni-freiburg.de> wrote:
> 
>>David Walthall <david.nospam.walthall@stanford.edu> wrote:
>>
>>> Also, thumbpdf has a list of known problems.
>>
>>Which?
> 
> http://www.ctan.org/tex-archive/support/thumbpdf/
> Specifically section "I. Known Problems" of readme.txt
> 
>>> The only one that sounds
>>> vaguely like yours is that 'pdfpagetransition' in hyperref is
>>> incompatible.
>>
>>Example?
>>And pdfpagetransition does not have anything to do with bookmarks.
> 
> Ah, thank you.  I was merely suggesting that the known incompatibility
> between that option in hyperref and thumbpdf could cause an issue.
> Without a (minimal) listing of your tex file, it is I did not know
> which options you were using.
> 
> David

I am using :

\documentclass[12pt]{report}
\usepackage{times}
\usepackage{rac}
\usepackage{dbl12}
\usepackage[pdftex]{graphicx}
\usepackage{subfigure}
\usepackage{dcolumn}
\usepackage{thumbpdf}
\usepackage{amsmath}
\usepackage{amscd}
\usepackage{makeidx}
\makeindex
\usepackage{listings}
\usepackage{wasysym}
\usepackage{caption}
\usepackage{hyperref}

And :

\newcommand{\hyperrefoptions}{pdftex,linkbordercolor={1 0.5
0.5},citebordercolor={0.4 1 0.4},urlbordercolor={0.3 1
1},pdfauthor={Madhusudan Singh},pdftitle={abc}}