Bug: Generation of pdf when using OPTIONS: H: faulty [7.9.2 (release_7.9.2-588-g8fb2cb @ /home/rkrug/.emacs.d/org-mode/lisp/)]

[Rainer M Krug <r.m.krug@gmail.com>]

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Hi

When exporting the tree below (Linear Mixed Effect Models) as pdf, the
some headers are omitted when OPTIONS: H: is used. When this option is
removed, the export is fine, but as expected the fourth level headers
are converted to lists, but I would like to have them as headers in the
toc. This worked in earlier versions of org, but unfortunately I can not
tell you when it changed.

I attach the org file, tex and pdf

Cheers,

Rainer


#+OPTIONS: toc:5
#+OPTIONS: H:5

* Linear Mixed Effect Models
Load the package nlme
#+begin_src R
  #
#+end_src

** Brunia laevis
*** Height
Clean old =dat.*= objects out
#+begin_src R
  #
#+end_src

**** Define the "default" models
#+begin_src R
  #
#+end_src

**** Fit a linear model as a baseline
#+begin_src R
  #
#+end_src

**** Fit the lme for different random effects
random intercept and slope
#+begin_src R
  #
#+end_src

only random intercept
#+begin_src R
  #
#+end_src



Emacs  : GNU Emacs 24.2.1 (i686-pc-linux-gnu, GTK+ Version 2.24.13)
 of 2012-11-06 on dubnium, modified by Debian
Package: Org-mode version 7.9.2 (release_7.9.2-588-g8fb2cb @ /home/rkrug/.emacs.d/org-mode/lisp/)

current state:
==============
(setq
 org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point org-babel-execute-safely-maybe)
 org-export-latex-packages-alist '(("" "color" t) ("" "listings" t))
 org-src-fontify-natively t
 org-plantuml-jar-path "/home/rkrug/jar/plantuml.jar"
 org-export-kill-product-buffer-when-displayed t
 org-export-with-drawers nil
 org-ellipsis "? ? ?"
 org-export-with-tags 'not-in-toc
 org-export-preprocess-before-selecting-backend-code-hook '(org-beamer-select-beamer-code)
 org-tab-first-hook '(org-hide-block-toggle-maybe org-src-native-tab-command-maybe
		      org-babel-hide-result-toggle-maybe org-babel-header-arg-expand)
 org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers
		  org-cycle-hide-inline-tasks org-cycle-show-empty-lines
		  org-optimize-window-after-visibility-change)
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-confirm-babel-evaluate nil
 org-speed-command-hook '(org-speed-command-default-hook org-babel-speed-command-hook)
 org-src-window-setup 'current-window
 org-babel-pre-tangle-hook '(save-buffer)
 org-occur-hook '(org-first-headline-recenter)
 org-structure-template-alist '(("lua" "#+begin_src lua \n  ?\n#+end_src"
				 "<src lang=\"lua\">\n\n</src>")
				("r" "#+begin_src R ?\n\n#+end_src" "<src lang=\"R\">\n\n</src>")
				("s" "#+BEGIN_SRC ?\n\n#+END_SRC" "<src lang=\"?\">\n\n</src>")
				("e" "#+BEGIN_EXAMPLE\n?\n#+END_EXAMPLE" "<example>\n?\n</example>")
				("q" "#+BEGIN_QUOTE\n?\n#+END_QUOTE" "<quote>\n?\n</quote>")
				("v" "#+BEGIN_VERSE\n?\n#+END_VERSE" "<verse>\n?\n</verse>")
				("c" "#+BEGIN_CENTER\n?\n#+END_CENTER" "<center>\n?\n</center>")
				("l" "#+BEGIN_LaTeX\n?\n#+END_LaTeX"
				 "<literal style=\"latex\">\n?\n</literal>")
				("L" "#+LaTeX: " "<literal style=\"latex\">?</literal>")
				("h" "#+BEGIN_HTML\n?\n#+END_HTML"
				 "<literal style=\"html\">\n?\n</literal>")
				("H" "#+HTML: " "<literal style=\"html\">?</literal>")
				("a" "#+BEGIN_ASCII\n?\n#+END_ASCII") ("A" "#+ASCII: ")
				("i" "#+INDEX: ?" "#+INDEX: ?")
				("I" "#+INCLUDE: %file ?" "<include file=%file markup=\"?\">"))
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-confirm-elisp-link-function 'yes-or-no-p
 org-export-latex-format-toc-function 'org-export-latex-format-toc-default
 org-hide-leading-stars t
 org-capture-templates '(("p" "Problem to be logged in buffer" entry
			  (file+headline (buffer-file-name) "QUESTIONS")
			  "* %?\n- revision :: %(symbol-name (vc-working-revision (buffer-file-name (org-capture-get
:original-buffer))))\n- state    :: %(symbol-name (vc-state (buffer-file-name (org-capture-get
:original-buffer))))\n- link     :: %a \n- author   :: Rainer M Krug, email: Rainer@krugs.de")
			 ("c" "Changes to be logged in buffer" entry
			  (file+headline (buffer-file-name) "CHANGES")
			  "* %T %? \n- revision :: %(symbol-name (vc-working-revision (buffer-file-name
(org-capture-get :original-buffer))))\n- state    :: %(symbol-name (vc-state (buffer-file-name
(org-capture-get :original-buffer))))\n- link     :: %a \n- author   :: Rainer M Krug, email:
Rainer@krugs.de %n")
			 ("t" "TODO to be logged in buffer" entry
			  (file+headline (buffer-file-name) "TODOs")
			  "* TODO %?\n- revision :: %(symbol-name (vc-working-revision (buffer-file-name
(org-capture-get :original-buffer))))\n- state    :: %(symbol-name (vc-state (buffer-file-name
(org-capture-get :original-buffer))))\n- link     :: %a \n- author   :: Rainer M Krug, email:
Rainer@krugs.de")
			 ("T" "Todo to be logged in Notes.org" entry
			  (file+headline (concat org-directory "/Notes.org") "Tasks")
			  "* TODO %?\n  %i\n %T\n %a")
			 ("M" "Misc to be logged in Notes.org" entry
			  (file+headline (concat org-directory "/Notes.org") "Misc")
			  "* %?\n  %i\n %T\n  %a")
			 ("I" "Info to be logged in Notes.org" entry
			  (file+headline (concat org-directory "/Notes.org") "Information")
			  "* %?\n  %i\n %T\n  %a")
			 ("B" "Things I can blog about to be logged in Notes.org" entry
			  (file+headline (concat org-directory "/Notes.org") "To Blog")
			  "* %?\n  %i\n %T\n  %a")
			 ("S" "Useful code snippets logged in Programming.org" entry
			  (file+headline (concat org-directory "/Programming.org") "Code Snippet")
			  "* %?  %^g\n%T\n#+begin_src %^{Programming Language|R|R|C|elisp} \n%i\n#+end_src\n%a")
			 )
 org-export-preprocess-before-normalizing-links-hook '(org-remove-file-link-modifiers)
 org-ctrl-k-protect-subtree "ask"
 org-format-latex-options '(:foreground default :background default :scale 1.3 :html-foreground
			    "Black" :html-background "Transparent" :html-scale 1.0 :matchers
			    ("begin" "$1" "$" "$$" "\\(" "\\["))
 org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
 org-export-first-hook '(org-beamer-initialize-open-trackers)
 org-mode-hook '((lambda nil (local-set-key "\357" (quote org-mime-org-buffer-htmlize)))
		 #[nil "\300\301\302\303\304$\207"
		   [org-add-hook change-major-mode-hook org-show-block-all append local] 5]
		 #[nil "\300\301\302\303\304$\207"
		   [org-add-hook change-major-mode-hook org-babel-show-result-all append local] 5]
		 org-babel-result-hide-spec org-babel-hide-all-hashes)
 org-directory "~/Documents/orgfiles"
 org-from-is-user-regexp "\\<Rainer M Krug\\>"
 org-export-latex-final-hook '(org-beamer-amend-header org-beamer-fix-toc
			       org-beamer-auto-fragile-frames
			       org-beamer-place-default-actions-for-lists)
 org-export-latex-listings t
 org-export-latex-after-initial-vars-hook '(org-beamer-after-initial-vars)
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-startup-indented t
 org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer)
 org-after-todo-state-change-hook '(org-clock-out-if-current)
 org-babel-tangle-lang-exts '(("latex" . "tex") ("emacs-lisp" . "el"))
 org-confirm-shell-link-function 'y-or-n-p
 )


- -- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys.
(Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer@krugs.de

Skype:      RMkrug
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#+OPTIONS: toc:5
#+OPTIONS: H:5

* Linear Mixed Effect Models
Load the package nlme
#+begin_src R 
  #
#+end_src

** Brunia laevis
*** Height
Clean old =dat.*= objects out
#+begin_src R 
  #
#+end_src

**** Define the "default" models
#+begin_src R 
  #
#+end_src

**** Fit a linear model as a baseline
#+begin_src R 
  #
#+end_src

**** Fit the lme for different random effects
random intercept and slope
#+begin_src R 
  #
#+end_src

only random intercept
#+begin_src R 
  #
#+end_src

[-- Attachment #3: test.tex --]
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% Created 2012-11-15 Thu 14:54
\documentclass[11pt]{article}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{fixltx2e}
\usepackage{graphicx}
\usepackage{longtable}
\usepackage{float}
\usepackage{wrapfig}
\usepackage{soul}
\usepackage{textcomp}
\usepackage{marvosym}
\usepackage{wasysym}
\usepackage{latexsym}
\usepackage{amssymb}
\usepackage{hyperref}
\tolerance=1000
\usepackage{color}
\usepackage{listings}
\providecommand{\alert}[1]{\textbf{#1}}

\title{test}
\author{Rainer M. Krug}
\date{\today}
\hypersetup{
  pdfkeywords={},
  pdfsubject={},
  pdfcreator={Emacs Org-mode version 7.9.2}}

\begin{document}

\maketitle

\setcounter{tocdepth}{5}
\tableofcontents
\vspace*{1cm}

\section{Linear Mixed Effect Models}
\label{sec-1}

Load the package nlme

\lstset{language=R}
\begin{lstlisting}
#
\end{lstlisting}
\subsection{Brunia laevis}
\label{sec-1-1}
\subsubsection{Height}
\label{sec-1-1-1}

Clean old \texttt{dat.*} objects out

\lstset{language=R}
\begin{lstlisting}
#
\end{lstlisting}
\paragraph{Define the ``default'' models}
\label{sec-1-1-1-1}

Test Text

\lstset{language=R}
\begin{lstlisting}
#
\end{lstlisting}
\paragraph{Fit a linear model as a baseline}
\label{sec-1-1-1-2}


\lstset{language=R}
\begin{lstlisting}
#
\end{lstlisting}
\paragraph{Fit the lme for different random effects}
\label{sec-1-1-1-3}

random intercept and slope

\lstset{language=R}
\begin{lstlisting}
#
\end{lstlisting}

only random intercept

\lstset{language=R}
\begin{lstlisting}
#
\end{lstlisting}

\end{document}

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