Re: Re: Re: Org Babel and R issue with pdf latex export

From: Erik Iverson <eriki@ccbr.umn.edu>
To: Ben Ward <benjamin.ward@bathspa.org>
Cc: emacs-orgmode@gnu.org, Dan Davison <dandavison7@gmail.com>,
	Rainer M Krug <r.m.krug@gmail.com>
Subject: Re: Re: Re: Org Babel and R issue with pdf latex export
Date: Mon, 28 Feb 2011 13:31:00 -0600	[thread overview]
Message-ID: <4D6BF7F4.5000906@ccbr.umn.edu> (raw)
In-Reply-To: <4D6BE1DC.5070409@ccbr.umn.edu>

Erik Iverson wrote:
> Ben,
> 
> And what about your .Rprofile. Since your R code does produce
> a warning, I wonder if you have instructed R to take some
> special action when it sees one?

Related, how does the export process that's not working affect
the *R* buffer in Emacs?  Can you paste that buffer (or at least
the relevant portions?)

Thanks!

> 
> --Erik
> 
> Ben Ward wrote:
>> On 28/02/2011 11:24, Rainer M Krug wrote:
>>> On Mon, Feb 28, 2011 at 8:07 AM, Ben Ward<benjamin.ward@bathspa.org>  
>>> wrote:
>>>> On Sun, 2011-02-27 at 21:35 -0800, Dan Davison wrote:
>>>>> Ben Ward<benjamin.ward@bathspa.org>  writes:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I recently installed emacs, org-mode fresh on a new install of Arch
>>>>>> Linux. Before I had it working on Ubuntu.
>>>>>>
>>>>>> I've installed everything as before and used the same .emacs file 
>>>>>> I had,
>>>>>> but if I use org to write out some R script and export to pdf via 
>>>>>> latex,
>>>>>> then I get an empty pdf document, with only the title and Contents
>>>>>> heading. However if I export to anything else such as html it 
>>>>>> works, and
>>>>>> shows me code and results.
>>>>> Hi Ben,
>>>>>
>>>>> Are you sure this problem concerns babel/R? What happens when you 
>>>>> export
>>>>> an Org document to pdf without any babel stuff?
>>>>>
>>>>> Can you provide an example Org file that you are having trouble
>>>>> exporting to pdf? The problem is probably in your local configuration,
>>>>> so if no-one can jump to the solution then start from a minimal 
>>>>> working
>>>>> config and try to find the part of your .emacs which is causing the
>>>>> problem.
>>>>>
>>>>> Dan
>>>>>
>>>> Hi, I've tried exporting an org file that has no code in it to PDF and
>>>> it works without any trouble.
>>>>
>>>> The file I'm trying to export is:
>>>> #+TITLE: Test
>>>> #+AUTHOR: Ben J. Ward
>>>> #+LATEX_CLASS: article
>>>> #+BABEL: :session *R* :results output
>>>> \pagebreak
>>>>
>>>> Test:
>>>>
>>>> #+begin_src R :exports both
>>>> x<-c(1,2,3,4,5)
>>>> y<-c(5,10,15,20)
>>>> x
>>>> y
>>>> xy<-(x*y)
>>>> xy
>>>> #+end_src
>>> When I use your example and export it to LaTeX,
>>>
>>> I get this:
>>>
>>> #########################################
>>> % Created 2011-02-28 Mon 12:21
>>> \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}}
>>> \begin{document}
>>>
>>>
>>>
>>> \title{Test}
>>> \author{Ben J. Ward}
>>> \date{28 February 2011}
>>> \maketitle
>>>
>>> \setcounter{tocdepth}{3}
>>> \tableofcontents
>>> \vspace*{1cm}
>>> The file I'm trying to export is:
>>> \pagebreak
>>>
>>> Test:
>>>
>>> \lstset{language=R}
>>> \begin{lstlisting}
>>> x<-c(1,2,3,4,5)
>>> y<-c(5,10,15,20)
>>> x
>>> y
>>> xy<-(x*y)
>>> xy
>>> \end{lstlisting}
>>>
>>> \begin{verbatim}
>>>   [1] 1 2 3 4 5
>>>   [1]  5 10 15 20
>>>   Warning message:
>>>   In x * y : longer object length is not a multiple of shorter object 
>>> length
>>>   [1]  5 20 45 80 25
>>> \end{verbatim}
>>>
>>>
>>>
>>> \end{document}
>>> #########################################
>>> So it works for me - have you tried to export to LaTex? If that works,
>>> it is a LaTeX / pdf issue.
>>>
>>> Rainer
>>>
>> Hi, I've just tried and I still get the same as before, but it works 
>> to latex, when there is no src code chunks.
>> This is my .emacs:
>>
>> (require 'ess-site)
>> (require 'org-install)
>> (add-to-list 'auto-mode-alist '("\\.org\\'" . org-mode))
>> (global-set-key "\C-cl" 'org-store-link)
>> (global-set-key "\C-cc" 'org-capture)
>> (global-set-key "\C-ca" 'org-agenda)
>> (global-set-key "\C-cb" 'org-iswitchb)
>> (transient-mark-mode 1)
>> (org-babel-do-load-languages
>>  'org-babel-load-languages
>>  '((R . t)
>>    (emacs-lisp . t)
>>    ))
>>
>> (custom-set-variables
>>   ;; custom-set-variables was added by Custom.
>>   ;; If you edit it by hand, you could mess it up, so be careful.
>>   ;; Your init file should contain only one such instance.
>>   ;; If there is more than one, they won't work right.
>>  '(org-confirm-babel-evaluate nil))
>> (custom-set-faces
>>   ;; custom-set-faces was added by Custom.
>>   ;; If you edit it by hand, you could mess it up, so be careful.
>>   ;; Your init file should contain only one such instance.
>>   ;; If there is more than one, they won't work right.
>>  )
>>
>> Thanks,
>> Ben W.
>>
>>>> I can include my .emacs although it's lengthy.
>>>>
>>>> I uninstalled all of my emacs stuff, and installed it from the vanilla
>>>> downloads on their respective sites, and I'm still getting the same
>>>> result. I'm considering removing all my tex stuff and installing the
>>>> vanilla texlive too.
>>>>
>>>> Thanks,
>>>> Ben W.
>>>>
>>>>>> I've tried even installing a version of org
>>>>>> mode from source, using the build system my distro has, so as it's 
>>>>>> made
>>>>>> and installed to exactly the right place, but I still don't have any
>>>>>> luck. The texlive version I'm using is from my distro's package 
>>>>>> manager.
>>>>>> Using C-c C-c to evaluate on the fly works. I had an issue getting 
>>>>>> org
>>>>>> and babel to work with R on Windows 7 as well, but it was because
>>>>>> certain tex packages were missing and I recieved a message when I 
>>>>>> tried
>>>>>> to export, but nothing comes up here.
>>>>>>
>>>>>> Would the recent change:
>>>>>> Org-babel is now inside org, remove (require 'org-babel-init)
>>>>>>    and alike from your .emacs.
>>>>>>    Look at http://orgmode.org/Changes.html#ob-configuration-changes
>>>>>>    for overview of the settings.
>>>>>> Be causing the entire issue?
>>>>>>
>>>>>> The .tex file I get out is thus:
>>>>>> % Created 2011-02-28 Mon 03:47
>>>>>> \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
>>>>>> \providecommand{\alert}[1]{\textbf{#1}}
>>>>>> \begin{document}
>>>>>>
>>>>>>
>>>>>>
>>>>>> \title{Test}
>>>>>> \author{Ben J. Ward}
>>>>>> \date{28 February 2011}
>>>>>> \maketitle
>>>>>>
>>>>>> \setcounter{tocdepth}{3}
>>>>>> \tableofcontents
>>>>>> \vspace*{1cm}
>>>>>>
>>>>>> \end{document}
>>>>>>
>>>>>> Thanks,
>>>>>> Ben W.
>>>>>> (Apologies if this has been sent twice, first time an error occured)
>>>>>>
>>>>>>
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>>
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