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 11:56:44 -0600	[thread overview]
Message-ID: <4D6BE1DC.5070409@ccbr.umn.edu> (raw)
In-Reply-To: <BLU0-SMTP112064FB709887465108B53F5DE0@phx.gbl>

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?

--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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>>
> 
> 
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