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

[Ben Ward <benjamin.ward@bathspa.org>]

On Mon, 2011-02-28 at 11:56 -0600, 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?
> 

R on my system is as default with no special instruction by me. Tried
removing the source of error in the code block, still no luck. My *R*
Buffer contains:

> options(STERM='iESS', editor='emacsclient')
> x<-c(1,2,3,4,5)
y<-c(5,10,15,20)
x
y
'org_babel_R_eoe'
x<-c(1,2,3,4,5)
> y<-c(5,10,15,20)
> x
[1] 1 2 3 4 5
> y
[1]  5 10 15 20
> 'org_babel_R_eoe'
[1] "org_babel_R_eoe"
> 

Thanks,
Ben.

> --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)
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> Emacs-orgmode mailing list
> >>>>> Please use `Reply All' to send replies to the list.
> >>>>> Emacs-orgmode@gnu.org
> >>>>> http://lists.gnu.org/mailman/listinfo/emacs-orgmode
> >>>
> >>>
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> >>>
> >>
> >>
> > 
> > 
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