From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Ward Subject: Re: Re: Re: Org Babel and R issue with pdf latex export Date: Mon, 28 Feb 2011 22:21:56 +0000 Message-ID: References: <4D6BE1DC.5070409@ccbr.umn.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 7bit Return-path: Received: from [140.186.70.92] (port=55749 helo=eggs.gnu.org) by lists.gnu.org with esmtp (Exim 4.43) id 1PuBQr-0007qq-U9 for emacs-orgmode@gnu.org; Mon, 28 Feb 2011 17:19:11 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1PuBQq-0004En-4h for emacs-orgmode@gnu.org; Mon, 28 Feb 2011 17:19:09 -0500 Received: from blu0-omc1-s17.blu0.hotmail.com ([65.55.116.28]:11529) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1PuBQq-0004Eg-25 for emacs-orgmode@gnu.org; Mon, 28 Feb 2011 17:19:08 -0500 In-Reply-To: <4D6BE1DC.5070409@ccbr.umn.edu> List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: Erik Iverson Cc: emacs-orgmode@gnu.org, Dan Davison , Rainer M Krug 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 > >> wrote: > >>> On Sun, 2011-02-27 at 21:35 -0800, Dan Davison wrote: > >>>> Ben Ward 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 > >>> > >>> > >>> _______________________________________________ > >>> 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 > >>> > >> > >> > > > > > > _______________________________________________ > > 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 >