Re: [O] Problems with Org-Mode export

[Nick Dokos]

Michael Hannon <address@hidden> wrote:

> Another bit of information about this:  if I remove:
> 
>     :session *R*
> 
> from the line starting with:
> 
>     #+BABEL
> 
> then I don't see any error message.
> 
> OTOH, this isn't much of a workaround, because without a "session", the 
> values of the variables are
> not preserved between source-code blocks, so that, for instance, the 
> combination:
> 
>     x <- c(1, 3, 5)    #### defined in one block
> 
> and
> 
>     q <- c(x, 8, 8)    #### defined in another block
> 
> raises an R error ('x' is not defined when the assignment to 'q' is made).
> 
> Also, in grasping at straws, I've tried renaming the R session, as:
> 
>     ... :session mTest
> 
> (on the theory that the '*' is used for emphasis in Org-Mode markup and 
> might, therefore, somehow
> confuse things).  That didn't help.
> 

FWIW, I don't get any error messages. I have no idea what the exported
file should look like: I attach both the exported pdf and the exported
html below (as well as the org file, which is just cut-n-pasted from
what you posted).

Versions:

Org-mode version 7.7 (release_7.7.224.g6e14)
GNU Emacs 24.0.50.2 (x86_64-unknown-linux-gnu, GTK+ Version 2.22.0) of 
2011-09-13

I'll pull the newest bits and try again.

Nick

> 
>     
> -------------------------------------------------------------------------------------------------
>     From: Michael Hannon <address@hidden>
>     To: Org-Mode List <address@hidden>
>     Sent: Friday, September 16, 2011 10:50 AM
>     Subject: [O] Problems with Org-Mode export
>    
>     Greetings.  I've been having problems lately in exporting Org-Mode 
> source-code
>     documents to HTML and/or PDF.
>    
>     I'm running Org-Mode 7.7 with Emacs 23 on 64-bit linux (Fedora 15).
>    
>     I've appended a document that exhibits at least some of the problem.  The
>     problems are similar to the problem described at:
>    
>         http://comments.gmane.org/gmane.emacs.orgmode/45316
>    
>     and can *sometimes* be circumvented by executing org-reload.
>    
>     In the particular example shown below, the HTML export works as expected, 
> but
>     the PDF export fails with message:
>    
>         org-export-latex-preprocess: Wrong type argument: stringp, nil
>    
>     By the way, everything worked fine in the example until I added the last
>     source block:
>    
>         #+begin_src R
>    
>           x
>    
>         #+end_src
>    
>     I tried using what I take to be the latest version of Org-Mode:
>    
>         Org-mode version 7.7 (release_7.7.290.g65d05)
>    
>     but that only made things worse.  I tried an HTML export with this 
> version, and
>     it generated a horrendous-looking message that begins with:
>    
>     org-babel-R-evaluate: Wrong number of arguments: #[(session body 
> result-type
>     result-params column-names-p row-names-p) Æ=}...
>    
>     followed by a bunch of stuff containing enough non-printing characters 
> that
>     it's hard to reproduce in email, and ending with:
>    
>     ...org-mode/lisp/ob-R.elc" . 9734)], 5
>    
>     I'd welcome any help/advice that anybody can provide.
>    
>     Thanks,
>    
>     -- Mike
>    
>     ########## Sample file that exhibits some export problems
>    
>     #+TITLE: This is a test
>    
>     #+AUTHOR: Michael Hannon
>     #+email: address@hidden
>    
>     #+BABEL: :session *R* :cache yes :results output graphics :exports both 
> :tangle yes
>    
>     * Getting Started
>    
>     ** Batch Mode
> 
>     #+begin_src R :exports code
>    
>     pdf("xh.pdf") # set graphical output file
>     hist(rnorm(100)) # generate 100 N(0,1) variates and plot their histogram
>     dev.off() # close the graphical output file
>    
>     #+end_src
>    
>     If we put the code above in a file called =z.R=, we can execute the
>     code from the command line via: =R CMD BATCH z.R=
> 
>     #+begin_src R
>      
>       x <- c(1, 3, 5)
>      
>     #+end_src
>    
>     #+begin_src R
>    
>       x[3]
>    
>     #+end_src
>    
>     #+begin_src R
>    
>       q <- c(x,x,8)
>    
>     #+end_src
>    
>     #+begin_src R
>    
>       x
>    
>     #+end_src

michael-hannon.org
Description: org file

michael-hannon.html
Description: html file

michael-hannon.pdf
Description: pdf file