Re: [O] Problems with Org-Mode export
Michael Hannon jm_han...@yahoo.com wrote: Nick Dokos nicholas.do...@hp.com wrote: 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. I pulled from latest and reran both the original test file and the test file below. I get no errors either with my standard config or with a minimal .emacs in either case. Version info for reference: Org-mode version 7.7 (release_7.7.311.g0c099) GNU Emacs 24.0.50.2 (x86_64-unknown-linux-gnu, GTK+ Version 2.22.0) of 2011-09-13 This is on Ubuntu 10.10. Nick Thanks, Nick. This is getting curiouser and curiouser. I can now reliably get documents exported using the vanilla 7.7 Org-Mode, but not with the development version I currently have installed: Org-mode version 7.7 (release_7.7.304.g9da4) I suspect that the following bit of the error message is the relevant one: org-babel-R-evaluate: Wrong number of arguments: #[(session body result-type result-params column-names-p row-names-p but I don't know what to make of it. In order to simplify the discussion, I've been working with some Org code that I took from the worg web site. Please see below for details. I've also appended the pieces of my .emacs file that relate to finding Org files. At this point I guess I'm ready to declare victory and slink away, but it WOULD be interesting to know what's going on. -- Mike -- #+TITLE: Test #+AUTHOR: Michael Hannon #+EMAIL: jm_han...@yahoo.com #+BABEL: :session *R* :cache yes :results output graphics :exports both :tangle yes Example taken from: http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.html * Example of Org-Babel for R Literate Programming ** R text output A simple summary. #+begin_src R x - rnorm(10) summary(x) #+end_src ** R graphics output Note we use the object =x= generated in previous code block, thanks to the header option =:session *R*=. The output graphics file is =a.png=. #+begin_src R :file a.png y - rnorm(10) plot(x, y) #+end_src Same plot with larger dimension: #+begin_src R :file b.png :width 800 :height 800 plot(x, y) #+end_src -- Org-Mode path variables, standard and devel versions (setq load-path (cons /usr/local/emacs.d/ssh load-path)) (require 'ssh) ;;(setq load-path (cons /usr/local/emacs.d/org-mode/org-7.7/lisp load-path)) ;;(setq load-path (cons /usr/local/emacs.d/org-mode/org-7.7/contrib/lisp load-path)) (setq load-path (cons /usr/local/emacs.d/org-mode/org-devel/org-mode/lisp load-path)) (setq load-path (cons /usr/local/emacs.d/org-mode/org-devel/org-mode/contrib/lisp load-path)) (require 'org-install)
Re: [O] Problems with Org-Mode export
Thanks, Nick. I just grabbed: Org-mode version 7.7 (release_7.7.314.g12f0) and don't seem to have the problem any more. -- Mike From: Nick Dokos nicholas.do...@hp.com To: Michael Hannon jm_han...@yahoo.com Cc: nicholas.do...@hp.com; Org-Mode List emacs-orgmode@gnu.org Sent: Wednesday, September 21, 2011 7:37 AM Subject: Re: [O] Problems with Org-Mode export Michael Hannon jm_han...@yahoo.com wrote: Nick Dokos nicholas.do...@hp.com wrote: 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. I pulled from latest and reran both the original test file and the test file below. I get no errors either with my standard config or with a minimal .emacs in either case. Version info for reference: Org-mode version 7.7 (release_7.7.311.g0c099) GNU Emacs 24.0.50.2 (x86_64-unknown-linux-gnu, GTK+ Version 2.22.0) of 2011-09-13 This is on Ubuntu 10.10. Nick Thanks, Nick. This is getting curiouser and curiouser. I can now reliably get documents exported using the vanilla 7.7 Org-Mode, but not with the development version I currently have installed: Org-mode version 7.7 (release_7.7.304.g9da4) I suspect that the following bit of the error message is the relevant one: org-babel-R-evaluate: Wrong number of arguments: #[(session body result-type result-params column-names-p row-names-p but I don't know what to make of it. In order to simplify the discussion, I've been working with some Org code that I took from the worg web site. Please see below for details. I've also appended the pieces of my .emacs file that relate to finding Org files. At this point I guess I'm ready to declare victory and slink away, but it WOULD be interesting to know what's going on. -- Mike -- #+TITLE: Test #+AUTHOR: Michael Hannon #+EMAIL: jm_han...@yahoo.com #+BABEL: :session *R* :cache yes :results output graphics :exports both :tangle yes Example taken from: http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.html * Example of Org-Babel for R Literate Programming ** R text output A simple summary. #+begin_src R x - rnorm(10) summary(x) #+end_src ** R graphics output Note we use the object =x= generated in previous code block, thanks to the header option =:session *R*=. The output graphics file is =a.png=. #+begin_src R :file a.png y - rnorm(10) plot(x, y) #+end_src Same plot with larger dimension: #+begin_src R :file b.png :width 800 :height 800 plot(x, y) #+end_src -- Org-Mode path variables, standard and devel versions (setq load-path (cons /usr/local/emacs.d/ssh load-path)) (require 'ssh) ;;(setq load-path (cons /usr/local/emacs.d/org-mode/org-7.7/lisp load-path)) ;;(setq load-path (cons /usr/local/emacs.d/org-mode/org-7.7/contrib/lisp load-path)) (setq load-path (cons /usr/local/emacs.d/org-mode/org-devel/org-mode/lisp load-path)) (setq load-path (cons /usr/local/emacs.d/org-mode/org-devel/org-mode/contrib/lisp load-path)) (require 'org-install)
Re: [O] Problems with Org-Mode export
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.
-- Mike
From: Michael Hannon jm_han...@yahoo.com
To: Org-Mode List emacs-orgmode@gnu.org
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: jm_han...@yahoo.com
#+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
Re: [O] Problems with Org-Mode export
Nick Dokos nicholas.do...@hp.com wrote: [...] 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. Thanks, Nick. This is getting curiouser and curiouser. I can now reliably get documents exported using the vanilla 7.7 Org-Mode, but not with the development version I currently have installed: Org-mode version 7.7 (release_7.7.304.g9da4) I suspect that the following bit of the error message is the relevant one: org-babel-R-evaluate: Wrong number of arguments: #[(session body result-type result-params column-names-p row-names-p but I don't know what to make of it. In order to simplify the discussion, I've been working with some Org code that I took from the worg web site. Please see below for details. I've also appended the pieces of my .emacs file that relate to finding Org files. At this point I guess I'm ready to declare victory and slink away, but it WOULD be interesting to know what's going on. -- Mike -- #+TITLE: Test #+AUTHOR: Michael Hannon #+EMAIL: jm_han...@yahoo.com #+BABEL: :session *R* :cache yes :results output graphics :exports both :tangle yes Example taken from: http://orgmode.org/worg/org-contrib/babel/how-to-use-Org-Babel-for-R.html * Example of Org-Babel for R Literate Programming ** R text output A simple summary. #+begin_src R x - rnorm(10) summary(x) #+end_src ** R graphics output Note we use the object =x= generated in previous code block, thanks to the header option =:session *R*=. The output graphics file is =a.png=. #+begin_src R :file a.png y - rnorm(10) plot(x, y) #+end_src Same plot with larger dimension: #+begin_src R :file b.png :width 800 :height 800 plot(x, y) #+end_src -- Org-Mode path variables, standard and devel versions (setq load-path (cons /usr/local/emacs.d/ssh load-path)) (require 'ssh) ;;(setq load-path (cons /usr/local/emacs.d/org-mode/org-7.7/lisp load-path)) ;;(setq load-path (cons /usr/local/emacs.d/org-mode/org-7.7/contrib/lisp load-path)) (setq load-path (cons /usr/local/emacs.d/org-mode/org-devel/org-mode/lisp load-path)) (setq load-path (cons /usr/local/emacs.d/org-mode/org-devel/org-mode/contrib/lisp load-path)) (require 'org-install)
Re: [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. Could I ask you to provide the entire backtrace for both errors? M-x toggle-debug-on-error RET The backtrace might contain information about the exact place where a string is expected. If you can't copy it into the email program save to disk + gzip + attach should do the trick. Hi, David. I've attached the backtrace for: Org-mode version 7.7 (release_7.7.304.g9da4) (I was traveling when I worked on this previously, and my environment has now changed. The version I'm using now exhibits the same kind of error.) Thanks, -- Mike backtrace.txt.gz Description: GNU Zip compressed data
Re: [O] Problems with Org-Mode export
FYI: the problem described below is worse with: Org-mode version 7.7 (release_7.7.298.gbf3e9) -- Mike From: Michael Hannon jm_han...@yahoo.com To: Org-Mode List emacs-orgmode@gnu.org 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: jm_han...@yahoo.com #+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
Re: [O] Problems with Org-Mode export
At Fri, 16 Sep 2011 10:50:01 -0700 (PDT), Michael Hannon wrote: 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. Could I ask you to provide the entire backtrace for both errors? M-x toggle-debug-on-error RET The backtrace might contain information about the exact place where a string is expected. If you can't copy it into the email program save to disk + gzip + attach should do the trick. Best, -- David -- OpenPGP... 0x99ADB83B5A4478E6 Jabber dmj...@jabber.org Email. dm...@ictsoc.de pgpAA75epbMNO.pgp Description: PGP signature
