* Running "org-babel-tangle" and/or "org-export-as-pdf" in Emacs batch mode
@ 2012-04-10 13:20 Bernd Weiss
2012-04-11 14:14 ` Eric Schulte
0 siblings, 1 reply; 3+ messages in thread
From: Bernd Weiss @ 2012-04-10 13:20 UTC (permalink / raw)
To: emacs-orgmode
Dear all,
I am not sure if this an orgmode-, an ESS- or an Emacs-related question.
I am working on an orgmode-file with embedded R code. Since I am using a
build tool called waf, I would like to call Emacs from command line like
this:
emacs --batch --load "e:/config/.emacs" --visit test.org --funcall
org-export-as-pdf
(or call org-babel-tangle)
However, it stops with "Type C-h m for help on ESS version 12.03". If I
remove the R part (#+begin_src etc.), everything works as expected.
This is my (hopefully) minimal example, the command line output and the
orgmode related infos.
Thanks,
Bernd
-------------------minimal example: test.org---------------------------
# Babel settings
#+PROPERTY: session *R*
#+PROPERTY: tangle test.R
#+PROPERTY: comments yes
#+PROPERTY: results output
#+PROPERTY: exports both
#+BEAMER_FRAME_LEVEL: 1
#+startup: beamer
#+LaTeX_CLASS: beamer
#+LaTeX_CLASS_OPTIONS: [bigger]
#+latex_header: %%\mode<beamer>{\usetheme{Madrid}}
* test heading
lsals
#+begin_src R
1+1
#+end_src
-------------------minimal example: text.org---------------------------
-------------------cl-output------------------------------------------
wmx336@fi-weiss-50 /cygdrive/e/projects/software/ps2012r_intro/test
$ emacs --batch --load "e:/config/.emacs" --visit test.org --funcall
org-export-as-pdf
customizing GNU Emacs
customizing GNU Emacs for Win 7
Loading e:/config/.recentf...
Cleaning up the recentf list...
Cleaning up the recentf list...done (0 removed)
Loading tex-mik...
Ido mode enabled
Source file
`d:/programme/emacs/site-lisp/org-mode/contrib/lisp/org-contacts.el'
newer than byte-compiled file
Ido mode enabled
Loading
d:/programme/emacs/site-lisp/color-theme/themes/color-theme-example.el
(source)...
Loading
d:/programme/emacs/site-lisp/color-theme/themes/color-theme-example.elc...
Loading
d:/programme/emacs/site-lisp/color-theme/themes/color-theme-library.el
(source)...
Loading
d:/programme/emacs/site-lisp/color-theme/themes/color-theme-library.elc...
Loading
d:/programme/emacs/site-lisp/color-theme/themes/color-theme-tango.el
(source)...
Loading
d:/programme/emacs/site-lisp/color-theme/themes/color-theme-tango.elc...
[yas] warning: keybinding "(rinari-minor-mode-map . C-c C-c C-r)"
invalid for snippet "#+begin_src R...#+end_" since keymap
"rinari-minor-mode-map" does not (yet?) exist.
[yas] warning: keybinding "(rinari-minor-mode-map . C-c C-c C-b)"
invalid for snippet "beamer_envargs" since keymap
"rinari-minor-mode-map" does not (yet?) exist.
Loading d:/programme/emacs/site-lisp/graphviz-dot-mode.el (source)...
OVERVIEW
Local Ispell dictionary set to nil
Starting new Ispell process [default] ...
File mode specification error: (error
"d:\\programme\\Aspell\\bin\\aspell.exe did not output version line")
Loading vc-git...
Exporting to PDF...
Exporting to LaTeX...
Local Ispell dictionary set to nil
Automatic display of crossref information was turned on
Applying style hooks...
Applying style hooks... done
Local Ispell dictionary set to nil
Local Ispell dictionary set to nil
executing R code block...
Type C-h m for help on ESS version 12.03
-------------------cl-output------------------------------------------
-------------------org-related-infos-----------------------------------
Emacs : GNU Emacs 23.3.1 (i386-mingw-nt5.1.2600)
of 2011-03-10 on 3249CTO
Package: Org-mode version 7.8.06 (release_7.8.06.180.g22bfd)
current state:
==============
(setq
org-export-preprocess-before-backend-specifics-hook
'(org-inlinetask-export-handler)
org-export-latex-after-initial-vars-hook '(org-beamer-after-initial-vars)
org-export-latex-listings t
org-speed-command-hook '(org-speed-command-default-hook
org-babel-speed-command-hook)
org-agenda-custom-commands '(("c" "conferences" ((tags "CONFERENCE"))
((org-tags-match-list-sublevels nil))
((org-columns-default-format "%DATE %LOCATION")))
("d" "Upcoming deadlines" agenda ""
((org-agenda-time-grid nil) (org-deadline-warning-days 365)
(org-agenda-entry-types (quote (:deadline)))))
("W" "Weekly Review" ((agenda "" ((org-agenda-ndays 14))) (todo
"WRITING"))))
org-agenda-files '("e:/projects/habilitation/org/prHabilitation.org"
"e:/projects/org/agendas/2011fall.org"
"e:/projects/org/agendas/2011springterm.org"
"e:/projects/org/agendas/SynRG.org"
"e:/projects/org/agendas/capture.org" "e:/projects/org/agendas/d_2011a.org"
"e:/projects/org/agendas/prDAAD-ipd-ma-divorce.org"
"e:/projects/org/agendas/prDAAD-ma-simulation.org"
"e:/projects/org/agendas/privat.org"
"e:/projects/org/agendas/pu2012bbbook_basic_meta-analysis.org"
"e:/projects/org/agendas/te2012sose.org"
"e:/projects/org/agendas/te2012spring.org"
"e:/projects/org/agendas/work.org")
org-blocker-hook '(org-block-todo-from-children-or-siblings-or-parent)
org-src-fontify-natively t
org-babel-load-languages '((emacs-lisp . t) (maxima . t) (R . t)
(python . t) (latex . t) (dot . t) (sh . t))
org-ctrl-k-protect-subtree t
org-completion-use-ido t
org-metaup-hook '(org-babel-load-in-session-maybe)
org-after-todo-state-change-hook '(org-clock-out-if-current)
org-babel-tangle-lang-exts '(("python" . "py") ("maxima" . "max")
("emacs-lisp" . "el"))
org-edit-src-content-indentation 0
org-export-latex-format-toc-function 'org-export-latex-format-toc-default
org-tab-first-hook '(yas/org-very-safe-expand
org-hide-block-toggle-maybe org-src-native-tab-command-maybe
org-babel-hide-result-toggle-maybe)
org-src-mode-hook '(org-src-babel-configure-edit-buffer
org-src-mode-configure-edit-buffer)
org-confirm-shell-link-function 'yes-or-no-p
org-export-first-hook '(org-beamer-initialize-open-trackers)
org-agenda-before-write-hook '(org-agenda-add-entry-text)
org-export-latex-packages-alist '(("" "color") ("" "listings"))
org-default-notes-file "e:/projects/org/agendas/capture.org"
org-directory "e:/projects/org/"
org-babel-pre-tangle-hook '(save-buffer)
org-cycle-hook '(org-cycle-hide-archived-subtrees
org-cycle-hide-drawers org-cycle-show-empty-lines
org-optimize-window-after-visibility-change)
org-export-preprocess-before-normalizing-links-hook
'(org-remove-file-link-modifiers)
org-mode-hook '((lambda nil (make-variable-buffer-local (quote
yas/trigger-key)) (setq yas/trigger-key [tab])
(add-to-list (quote org-tab-first-hook) (quote
yas/org-very-safe-expand)) (define-key yas/keymap [tab] (quote
yas/next-field)))
turn-on-org-cdlatex turn-on-auto-fill turn-on-font-lock
#[nil "\300\301\302\303\304$\207" [org-add-hook
change-major-mode-hook org-show-block-all append local] 5]
#[nil "\300\301\302\303\304$\207" [org-add-hook
change-major-mode-hook org-babel-show-result-all append local] 5]
org-babel-result-hide-spec org-babel-hide-all-hashes
turn-on-visual-line-mode)
org-font-lock-hook '(org-inlinetask-fontify)
org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point
org-babel-execute-safely-maybe)
org-confirm-elisp-link-function 'yes-or-no-p
org-export-interblocks '((src org-babel-exp-non-block-elements))
org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
org-enforce-todo-dependencies t
org-occur-hook '(org-first-headline-recenter)
org-from-is-user-regexp nil
org-export-preprocess-before-selecting-backend-code-hook
'(org-beamer-select-beamer-code)
org-confirm-babel-evaluate nil
org-hierarchical-checkbox-statistics nil
org-src-tab-acts-natively t
org-export-latex-final-hook '(org-beamer-amend-header
org-beamer-fix-toc org-beamer-auto-fragile-frames
org-beamer-place-default-actions-for-lists)
org-metadown-hook '(org-babel-pop-to-session-maybe)
org-export-blocks '((src org-babel-exp-src-block nil) (export-comment
org-export-blocks-format-comment t) (ditaa
org-export-blocks-format-ditaa nil)
(dot org-export-blocks-format-dot nil))
)
-------------------org-related-infos-----------------------------------
^ permalink raw reply [flat|nested] 3+ messages in thread* Re: Running "org-babel-tangle" and/or "org-export-as-pdf" in Emacs batch mode
2012-04-10 13:20 Running "org-babel-tangle" and/or "org-export-as-pdf" in Emacs batch mode Bernd Weiss
@ 2012-04-11 14:14 ` Eric Schulte
2012-04-12 15:45 ` Bernd Weiss
0 siblings, 1 reply; 3+ messages in thread
From: Eric Schulte @ 2012-04-11 14:14 UTC (permalink / raw)
To: Bernd Weiss; +Cc: emacs-orgmode
Bernd Weiss <bernd.weiss@uni-koeln.de> writes:
> Dear all,
>
> I am not sure if this an orgmode-, an ESS- or an Emacs-related question.
>
> I am working on an orgmode-file with embedded R code. Since I am using a
> build tool called waf, I would like to call Emacs from command line like
> this:
>
> emacs --batch --load "e:/config/.emacs" --visit test.org --funcall
> org-export-as-pdf
>
> (or call org-babel-tangle)
>
> However, it stops with "Type C-h m for help on ESS version 12.03". If I
> remove the R part (#+begin_src etc.), everything works as expected.
>
> This is my (hopefully) minimal example, the command line output and the
> orgmode related infos.
>
> Thanks,
>
> Bernd
>
Hi Bernd,
I can't recreate this hanging issue locally (I don't have access to a
windows box). This sounds like an ESS issue to me since ESS seems to be
the hanging process. Perhaps a good first step would be to try to
evaluate "(require 'ess) (R)" in a batch Emacs session without Emacs
hanging. Once this is working then it should be clear how to run ESS
sessions from code blocks.
Best,
>
>
> -------------------minimal example: test.org---------------------------
> # Babel settings
> #+PROPERTY: session *R*
> #+PROPERTY: tangle test.R
> #+PROPERTY: comments yes
> #+PROPERTY: results output
> #+PROPERTY: exports both
>
> #+BEAMER_FRAME_LEVEL: 1
>
> #+startup: beamer
> #+LaTeX_CLASS: beamer
> #+LaTeX_CLASS_OPTIONS: [bigger]
> #+latex_header: %%\mode<beamer>{\usetheme{Madrid}}
>
> * test heading
> lsals
>
> #+begin_src R
> 1+1
> #+end_src
> -------------------minimal example: text.org---------------------------
>
>
>
>
>
> -------------------cl-output------------------------------------------
> wmx336@fi-weiss-50 /cygdrive/e/projects/software/ps2012r_intro/test
> $ emacs --batch --load "e:/config/.emacs" --visit test.org --funcall
> org-export-as-pdf
> customizing GNU Emacs
> customizing GNU Emacs for Win 7
> Loading e:/config/.recentf...
> Cleaning up the recentf list...
> Cleaning up the recentf list...done (0 removed)
> Loading tex-mik...
> Ido mode enabled
> Source file
> `d:/programme/emacs/site-lisp/org-mode/contrib/lisp/org-contacts.el'
> newer than byte-compiled file
> Ido mode enabled
> Loading
> d:/programme/emacs/site-lisp/color-theme/themes/color-theme-example.el
> (source)...
> Loading
> d:/programme/emacs/site-lisp/color-theme/themes/color-theme-example.elc...
> Loading
> d:/programme/emacs/site-lisp/color-theme/themes/color-theme-library.el
> (source)...
> Loading
> d:/programme/emacs/site-lisp/color-theme/themes/color-theme-library.elc...
> Loading
> d:/programme/emacs/site-lisp/color-theme/themes/color-theme-tango.el
> (source)...
> Loading
> d:/programme/emacs/site-lisp/color-theme/themes/color-theme-tango.elc...
> [yas] warning: keybinding "(rinari-minor-mode-map . C-c C-c C-r)"
> invalid for snippet "#+begin_src R...#+end_" since keymap
> "rinari-minor-mode-map" does not (yet?) exist.
> [yas] warning: keybinding "(rinari-minor-mode-map . C-c C-c C-b)"
> invalid for snippet "beamer_envargs" since keymap
> "rinari-minor-mode-map" does not (yet?) exist.
> Loading d:/programme/emacs/site-lisp/graphviz-dot-mode.el (source)...
> OVERVIEW
> Local Ispell dictionary set to nil
> Starting new Ispell process [default] ...
> File mode specification error: (error
> "d:\\programme\\Aspell\\bin\\aspell.exe did not output version line")
> Loading vc-git...
> Exporting to PDF...
> Exporting to LaTeX...
> Local Ispell dictionary set to nil
> Automatic display of crossref information was turned on
> Applying style hooks...
> Applying style hooks... done
> Local Ispell dictionary set to nil
> Local Ispell dictionary set to nil
> executing R code block...
> Type C-h m for help on ESS version 12.03
> -------------------cl-output------------------------------------------
>
>
>
>
> -------------------org-related-infos-----------------------------------
> Emacs : GNU Emacs 23.3.1 (i386-mingw-nt5.1.2600)
> of 2011-03-10 on 3249CTO
> Package: Org-mode version 7.8.06 (release_7.8.06.180.g22bfd)
>
> current state:
> ==============
> (setq
> org-export-preprocess-before-backend-specifics-hook
> '(org-inlinetask-export-handler)
> org-export-latex-after-initial-vars-hook '(org-beamer-after-initial-vars)
> org-export-latex-listings t
> org-speed-command-hook '(org-speed-command-default-hook
> org-babel-speed-command-hook)
> org-agenda-custom-commands '(("c" "conferences" ((tags "CONFERENCE"))
> ((org-tags-match-list-sublevels nil))
> ((org-columns-default-format "%DATE %LOCATION")))
> ("d" "Upcoming deadlines" agenda ""
> ((org-agenda-time-grid nil) (org-deadline-warning-days 365)
> (org-agenda-entry-types (quote (:deadline)))))
> ("W" "Weekly Review" ((agenda "" ((org-agenda-ndays 14))) (todo
> "WRITING"))))
> org-agenda-files '("e:/projects/habilitation/org/prHabilitation.org"
> "e:/projects/org/agendas/2011fall.org"
> "e:/projects/org/agendas/2011springterm.org"
> "e:/projects/org/agendas/SynRG.org"
> "e:/projects/org/agendas/capture.org" "e:/projects/org/agendas/d_2011a.org"
> "e:/projects/org/agendas/prDAAD-ipd-ma-divorce.org"
> "e:/projects/org/agendas/prDAAD-ma-simulation.org"
> "e:/projects/org/agendas/privat.org"
> "e:/projects/org/agendas/pu2012bbbook_basic_meta-analysis.org"
> "e:/projects/org/agendas/te2012sose.org"
> "e:/projects/org/agendas/te2012spring.org"
> "e:/projects/org/agendas/work.org")
> org-blocker-hook '(org-block-todo-from-children-or-siblings-or-parent)
> org-src-fontify-natively t
> org-babel-load-languages '((emacs-lisp . t) (maxima . t) (R . t)
> (python . t) (latex . t) (dot . t) (sh . t))
> org-ctrl-k-protect-subtree t
> org-completion-use-ido t
> org-metaup-hook '(org-babel-load-in-session-maybe)
> org-after-todo-state-change-hook '(org-clock-out-if-current)
> org-babel-tangle-lang-exts '(("python" . "py") ("maxima" . "max")
> ("emacs-lisp" . "el"))
> org-edit-src-content-indentation 0
> org-export-latex-format-toc-function 'org-export-latex-format-toc-default
> org-tab-first-hook '(yas/org-very-safe-expand
> org-hide-block-toggle-maybe org-src-native-tab-command-maybe
> org-babel-hide-result-toggle-maybe)
> org-src-mode-hook '(org-src-babel-configure-edit-buffer
> org-src-mode-configure-edit-buffer)
> org-confirm-shell-link-function 'yes-or-no-p
> org-export-first-hook '(org-beamer-initialize-open-trackers)
> org-agenda-before-write-hook '(org-agenda-add-entry-text)
> org-export-latex-packages-alist '(("" "color") ("" "listings"))
> org-default-notes-file "e:/projects/org/agendas/capture.org"
> org-directory "e:/projects/org/"
> org-babel-pre-tangle-hook '(save-buffer)
> org-cycle-hook '(org-cycle-hide-archived-subtrees
> org-cycle-hide-drawers org-cycle-show-empty-lines
> org-optimize-window-after-visibility-change)
> org-export-preprocess-before-normalizing-links-hook
> '(org-remove-file-link-modifiers)
> org-mode-hook '((lambda nil (make-variable-buffer-local (quote
> yas/trigger-key)) (setq yas/trigger-key [tab])
> (add-to-list (quote org-tab-first-hook) (quote
> yas/org-very-safe-expand)) (define-key yas/keymap [tab] (quote
> yas/next-field)))
> turn-on-org-cdlatex turn-on-auto-fill turn-on-font-lock
> #[nil "\300\301\302\303\304$\207" [org-add-hook
> change-major-mode-hook org-show-block-all append local] 5]
> #[nil "\300\301\302\303\304$\207" [org-add-hook
> change-major-mode-hook org-babel-show-result-all append local] 5]
> org-babel-result-hide-spec org-babel-hide-all-hashes
> turn-on-visual-line-mode)
> org-font-lock-hook '(org-inlinetask-fontify)
> org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point
> org-babel-execute-safely-maybe)
> org-confirm-elisp-link-function 'yes-or-no-p
> org-export-interblocks '((src org-babel-exp-non-block-elements))
> org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
> org-enforce-todo-dependencies t
> org-occur-hook '(org-first-headline-recenter)
> org-from-is-user-regexp nil
> org-export-preprocess-before-selecting-backend-code-hook
> '(org-beamer-select-beamer-code)
> org-confirm-babel-evaluate nil
> org-hierarchical-checkbox-statistics nil
> org-src-tab-acts-natively t
> org-export-latex-final-hook '(org-beamer-amend-header
> org-beamer-fix-toc org-beamer-auto-fragile-frames
> org-beamer-place-default-actions-for-lists)
> org-metadown-hook '(org-babel-pop-to-session-maybe)
> org-export-blocks '((src org-babel-exp-src-block nil) (export-comment
> org-export-blocks-format-comment t) (ditaa
> org-export-blocks-format-ditaa nil)
> (dot org-export-blocks-format-dot nil))
> )
> -------------------org-related-infos-----------------------------------
>
>
>
--
Eric Schulte
http://cs.unm.edu/~eschulte/
^ permalink raw reply [flat|nested] 3+ messages in thread* Re: Running "org-babel-tangle" and/or "org-export-as-pdf" in Emacs batch mode
2012-04-11 14:14 ` Eric Schulte
@ 2012-04-12 15:45 ` Bernd Weiss
0 siblings, 0 replies; 3+ messages in thread
From: Bernd Weiss @ 2012-04-12 15:45 UTC (permalink / raw)
To: Eric Schulte; +Cc: emacs-orgmode
On 11.04.2012 16:14, Eric Schulte wrote:
[...]
> Hi Bernd,
>
> I can't recreate this hanging issue locally (I don't have access to a
> windows box). This sounds like an ESS issue to me since ESS seems to be
> the hanging process. Perhaps a good first step would be to try to
> evaluate "(require 'ess) (R)" in a batch Emacs session without Emacs
> hanging. Once this is working then it should be clear how to run ESS
> sessions from code blocks.
>
Eric,
Thanks for your answer!
I am not sure if you had the following in mind but it again causes Emacs
to hang:
emacs -batch -l e:/config/.emacs --visit test.R --eval="(progn (require
'ess) (R) (ess-eval-buffer))"
This is test.R
---- test.R ------------------
pdf("testplot.pdf")
hist(rnorm(100))
dev.off()
---- test.R ------------------
I wrote another email to the ESS list, which is currently awaiting
moderator approval.
However, I am still wondering that I seem to be the first person to
stumble upon this problem...
Thanks,
Bernd
^ permalink raw reply [flat|nested] 3+ messages in thread
end of thread, other threads:[~2012-04-12 15:45 UTC | newest]
Thread overview: 3+ messages (download: mbox.gz / follow: Atom feed)
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2012-04-10 13:20 Running "org-babel-tangle" and/or "org-export-as-pdf" in Emacs batch mode Bernd Weiss
2012-04-11 14:14 ` Eric Schulte
2012-04-12 15:45 ` Bernd Weiss
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