Re: [Update Config] Babel changes -- security updates and final integration push

["Eric Schulte" <schulte.eric@gmail.com>]

Hi Tom,

Thanks for finding this error, the problem is that org-table is not
being required before the source-code block is run.  As a temporary fix
you can put

  (require 'org-table)

somewhere in your configuration.

As a long term solution I would want to talk to Carsten about how best
to ensure that org-table is required when org-babel has been required as
I believe it may require some change in the org require tree.

Carsten, do you have any suggestion?  I've tried a couple of approaches
but most result in a recursive require error.

Thanks -- Eric

"Thomas S. Dye" <tsd@tsdye.com> writes:

> Hi Eric,
>
> Thanks for all your work integrating Babel into Org-mode.
>
> I've pulled the latest Org-mode and changed my initialization
> according to your message.  I also pulled the latest starter-kit, so I
> think I have all the latest code.
>
> When I try to evaluate this code block I get an error that orgtbl-to-
> orgtbl is void.
>
> #+begin_src emacs-lisp
>   (list 1 (+ 2 3))
> #+end_src
>
> Here is a backtrace:
>
> Debugger entered--Lisp error: (void-function orgtbl-to-orgtbl)
>   (orgtbl-to-orgtbl (if (or ... ...) result (list result)) (quote
> (:fmt ...)))
>   (concat (orgtbl-to-orgtbl (if ... result ...) (quote ...)) "\n")
>   (insert (concat (orgtbl-to-orgtbl ... ...) "\n"))
>   (cond ((not ...) (insert ...) (goto-char beg) (when ... ...))
> ((member "file" result-params) (insert result)) ((member "html"
> result- 
> params) (insert ...)) ((member "latex" result-params) (insert ...))
> ((member "code" result-params) (insert ...)) ((or ... ...) (save- 
> excursion ...) (if ... ...)) (t (org-babel-examplize-region
> ... ... results-switches)))
>   (let ((existing-result ...) (results-switches ...) beg end) (when
> existing-result (goto-char existing-result) (save-excursion ... ...)
> (forward-line 1) (setq beg ...) (cond ... ... ...)) (setq results- 
> switches (if results-switches ... "")) (cond (... ... ... ...)
> (... ...) (... ...) (... ...) (... ...) (... ... ...) (t ...)) (setq
> end (if ... ... ...)) (when (and indent ... ...) (indent-rigidly beg
> end indent)))
>   (save-excursion (let (... ... beg end) (when existing-
> result ... ... ... ... ...) (setq results-switches ...) (cond
> ... ... ... ... ... ... ...) (setq end ...) (when ... ...)))
>   (if (and result-params (member "silent" result-params)) (progn
> (message ...) result) (when (and ... ...) (setq result ...)) (save- 
> excursion (let ... ... ... ... ... ...)) (message "finished"))
>   (if (= (length result) 0) (if (member "value" result-params)
> (message "No result returned by source block") (message "Source block
> produced no output")) (if (and result-params ...) (progn ... result)
> (when ... ...) (save-excursion ...) (message "finished")))
>   org-babel-insert-result((1 5) ("replace") ("emacs-lisp" "(list 1 (+
> 2 3))\n" ((:cache . "no") (:colnames . "no") (:comments . "")
> (:exports . "code") (:hlines . "yes") (:noweb . "yes") (:results .
> "replace") (:session . "none") (:shebang . "") (:tangle . "")) "" nil
> nil 0) nil 0 "emacs-lisp")
>   (if (and (not arg) new-hash (equal new-hash old-hash)) (save-
> excursion (goto-char ...) (end-of-line 1) (forward-char 1) (setq
> result ...) (message ...) result) (setq result (funcall cmd body
> params)) (if (eq result-type ...) (setq result ...))
> (org-babel-insert- 
> result result result-params info new-hash indent lang) (run-hooks
> (quote org-babel-after-execute-hook)) result)
>   (progn (fset (quote call-process-region) (function* ...)) (unless
> (fboundp cmd) (error "No org-babel-execute function for %s!" lang))
> (if (and ... new-hash ...) (save-excursion ... ... ... ... ... result)
> (setq result ...) (if ... ...) (org-babel-insert-result result result- 
> params info new-hash indent lang) (run-hooks ...) result))
>   (unwind-protect (progn (fset ... ...) (unless ... ...) (if ... ... ... ... ... ... result)) (if --cl-letf-bound-- (fset ... -- 
> cl-letf-save--) (fmakunbound ...)))
>   (let* ((--cl-letf-bound-- ...) (--cl-letf-save-- ...)) (unwind-
> protect (progn ... ... ...) (if --cl-letf-bound-- ... ...)))
>   (letf ((... ...)) (unless (fboundp cmd) (error "No org-babel-
> execute function for %s!" lang)) (if (and ... new-hash ...) (save-
> excursion ... ... ... ... ... result) (setq result ...) (if ... ...)
> (org-babel-insert-result result result-params info new-hash indent
> lang) (run-hooks ...) result))
>   (letf* ((... ...)) (unless (fboundp cmd) (error "No org-babel-
> execute function for %s!" lang)) (if (and ... new-hash ...) (save-
> excursion ... ... ... ... ... result) (setq result ...) (if ... ...)
> (org-babel-insert-result result result-params info new-hash indent
> lang) (run-hooks ...) result))
>   (flet ((call-process-region ... ...)) (unless (fboundp cmd) (error
> "No org-babel-execute function for %s!" lang)) (if (and ... new- 
> hash ...) (save-excursion ... ... ... ... ... result) (setq result
> ...) (if ... ...) (org-babel-insert-result result result-params  info
> new-hash indent lang) (run-hooks ...) result))
>   (unwind-protect (flet (...) (unless ... ...) (if
> ... ... ... ... ... ... result)) (setq call-process-region (quote
> org-babel-call-process-region-original)))
>   (let* ((info ...) (evaluation-confirmed ...) (lang ...) (params ...)
> (new-hash ...) (old-hash ...) (body ...) (result- 
> params ...) (result-type ...) (cmd ...) (dir ...) (default-
> directory ...) (org-babel-call-process-region-original ...) (indent
> ...) result) (unwind-protect (flet ... ... ...) (setq call- 
> process-region ...)))
>   org-babel-execute-src-block(nil ("emacs-lisp" "(list 1 (+ 2 3))
> \n" ((:cache . "no") (:colnames . "no") (:comments . "") (:exports
> . "code") (:hlines . "yes") (:noweb . "yes") (:results . "replace")
> (:session . "none") (:shebang . "") (:tangle . "")) "" nil nil 0))
>   (progn (org-babel-execute-src-block current-prefix-arg info) t)
>   (if info (progn (org-babel-execute-src-block current-prefix-arg
> info) t) nil)
>   (let ((info ...)) (if info (progn ... t) nil))
>   (if (not org-babel-no-eval-on-ctrl-c-ctrl-c) (let (...) (if info
> ... nil)) nil)
>   org-babel-execute-src-block-maybe()
>   run-hook-with-args-until-success(org-babel-execute-src-block-maybe)
>   (cond ((or ... org-occur-highlights org-latex-fragment-image-
> overlays) (and ... ...) (org-remove-occur-highlights) (org-remove-
> latex-fragment-image-overlays) (message "Temporary highlights/overlays
> removed from current buffer")) ((and ... ...) (funcall org-finish- 
> function)) ((run-hook-with-args-until-success ...)) ((or ... ...)
> (call-interactively ...)) ((org-on-target-p) (call-interactively ...))
> ((and ... ...) (call-interactively ...)) ((org-on-heading-p) (call- 
> interactively ...)) ((org-at-table\.el-p) (message "Use C-c ' to edit
> table.el tables")) ((org-at-table-p) (org-table-maybe-eval-formula)
> (if arg ... ...) (call-interactively ...)) ((or ... ...) (call- 
> interactively ...)) ((org-at-item-checkbox-p) (call-
> interactively ...)) ((org-at-item-p) (if arg ... ...)) ((save-
> excursion ... ...) (beginning-of-line 1) (save-excursion ...)) ((save-
> excursion ... ...) (cond ... ...)) ((org-clock-update-time-maybe)) (t
> (error "C-c C-c can do nothing useful at this location")))
>   (let ((org-enable-table-editor t)) (cond (... ... ... ... ...)
> (... ...) (...) (... ...) (... ...) (... ...) (... ...) (... ...)
> (... ... ... ...) (... ...) (... ...) (... ...) (... ... ...)
> (... ...) (...) (t ...)))
>   org-ctrl-c-ctrl-c(nil)
>   call-interactively(org-ctrl-c-ctrl-c nil nil)
>
>
> All the best,
> Tom
> On Jul 5, 2010, at 8:31 AM, Eric Schulte wrote:
>
>> Hi,
>>
>> I've just merged a large set of Babel related security measures and
>> layout/initialization updates into the master branch of the git
>> repository.
>>
>> These changes will require existing babel users to update their
>> configuration, see the following instructions for details -- even if
>> you
>> think you've read similar instructions before these are worth reading.
>> http://eschulte.github.com/babel-dev/DONE-document-configuration-changes-for-Babel-integration.html
>>
>> From here on out Babel development in the master branch will settle
>> down
>> along with the rest of the current Org-mode feature freeze.
>>
>> Thanks -- Eric
>>
>> please reply to this email with any question or problems you
>> encounter,
>> a text export of the contents of the web page linked above is provided
>> below.
>>
>> DONE document configuration changes for Babel integration
>> ==========================================================
>> Babel took the integration into Org-mode as an opportunity to do
>> some much needed house cleaning.  Most importantly we have
>> simplified the enabling of language support, and cleared out
>> unnecessary configuration variables -- which is great unless you
>> already have a working configuration under the old model.
>>
>> The most important changes regard the /location/ and /enabling/
>> of Babel (both core functionality and language specific support).
>>
>> Babel: Babel is now part of the core of Org-mode, so it is
>>     now loaded along with the rest of Org-mode.  That means that
>>     there is /no configuration/ required to enable the main
>>     Babel functionality.  For current users, this means that
>>     statements like
>>
>>     (require 'org-babel)
>>
>>     or
>>
>>     (require 'org-babel-init)
>>
>>     that may by lying around in your configuration must now be
>>     removed.
>>
>> load path: Babel (including all language specific files --
>>     aside from those which are located in the =contrib/=
>>     directory for reasons of licencing) now lives in the base of
>>     the Org-mode lisp directory, so /no additional directories/
>>     need to be added to your load path to use babel.  For Babel
>>     users this means that statements adding babel-specific
>>     directories to your load-path should now be removed from
>>     your config.
>>
>> language support: It is no longer necessary to require
>>     language specific support on a language-by-language basis.
>>     Specific language support should now be managed through the
>>     `org-babel-load-languages' variable.  This variable can be
>>     customized using the Emacs customization interface, or
>>     through the addition of something like the following to your
>>     configuration (note: any language not mentioned will /not/
>>     be enabled, aside from =emacs-lisp= which is enabled by
>>     default)
>>
>>     (org-babel-do-load-languages
>>      'org-babel-load-languages
>>      '((R . t)
>>        (ditaa . t)
>>        (dot . t)
>>        (emacs-lisp . t)
>>        (gnuplot . t)
>>        (haskell . nil)
>>        (ocaml . nil)
>>        (python . t)
>>        (ruby . t)
>>        (screen . nil)
>>        (sh . t)
>>        (sql . nil)
>>        (sqlite . t)))
>>
>>     Despite this change it is still possible to add
>>     language support through the use of =require=
>>     statements, however to conform to Emacs file-name
>>     regulations all Babel language files have changed
>>     prefix from =org-babel-*= to =ob-*=, so the require
>>     lines must also change e.g.
>>
>>     (require 'org-babel-R)
>>
>>     should be changed to
>>
>>     (require 'ob-R)
>>
>> We have eliminated the =org-babel-tangle-w-comments= variable as
>> well as the two main internal lists of languages, namely
>> - =org-babel-interpreters= and
>> - =org-babel-tangle-langs=
>>
>> so any config lines which mention those variables, can/should be
>> stripped out in their entirety.  This includes any calls to the
>> =org-babl-add-interpreter= function, whose sole purpose was to
>> add languages to the =org-babel-interpreters= variable.
>>
>> With those calls stripped out, we may still in some cases want to
>> associate a file name extension with certain languages, for
>> example we want all of our emacs-lisp files to end in a =.el=, we
>> can do this will the =org-babel-tangle-lang-exts= variable.  In
>> general you shouldn't need to touch this as it already has
>> defaults for most common languages, and if a language is not
>> present in org-babel-tangle-langs, then babel will just use the
>> language name, so for example a file of =c= code will have a =.c=
>> extension by default, shell-scripts (identified with =sh=) will
>> have a =.sh= extension etc...
>>
>> The configuration of /shebang/ lines now lives in header
>> arguments.  So the shebang for a single file can be set at the
>> code block level, e.g.
>>
>>
>>  #+begin_src clojure :shebang #!/usr/bin/env clj
>>    (println "with a shebang line, I can be run as a script!")
>>  #+end_src
>>
>> Note that whenever a file is tangled which includes a /shebang/
>> line, Babel will make the file executable, so there is good
>> reason to only add /shebangs/ at the source-code block level.
>> However if you're sure that you want all of your code in some
>> language (say shell scripts) to tangle out with shebang lines,
>> then you can customize the default header arguments for that
>> language, e.g.
>>
>>
>>  ;; ensure this variable is defined defined
>>  (unless (boundp 'org-babel-default-header-args:sh)
>>    (setq org-babel-default-header-args:sh '()))
>>
>>  ;; add a default shebang header argument
>>  (add-to-list 'org-babel-default-header-args:sh
>>               '(:shebang . "#!/bin/bash"))
>>
>> The final important change included in this release is the
>> addition of new security measures into Babel.  These measures are
>> in place to protect users from the accidental or uninformed
>> execution of code.  Along these lines /every/ execution of a code
>> block will now require an explicit confirmation from the user.
>> These confirmations can be stifled through customization of the
>> `org-confirm-babel-evaluate' variable, e.g.
>>
>>  ;; I don't want to be prompted on every code block evaluation
>>  (setq org-confirm-babel-evaluate nil)
>>
>> In addition, it is now possible to remove code block evaluation
>> form the =C-c C-c= keybinding.  This can be done by setting the
>> =org-babel-no-eval-on-ctrl-c-ctrl-c= variable to a non-nil value,
>> e.g.
>>
>>  ;; I don't want to execute code blocks with C-c C-c
>>  (setq org-babel-no-eval-on-ctrl-c-ctrl-c t)
>>
>> An additional keybinding has been added for code block
>> evaluation, namely =C-c C-v e=.
>>
>> Whew! that seems like a lot of effort for a /simplification/ of
>> configuration.
>>
>> _______________________________________________
>> 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