Re: [Orgmode] [Update Config] Babel changes -- security updates and final integration push
Hi Eric, On Jul 6, 2010, at 3:09 AM, Eric Schulte wrote: 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. You are using only a few entry points from org-table, and I have just added these to the autoloads. This fixes the current issue. The require tree of Org could be better, but this is too complex an issue for the moment. - Carsten Thanks -- Eric Thomas S. Dye t...@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 ... ... ... ... ...
[Orgmode] [Update Config] Babel changes -- security updates and final integration push
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
Re: [Orgmode] [Update Config] Babel changes -- security updates and final integration push
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 .
Re: [Orgmode] [Update Config] Babel changes -- security updates and final integration push
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 t...@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 ... ... ... ... ... ...
Re: [Orgmode] [Update Config] Babel changes -- security updates and final integration push
Thanks Eric, That works. Tom On Jul 5, 2010, at 3:09 PM, Eric Schulte wrote: 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 t...@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))
