Re: [O] org babel before excute hook
if anyone is interested in this, a simple defadvice appears to be a good option, I put (defadvice org-babel-execute-maybe (around org-babel-stop-on-collision) stop execution of result file defined more than once (let ((info (org-babel-get-src-block-info))) (setq result-file (cdr (assoc :file (nth 2 info (if (save-excursion (goto-char 0) (re-search-forward (concat :file + result-file) nil t) (re-search-forward (concat :file + result-file) nil t)) (error (concat result-file defined in more than one source block)) ad-do-it))) (ad-activate 'org-babel-execute-maybe) in my .emacs and appear to get the desired functionality 2013/10/13 Samuel Wales samolog...@gmail.com In case it helps, there is org-confirm-babel-evaluate. (But I have not found it to be useful, because it does not seem to place point in a place where you can check properties, etc.) Samuel -- The Kafka Pandemic: http://thekafkapandemic.blogspot.com The disease DOES progress. MANY people have died from it. ANYBODY can get it. Denmark: free Karina Hansen NOW.
Re: [O] org babel before excute hook
Is it possible to add a function to org-ctrl-c-ctrl-c-hook without patching ob-core.el? If I just add something like (add-hook 'org-ctrl-c-ctrl-c-hook 'org-babel-stop-if-file-collision) in my .emacs I notice that my addition gets overwritten later via the autoloads (I think) that are defined in ob-core.el.. 2013/10/12 Charles Berry ccbe...@ucsd.edu John Kitchin jkitchin at andrew.cmu.edu writes: I have a related kind of problem. When preparing notes for a class, I may end up with 70 code blocks in an org file, many of which create graphics. I am always worried about accidentally using the same filename and overwriting a graphic from an earlier block. A unique, but reproducible filename would be sufficient for my needs. Header arg values can be elisp calls. You can use `make-temp-file'. So every time this block is executed, a new file is created and the file link is added to the results. #+BEGIN_SRC R :results output append :file (make-temp-file temp) cat(date(),\n) #+END_SRC #+RESULTS: [[file:/var/folders/kb/2hchpbyj7lb6z76l0q73w_fhgn/T/temp302IjV]] [[file:/var/folders/kb/2hchpbyj7lb6z76l0q73w_fhgn/T/temp3028Lu]] See `temporary-file-directory', too, if you want to use this, as the default may not be what you intend. You might want to use this: #+BEGIN_SRC emacs-lisp (defun local-tfile (file) (let ((temporary-file-directory .)) (make-temp-file file))) #+END_SRC Then the files go in the local directory when this is executed: #+BEGIN_SRC R :file (local-tfile tfile) :results output append cat(date(),\n) #+END_SRC You might not want `append' in this case. HTH, Chuck [rest deleted]
Re: [O] org babel before excute hook
I thought about temp files, but that makes the file names cryptic which is inconvenient for communication without people outside org.. also, I tend recompile figures many times which would cause a lot of cluttering files that are hard to delete since you don't know which file is the one currently linked in your org file... Anyway, I made this instead which appears to work as I intended (defun org-babel-about-to-overwrite-file () (let ((info (org-babel-get-src-block-info))) (setq result-file (cdr (assoc :file (nth 2 info (if (save-excursion (goto-char 0) (re-search-forward (concat :file + result-file) nil t) (re-search-forward (concat :file + result-file) nil t)) (message (concat result-file defined in more than one source block)) (org-babel-execute-maybe (add-hook 'org-ctrl-c-ctrl-c-hook 'org-babel-about-to-overwrite-file) 2013/10/12 Charles Berry ccbe...@ucsd.edu John Kitchin jkitchin at andrew.cmu.edu writes: I have a related kind of problem. When preparing notes for a class, I may end up with 70 code blocks in an org file, many of which create graphics. I am always worried about accidentally using the same filename and overwriting a graphic from an earlier block. A unique, but reproducible filename would be sufficient for my needs. Header arg values can be elisp calls. You can use `make-temp-file'. So every time this block is executed, a new file is created and the file link is added to the results. #+BEGIN_SRC R :results output append :file (make-temp-file temp) cat(date(),\n) #+END_SRC #+RESULTS: [[file:/var/folders/kb/2hchpbyj7lb6z76l0q73w_fhgn/T/temp302IjV]] [[file:/var/folders/kb/2hchpbyj7lb6z76l0q73w_fhgn/T/temp3028Lu]] See `temporary-file-directory', too, if you want to use this, as the default may not be what you intend. You might want to use this: #+BEGIN_SRC emacs-lisp (defun local-tfile (file) (let ((temporary-file-directory .)) (make-temp-file file))) #+END_SRC Then the files go in the local directory when this is executed: #+BEGIN_SRC R :file (local-tfile tfile) :results output append cat(date(),\n) #+END_SRC You might not want `append' in this case. HTH, Chuck [rest deleted]
[O] org babel before excute hook
I collaborate with different people on the same orgfile which contains many source blocks that generate graphics by e.g. :results graphics abc.pdf It can happen that I or someone else accidentally create another independent source block that overwrites my abc.pdf which is of course very bad. I would like to add functionality so that org-babel-execute-src-block checks if in :results graphics FILE, FILE is already referred to by another source block and if so refuse to evaluate. However, I only see a org-babel-after-execute-hook but no org-babel-before-execute-hook any reason for this? I could try to write a patch but thought I'd ask first. or if there is an even better approach to avoid overwriting output from different source blocks.. //Henning
[O] feature request: re-compute cache without evaluation
Hi, I write many source blocks that take a fairly long time to execute (several minutes). Sometimes I find myself wanting to do cosmetic changes to the code, that I know (for sure) do not change the output, after the first evaluation. Unfortunately, after having made these changes the cache obviously does not match the code anymore and I have to re-evaluate to update the cache. I know it goes against the strict 'reproducible research' idea but still I would like to be able to re-compute the cache without actually evaluating the block as it is not efficient to re-evaluate for the sole purpose of updating the cache. What do you think? -- /Henning
Re: [O] feature request: re-compute cache without evaluation
ah, this was easy, thanks! 2012/4/12 Eric Schulte eric.schu...@gmx.com: Henning Redestig henning@googlemail.com writes: Hi, I write many source blocks that take a fairly long time to execute (several minutes). Sometimes I find myself wanting to do cosmetic changes to the code, that I know (for sure) do not change the output, after the first evaluation. Unfortunately, after having made these changes the cache obviously does not match the code anymore and I have to re-evaluate to update the cache. I know it goes against the strict 'reproducible research' idea but still I would like to be able to re-compute the cache without actually evaluating the block as it is not efficient to re-evaluate for the sole purpose of updating the cache. What do you think? Press C-c C-v a (org-babel-sha1-hash) in the code block, then manually replace the original hash with the hash returned by that function. -- Eric Schulte http://cs.unm.edu/~eschulte/ -- /Henning
Re: [O] org-mode fontification error [6 times]
Better now but still some issues here, now if I start a new org buffer and type s [TAB] to complete the source block, I get org-mode fontification error again. 2012/4/4 Bastien b...@gnu.org: Hi Nick, Nick Dokos nicholas.do...@hp.com writes: Confirmed. It only happens when you start typing into an empty buffer. Looks like an off-by-one error in org.el:org-fontify-meta-lines-and-blocks-1, aroung line 5487: , | ;; just any other in-buffer setting, but not indented | (add-text-properties | beg (1+ (match-end 0)) | '(font-lock-fontified t face org-meta-line)) ` The second arg should probably be just (match-end 0). That's correct. I first thought (min (point-max) (1+ (match-end 0))) would have been safer, but I really don't see why the 1+. Please confirm this is fixed. Thanks, -- Bastien -- /Henning
Re: [O] org-mode fontification error [6 times]
+1 on this, I get 'org-mode fontification error' all the time after having typed just #+ in an org buffer. with org 7.8.08 and emacs 23.1.50.1 and running with emacs -Q 2011/8/18 Leo sdl@gmail.com: On 2011-08-18 15:22 +0800, Bastien wrote: Just a heads-up. I saw this in my *message* buffer. I don't know how it happened. Is this with emacs -Q? I am unable to reproduce this with emacs-23.3.1 and emacs-24.0.50.1. It is in my normal running emacs session. I haven't found a reproduction recipe. But I have been using the same org-mode setup for years. Leo -- /Henning
[Orgmode] org babel and alternative output file when using +call
Dear list, When I do #+source: test(myarg=blabla) #+begin_src R :session :file test.pdf plot(1:10, main=myarg) #+end_src I get the expected result: #+results: test [[file:test.pdf]] but if I later do #+call: test(myarg=hiho) :file test2.pdf I still get a file named according to the header argument specified in the original source block: #+results: test(myarg=hiho) [[file:test.pdf]] instead of what I hoped for: #+results: test(myarg=hiho) [[file:test2.pdf]] Is this intended? I think it would be very useful if I could change the file name in '+calls' like this to get different plots for different arguments. Using: GNU Emacs 23.1.50.1 (x86_64-pc-linux-gnu, GTK+ Version 2.18.0) of 2009-09-27 on crested, modified by Debian Org-mode version 7.01trans Best regards, -- /Henning Redestig Metabolome Informatics Unit | Yokohama RIKEN Plant Science Center ___ 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
