Re: [O] Emacs/ESS/org freezes/hangs on big data/ RAM(~256GB) processes when run in org/babel

2015-06-19 Thread Andreas Leha
Charles C. Berry ccbe...@ucsd.edu writes: On Thu, 18 Jun 2015, Andreas Leha wrote: Hi Chuck, [snip: all context about workflows for R projects] For example, the bioConductor package geneRxCluster [1] comes from an Org mode document that contains the C and R code as src blocks and a

Re: [O] Emacs/ESS/org freezes/hangs on big data/ RAM(~256GB) processes when run in org/babel

2015-06-19 Thread Andreas Leha
Hi Rainer, Rainer M Krug rai...@krugs.de writes: Charles C. Berry ccbe...@ucsd.edu writes: On Wed, 17 Jun 2015, William Denton wrote: On 17 June 2015, Xebar Saram wrote: I do alot of modeling work that involves using huge datasets and run process intensive R processes (such as complex

[O] Bug: [PATCH] org.texi: Fix typo

2015-06-19 Thread myq larson
* doc/org.texi (Diary-style sexp entries): Fix typo. TINYCHANGE --- doc/org.texi | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/org.texi b/doc/org.texi index 05d8666..5fc48d9 100644 --- a/doc/org.texi +++ b/doc/org.texi @@ -5925,7 +5925,7 @@ package@footnote{When working

Re: [O] Emacs/ESS/org freezes/hangs on big data/ RAM(~256GB) processes when run in org/babel

2015-06-19 Thread Charles C. Berry
On Thu, 18 Jun 2015, Andreas Leha wrote: Hi Chuck, [snip: all context about workflows for R projects] For example, the bioConductor package geneRxCluster [1] comes from an Org mode document that contains the C and R code as src blocks and a subtree with the vignette (Using geneRxCluster)

Re: [O] helm-bibtex questions

2015-06-19 Thread John Kitchin
Xebar Saram writes: Hi again Titus 2 quick questions that arose from using helm-bitex today extensively: how does one exclude in the search items? for example i want to search for xebar without keyword progress (I want to exclude in progress articles not published yet) Try this in the

Re: [O] helm-bibtex questions

2015-06-19 Thread John Kitchin
3.is it possible to ass an option to auto generate a bibkey for a selected citation based on user criteria such as author(date)short-title? Maintaining the content of the BibTeX file not really in the scope of helm-bibtex (I prefer to write my BibTeX entries by hand). Perhaps org-ref or

Re: [O] why org capture finalise asks for deleting bookmarks every time

2015-06-19 Thread Qiang Fang
Hi Kyle, Indeed bookmark-save-flag is 1 and org-capture-bookmark is t. I changed bookmark-save-flag to t and everything is working perfectly. Thank you! Qiang On Fri, Jun 19, 2015 at 3:14 PM, Kyle Meyer k...@kyleam.com wrote: Q godbles...@gmail.com wrote: When I finished typing in a capture

[O] What is the symbol/glyph that ... ?

2015-06-19 Thread Sharon Kimble
What is the symbol/glyph or whatever for clocking in on a task in the agenda please? The menu says that it is I, yet whatever I press on this UK keyboard I can't find it! I've tried I, 1, !, and even |, but none of them work! I can clock out okay using the keyboard, but just not able to clock in

Re: [O] org-babel-load-file fails with (wrong-type-argument stringp nil)

2015-06-19 Thread Marcelo de Moraes Serpa
*bump* does anyone have any idea? I'd like to save my current org setup, but looks like I'll need to do a clean install. Thanks! On Mon, Jun 15, 2015 at 12:43 PM, Marcelo de Moraes Serpa celose...@gmail.com wrote: Hi list, I'm using Org-mode version 8.2.10 (8.2.10-dist @

Re: [O] org-babel-load-file fails with (wrong-type-argument stringp nil)

2015-06-19 Thread Nick Dokos
Marcelo de Moraes Serpa celose...@gmail.com writes: *bump* does anyone have any idea? I'd like to save my current org setup, but looks like I'll need to do a clean install. Thanks! On Mon, Jun 15, 2015 at 12:43 PM, Marcelo de Moraes Serpa celose...@gmail.com wrote: Hi list,

Re: [O] another example of org being slow, with some analysis

2015-06-19 Thread Daniel Bausch
Daniel Bausch bau...@dvs.tu-darmstadt.de writes: I think it actually is not an org-mode problem but depends on how (count-lines 1 (point)) works, as it is using regex searches for the line endings. I can imagine that the regex parser for utf-8 can be inefficient. I just looked again at

Re: [O] another example of org being slow, with some analysis

2015-06-19 Thread Daniel Bausch
Hi! Nick Dokos ndo...@gmail.com writes: Eric S Fraga e.fr...@ucl.ac.uk writes: The output of the ELP profiler is here: ... org-goto-line 104 10.761145733 0.1034725551 .. org-current-line66 6.8422078910 0.1036698165 ... I find these two

Re: [O] another example of org being slow, with some analysis

2015-06-19 Thread Nicolas Goaziou
Hello, Daniel Bausch bau...@dvs.tu-darmstadt.de writes: Line 6000 is indeed quite lame. I have similar problems like Eric. A table recalculation at line 43868 takes about a minute at my quite fast machine. I also tracked that down to org-current-line. One interesting detail is that this

Re: [O] ox-koma-letter: how to use @@LaTeX:@@ specific commands in #+ directives

2015-06-19 Thread Eric S Fraga
On Thursday, 18 Jun 2015 at 23:01, Rasmus wrote: Eric S Fraga e.fr...@ucl.ac.uk writes: with this patch, exporting to koma-letter doesn't work for me. I've not investigated properly yet but thought I'd give you a heads up on this. Thanks. I don't really know where exactly it breaks with

Re: [O] exporter stopped working

2015-06-19 Thread Robert Klein
Hallo, are you using git master? If yes, this could be related to my issue described in issues with publishing to LaTeX... and follow-up mails. Could you test, if this happens with commit No. d1f9aa3a02c022baa9ded80ccca6589ba9d75669 ? (In org src do: git checkout

Re: [O] another example of org being slow, with some analysis

2015-06-19 Thread Nick Dokos
Eric S Fraga e.fr...@ucl.ac.uk writes: On Friday, 19 Jun 2015 at 08:19, Daniel Bausch wrote: [...] Line 6000 is indeed quite lame. I have similar problems like Eric. A table recalculation at line 43868 takes about a minute at my quite fast machine. I also tracked that down to

[O] exporter stopped working

2015-06-19 Thread Xebar Saram
Dear all the exporter seems to have stopped working in all configurations. i get the following error org-export-execute-babel-code: Wrong number of arguments: (lambda (reference-buffer) Execute all Babel blocks in current buffer. REFERENCE-BUFFER is the buffer containing a pristine copy of the

[O] help for summing column when exporting table

2015-06-19 Thread Charles Millar
How do you execute #+TBLFM: @$='(apply '+ '(@I$..@$));N%.2f while the following is being exported to LaTeX/pdf begin #+LATEX_CLASS: mysetup #+LaTeX: \setlength{\extrarowheight}{1.0ex} #+LaTeX: \begin{center} #+LaTeX: \textbf{SCHEDULE A}\\ #+LaTeX: \textbf{PRINCIPAL RECEIVED} #+LaTeX:

Re: [O] allow italic quote marks? org-emphasis-regexp-components

2015-06-19 Thread Myles English
Rasmus writes: Marcin Borkowski mb...@mbork.pl writes: On 2015-06-18, at 18:02, Kaushal kaushal.m...@gmail.com wrote: A quick google search comes up this these: http://tex.stackexchange.com/questions/83440/inputenc-error-unicode-char-u8-not-set-up-for-use-with-latex

Re: [O] helm-bibtex questions

2015-06-19 Thread Xebar Saram
Hi again Titus 2 quick questions that arose from using helm-bitex today extensively: how does one exclude in the search items? for example i want to search for xebar without keyword progress (I want to exclude in progress articles not published yet) is it possible to define default enter

[O] commit found, was: Re: ECM for: issues with publishing to LaTeX using #INCLUDE

2015-06-19 Thread Robert Klein
Hello, the first commit that doesn't work as expected is e900ebed08c444ad2813060195e9ece7f6bd910b ob-core: Small refactoring from Wednesday morning. Best regards Robert On Thu, 18 Jun 2015 20:51:10 +0200 Robert Klein rokl...@roklein.de wrote: Hello, now I've narrowed the org file(s)

Re: [O] another example of org being slow, with some analysis

2015-06-19 Thread Eric S Fraga
On Friday, 19 Jun 2015 at 08:19, Daniel Bausch wrote: [...] Line 6000 is indeed quite lame. I have similar problems like Eric. A table recalculation at line 43868 takes about a minute at my quite fast machine. I also tracked that down to org-current-line. One interesting detail is that

Re: [O] another example of org being slow, with some analysis

2015-06-19 Thread Daniel Bausch
Eric S Fraga e.fr...@ucl.ac.uk writes: On Friday, 19 Jun 2015 at 08:19, Daniel Bausch wrote: [...] Line 6000 is indeed quite lame. I have similar problems like Eric. A table recalculation at line 43868 takes about a minute at my quite fast machine. I also tracked that down to

Re: [O] no org-export-to-html-and-open since distribution, switch

2015-06-19 Thread Sven Ehret
Hi Nick, you deserve a medal. As I did experiment with xdg-open (never needed to fiddle with that before), adding a line to my mailcap file (also never was manually edited before. Perhaps once, for mc) and restarting emacs made the browser open again. A thousand thanks to you, not only for solving

Re: [O] another example of org being slow, with some analysis

2015-06-19 Thread Eric S Fraga
On Friday, 19 Jun 2015 at 10:28, Daniel Bausch wrote: [...] If anyone could give me a hint how to reliably set the preferred (or internal) encoding I could check wether it might have something to do with the system locale. I have (only) the following encoding related settings in my

Re: [O] another example of org being slow, with some analysis

2015-06-19 Thread Eric S Fraga
On Friday, 19 Jun 2015 at 09:53, Nick Dokos wrote: [...] What is the setting of cache-long-scans you are using? Does it differ on the two laptops? Ivan Andrus suggested setting it to nil, but it seems that for this case, leaving it at t (the default) should be much faster. But there may be

Re: [O] ox-koma-letter: how to use @@LaTeX:@@ specific commands in #+ directives

2015-06-19 Thread Eric S Fraga
On Thursday, 18 Jun 2015 at 23:01, Rasmus wrote: Eric S Fraga e.fr...@ucl.ac.uk writes: with this patch, exporting to koma-letter doesn't work for me. I've not investigated properly yet but thought I'd give you a heads up on this. Thanks. I don't really know where exactly it breaks with

[O] why org capture finalise asks for deleting bookmarks every time

2015-06-19 Thread Q
When I finished typing in a capture buffer, I hit C-c C-c, this is what I get in the message buffer, looks like emacs is trying to save all opened file and then delete backup of bookmarks. How do I avoid all this? Thank you for your help! Template key: Clipboard pasted as level 2 subtree Saving

[O] tentative patch Re: commit found, was: Re: ECM for: issues with publishing to LaTeX using #INCLUDE

2015-06-19 Thread Robert Klein
Hello, when I change a `symbol-value' in the commit back to `eval', export seems to work again. Patch is attached. Best regards Robert On Fri, 19 Jun 2015 09:51:40 +0200 Robert Klein rokl...@roklein.de wrote: Hello, the first commit that doesn't work as expected is

Re: [O] no org-export-to-html-and-open since distribution switch

2015-06-19 Thread Sven Ehret
Hi! The truth is, I not only switched from Mint to Arch, but also from Cinnamon to i3. So right, this should be taken into account. I have since been able to solve the problem by adding configuration to ~/.mailcap. Thanks! Best, Sven. Am 18.06.2015 um 17:42 schrieb Rasmus: Hi, What is your

Re: [O] why org capture finalise asks for deleting bookmarks every time

2015-06-19 Thread Kyle Meyer
Q godbles...@gmail.com wrote: When I finished typing in a capture buffer, I hit C-c C-c, this is what I get in the message buffer, looks like emacs is trying to save all opened file and then delete backup of bookmarks. How do I avoid all this? What are bookmark-save-flag and