Re: [O] [babel] return file from R

2016-01-19 Thread Andreas Leha
Hi Chuck, "Charles C. Berry" <ccbe...@ucsd.edu> writes: > On Tue, 19 Jan 2016, Andreas Leha wrote: > >> Hi Chuck, >> > > [snip] > >> I've tested your patch and it seems to work. But it does seem to need >> an analogous change in org-babel-R

Re: [O] [babel] return file from R

2016-01-19 Thread Andreas Leha
Hi Chuck, Thanks for following that up. And sorry for the long delay. "Charles C. Berry" <ccbe...@ucsd.edu> writes: > On Thu, 17 Dec 2015, Andreas Leha wrote: > >> Hi all, >> >> I think there is a bug in the handling of results of R src blocks. What &g

Re: [O] Changing org-block background with org-src-fontify-natively

2016-01-15 Thread Andreas Leha
Hi, John Kitchin writes: > It doesn't sounds like there is a way to do language specific colors. > Karl Voit writes: >> * Nick Dokos wrote: [ ... ] >> >> It would be fine to have both: org-src-fontify-natively *and* a >> background colour I can

[O] [babel] return file from R

2015-12-17 Thread Andreas Leha
Hi all, I think there is a bug in the handling of results of R src blocks. What is the suggested way to make an R block return a link to a file? The obvious way appends a newline character to the file link (which is broken because of that). Here is an example: --8<---cut

[O] cache and lint

2015-12-17 Thread Andreas Leha
Hi all, I just had an error (something including "search" and "wrong side" ...) during org-lint. As it turned out this error went away after I ran `org-element-cache-reset'. Hence my question: Would it make sense to include running `org-element-cache-reset' into `org-lint'? Best, Andreas

[O] [lint] imagemagick

2015-12-17 Thread Andreas Leha
Hi all, I get a spurious linting warning , | high Unknown header argument ":imagemagick" ` While that header argument should be valid for latex blocks. Regards, Andreas

Re: [O] [lint] imagemagick

2015-12-17 Thread Andreas Leha
Hi Nicolas, Nicolas Goaziou <m...@nicolasgoaziou.fr> writes: > Hello, > > Andreas Leha <andreas.l...@med.uni-goettingen.de> writes: > >> I get a spurious linting warning >> , >> | high Unknown header argument ":imagemagick" >> `

Re: [O] cache and lint

2015-12-17 Thread Andreas Leha
Hi Nicolas, Nicolas Goaziou <m...@nicolasgoaziou.fr> writes: > Hello, > > Andreas Leha <andreas.l...@med.uni-goettingen.de> writes: > >> I just had an error (something including "search" and "wrong side" ...) >> during org-lint. As it tur

Re: [O] [lint] imagemagick

2015-12-17 Thread Andreas Leha
Hi Nicolas, Nicolas Goaziou <m...@nicolasgoaziou.fr> writes: > Andreas Leha <andreas.l...@med.uni-goettingen.de> writes: > >> I am not sure about the possible values, though. babel header arguments >> usually take 'yes' and 'no' as values for TRUE and FALSE. >

Re: [O] [babel] return file from R

2015-12-17 Thread Andreas Leha
Hi Chuck, "Charles C. Berry" <ccbe...@ucsd.edu> writes: > On Thu, 17 Dec 2015, Andreas Leha wrote: > >> Hi all, >> >> I think there is a bug in the handling of results of R src blocks. What >> is the suggested way to make an R block return a link to

Re: [O] Problem with org-export--delete-comments

2015-12-17 Thread Andreas Leha
Hi Nicolas and Ethan, Nicolas Goaziou writes: > Hello, > > Ethan Ligon writes: > >> I've long used the following construction for displayed equations in org >> # >> \[ >> u_i(c)=p_i\lambda >> \] >> # >> which (i) gives nice space for reading

Re: [O] Problem with org-export--delete-comments

2015-12-17 Thread Andreas Leha
Hi Nicolas, Nicolas Goaziou <m...@nicolasgoaziou.fr> writes: > Hello, > > Andreas Leha <andreas.l...@med.uni-goettingen.de> writes: > >> I agree that the paragraph should not be broken in the exported >> document. There are also other use cases for com

[O] [babel] noweb reference with default values

2015-12-14 Thread Andreas Leha
Hi all, I'd like to hear your ideas on how to include noweb references to code blocks in a way that the default values are used as parameter values. Here is a little example: #+PROPERTY: header-args:R :session *testR* The background is that I like to use Org mode table to record small data.

Re: [O] [babel] noweb reference with default values

2015-12-14 Thread Andreas Leha
Hi Chuck, "Charles C. Berry" <ccbe...@ucsd.edu> writes: > On Mon, 14 Dec 2015, Andreas Leha wrote: > >> Hi all, >> >> I'd like to hear your ideas on how to include noweb references to code >> blocks in a way that the default values are used as pa

Re: [O] export subtree

2015-12-10 Thread Andreas Leha
Hi Skip, Skip Collins writes: > The export dispatcher allows me to export only the current subtree. > This is nice, but I would like to avoid having to put point in just > the right place before invoking the dispatcher. I have a document with > lots of things in it. One

Re: [O] export subtree

2015-12-10 Thread Andreas Leha
Hi Skip, Skip Collins <skip.coll...@gmail.com> writes: > Andreas Leha <andreas.l...@med.uni-goettingen.de> wrote: >>> The export dispatcher allows me to export only the current subtree. >>> This is nice, but I would like to avoid having to put point in just &g

Re: [O] Jumping between source blocks in a file

2015-12-02 Thread Andreas Leha
Hi Andrew, Martin Yrjölä writes: > Hi Andrew! > > Andrew Kirkpatrick writes: > >> If this is deemed useful, I'm happy to make changes suitable for >> inclusion in the project. > > Thanks for sharing! I would certainly want these functions included in > org-mode by

Re: [O] Jumping between source blocks in a file

2015-12-02 Thread Andreas Leha
Rainer M Krug <rai...@krugs.de> writes: > Rainer M Krug <rai...@krugs.de> writes: > >> Andreas Leha <andreas.l...@med.uni-goettingen.de> writes: >> >>> Hi Andrew, >>> >>> Martin Yrjölä <martin.yrj...@gmai

Re: [O] LATEX text in figure environment

2015-11-24 Thread Andreas Leha
Hi Rainer, Rainer M Krug writes: > Hi > > I want to add a todo note (from the todonotes package) in a figure > environment. What I want should look as follow, so that the to note sits > in the environment (based on [http://tex.stackexchange.com/a/256802/6941] > ): > > , > |

Re: [O] LATEX text in figure environment

2015-11-24 Thread Andreas Leha
Rainer M Krug writes: > Rasmus writes: > >> Rainer M Krug writes: >> >>> Hi >>> >>> I want to add a todo note (from the todonotes package) in a figure >>> environment. What I want should look as follow, so that the to note sits >>> in the

Re: [O] @@latex:...@@ syntax - where can I find info on it?

2015-11-24 Thread Andreas Leha
Hi Rainer, Rainer M Krug writes: > Hi > > I read at tha moment a lot of mails here regarding the @@latex:...@@ (or > @@html:...@@) syntax. I understand d=that these fragments are only > inserted when the corresponding backend is used - correct? > > Where can I find further

Re: [O] Org Babel resolution of `:var` value reference inconsistent

2015-11-05 Thread Andreas Leha
Hi Nicolas, Nicolas Goaziou <m...@nicolasgoaziou.fr> writes: > Hello, > > Martin Carlé <m...@aiguphonie.com> writes: > >> On 2015-11-04 Wed 14:14, Andreas Leha wrote: >> >>> ,-

Re: [O] Org Babel resolution of `:var` value reference inconsistent

2015-11-04 Thread Andreas Leha
Hi Nick, Nick Dokos <ndo...@gmail.com> writes: > Andreas Leha <andreas.l...@med.uni-goettingen.de> writes: > >> ... >> So, to me it is more surprising that the manual execution works. For >> instance, I might have two tables with the same name. Then, COM

Re: [O] Org Babel resolution of `:var` value reference inconsistent

2015-11-02 Thread Andreas Leha
Hi myq, myq writes: > Sometime since Org version 8.3beta and now, the way Org Babel resolves > the value of the `:var` header argument when assigned to a reference has > changed. > > Previously, the following would work when exporting: > > * test > > #+BEGIN_SRC R :var

Re: [O] problems with export and :cache

2015-10-30 Thread Andreas Leha
Hi all, As a follow-up. The caching produces un-expected results for call lines 'in the other direction' as well: Changes in the arguments to the called code block do not invalidate the cache. --8<---cut here---start->8--- * Test Cached Export ** A long

Re: [O] problems with export and :cache

2015-10-29 Thread Andreas Leha
Hi Aaron, Aaron Ecay <aarone...@gmail.com> writes: > Hi Andreas, > > 2015ko urriak 28an, Andreas Leha-ek idatzi zuen: >> >> Hi all, >> >> Andreas Leha <andreas.l...@med.uni-goettingen.de> writes: >>> Hi all, >>> >>&g

Re: [O] problems with export and :cache

2015-10-29 Thread Andreas Leha
Hi Thomas, Thomas S. Dye <t...@tsdye.com> writes: > Aloha all, > > Aaron Ecay <aarone...@gmail.com> writes: > >> Hi Nicolas, >> >> 2015ko urriak 29an, Nicolas Goaziou-ek idatzi zuen: >>> >>> Andreas Leha <andreas.l...@med.uni-g

[O] [babel] :eval and #+call lines

2015-10-29 Thread Andreas Leha
Hi all, Since this is not related to caching, I post this as a separate question from [1]. I want to argue that specifying ':eval never' as argument to a #+call line should transitively apply to the called block as well. Here is the example: --8<---cut

[O] problems with export and :cache

2015-10-28 Thread Andreas Leha
Hi all, babel's :cache seems to be ignored during export. At least on #+call lines. In the example below the caching works fine for interactive evaluation, i.e. C-c C-c on the #+call line returns immediately. If I export the subtree with the #+call line, however, the code block gets executed

Re: [O] problems with export and :cache

2015-10-28 Thread Andreas Leha
Hi all, Andreas Leha <andreas.l...@med.uni-goettingen.de> writes: > Hi all, > > babel's :cache seems to be ignored during export. At least on #+call > lines. > > In the example below the caching works fine for interactive evaluation, > i.e. C-c C-c on the #+ca

Re: [O] org-reveal questions

2015-10-23 Thread Andreas Leha
Hi, Fabrice Popineau writes: > I switched to org-reveal from beamer. > Beamer clutters your slides with too much markup. > (I ended up with much more markup than text in my slides). ... which of course can be changed by customizing the theme ... It seems that to

Re: [O] Bug: LaTeX export: internal target + \autoref{} broken [8.3.2 (8.3.2-elpaplus @ /home/myq/.emacs.d/elpa/org-plus-contrib-20150929/)]

2015-10-21 Thread Andreas Leha
Hi ☕◦m̰̱̐y̿q̟̽, ☕◦m̰̱̐y̿q̟̽ writes: > > Given the following Org document: > > , > | #+MACRO: refp \autoref{$1}, \autopageref{$1} > | > | > | * section > | > | Please see the results in {{{refp(sec:info)}}}. > | > | * info<> > | > | The results are here. > ` > > When

[O] order in agenda

2015-10-21 Thread Andreas Leha
Hi all, I am aware, that overlapping events cannot be displayed really well in the (linear) agenda view. But if I have two events starting at the same (day and) time, I'd prefer the one with the later end time to appear always below the other one. Is that already achievable? Here is an excerpt

Re: [O] order in agenda

2015-10-21 Thread Andreas Leha
Hi Nick, Nick Dokos <ndo...@gmail.com> writes: > Andreas Leha <andreas.l...@med.uni-goettingen.de> writes: > >> I am aware, that overlapping events cannot be displayed really well in >> the (linear) agenda view. But if I have two events starting at the same >>

Re: [O] Bug in latex export figure labels?

2015-10-16 Thread Andreas Leha
Nicolas Goaziou writes: > Hello, > > garj...@garjola.net writes: > >> I am having issues when exporting to LaTeX using labels in figures. The >> following snippet >> >>> > > >>> #+CAPTION: Comparison

Re: [O] SOLVED: LaTeX equation align in orgmode?

2015-09-30 Thread Andreas Leha
Rainer M Krug writes: > Eric S Fraga writes: > >> On Monday, 28 Sep 2015 at 21:10, Rainer M Krug wrote: >>> Hi >>> >>> I would need in a document several equations which are aligned as in >>> http://tex.stackexchange.com/a/167908/6941 >> >> I use align all

Re: [O] LaTeX equation align in orgmode?

2015-09-28 Thread Andreas Leha
Hi Rainer, Rainer M Krug writes: > Hi > > I would need in a document several equations which are aligned as in > http://tex.stackexchange.com/a/167908/6941 > > How can I use the following latex formula in orgmode? > > \begin{proof} The proof is a follows: > \begin{align} >

Re: [O] Beamer :BEAMER_envargs: [allowframebreaks] not working

2015-09-28 Thread Andreas Leha
Hi Jeremie, Jeremie Juste writes: > Hello, > > It's my first post here finally. Most of my questions were answered > before by you.:). I have the lastest version of org mode and search > with the best of my abilities if any had the same issue but couldn't > find anything.

Re: [O] export: noweb blocks substituted versus verbatim ?

2015-09-26 Thread Andreas Leha
Hi Brian, Brian Beckman writes: > Hello -- I have a situation where some code blocks with noweb references in > them <> are substituted inline when I export the document, and > other code blocks with noweb references, are copied verbatim into the > exported PDF. I do not

Re: [O] Tangle including code generating graphics for :results graphics

2015-09-24 Thread Andreas Leha
Hi Rainer, Rainer M Krug writes: > Hi > > Is it possible to tangle an R code block including the code which is > generating the graphs when using =:results graphics= ? > > I would like to tangle these code blocks generating the graphs as I > would like to have a script which I

Re: [O] tangle on export

2015-09-24 Thread Andreas Leha
Hi Alan, Alan Schmitt <alan.schm...@polytechnique.org> writes: > Hi Andreas, > > On 2015-09-24 14:14, Andreas Leha <andreas.l...@med.uni-goettingen.de> writes: > >> if all of this is for a single block, you can get away quite cheaply >> with sth along (un

Re: [O] tangle on export

2015-09-24 Thread Andreas Leha
Hi Alan, Rainer M Krug writes: > Alan Schmitt writes: > >> Hello, >> >> I have a question I feel is very basic but I did not find the answer in >> the manual. How can I trigger the tangling of a block upon export. > > Tangling and exporting are

Re: [O] [BUG] outshine and emacs 25.0.5.1 - Was: [error] orgmode git on emacs 25 - HEAD - org-global-cycle

2015-09-10 Thread Andreas Leha
Hi Rainer, Rainer M Krug writes: > Kyle Meyer writes: > >> Hi, >> >> Rainer M Krug writes: >> >>> Hi >>> >>> when doing global cycling using org in emacs 25.0.50.1, I get an "Before >>> first heading" error (see backtrace below). >>> >>> It

Re: [O] Block level specification for tex code html export method

2015-09-04 Thread Andreas Leha
Hi Nicolas, Nicolas Goaziou <m...@nicolasgoaziou.fr> writes: > Hello, > > Andreas Leha <andreas.l...@med.uni-goettingen.de> writes: > >> This macro is from Eric Schulte initially. And I guess I would be out >> of luck adapting it to new Org mode versions as

Re: [O] Block level specification for tex code html export method

2015-09-04 Thread Andreas Leha
Nicolas Goaziou <m...@nicolasgoaziou.fr> writes: > Andreas Leha <andreas.l...@med.uni-goettingen.de> writes: > >> Seems to work fine! >> >> Just note, that it works for me only after exporting >> (when tested under emacs -Q). > > `org-export-current

Re: [O] Block level specification for tex code html export method

2015-09-03 Thread Andreas Leha
il, or your html export will fail > silently (showing success on emacs, but no images generated). > > [1] http://tex.stackexchange.com/a/232739 > > -- > > Mail from Haochen Xie > > On Thu, Sep 3, 2015 at 9:30 PM, Andreas Leha > <andreas.l...@med.uni-goettinge

Re: [O] Block level specification for tex code html export method

2015-09-03 Thread Andreas Leha
Hi Eric, Thanks for following that up! Eric S Fraga <e.fr...@ucl.ac.uk> writes: > On Thursday, 3 Sep 2015 at 13:30, Andreas Leha wrote: >> Hi Alan, >> >> Glad you like the example. >> >> Three things: >> 1. It still works for me ;-) > > Andrea

Re: [O] Block level specification for tex code html export method

2015-09-03 Thread Andreas Leha
exported both to html and pdf, and in both cases I would have > a reference to the png instead of the svg/tikz code. > > I’m afraid I’m missing a step. Do you see what I’m doing wrong? > > Thanks, > > Alan > > On 2015-08-12 10:50, Andreas Leha <andreas.l...@med

[O] export (to gfm) with file local variables

2015-08-21 Thread Andreas Leha
Hi all, How can I make my toy sample file below export properly to github flavoured markdown (using ox-gfm)? (Of course including the file local variables in exported *.md file...) If I try I get , | hack-local-variables: Malformed local variable line: ` Thanks, Andreas PS: the

Re: [O] export (to gfm) with file local variables

2015-08-21 Thread Andreas Leha
I forgot... Andreas Leha andreas.l...@med.uni-goettingen.de writes: Hi all, How can I make my toy sample file below export properly to github flavoured markdown (using ox-gfm)? (Of course including the file local variables in exported *.md file...) ... and without having them apply

Re: [O] user-error: No language for src block: (unnamed) when running `org-icalendar-combine-agenda-files`

2015-08-21 Thread Andreas Leha
Hi, Ista Zahn istaz...@gmail.com writes: On Fri, Aug 21, 2015 at 10:20 AM, Nicolas Goaziou m...@nicolasgoaziou.fr wrote: Ista Zahn istaz...@gmail.com writes: Unless you've restored sanity by setting org-export-babel-evaluate to nil. Personally I think this is not a good default. Source

Re: [O] export (to gfm) with file local variables

2015-08-21 Thread Andreas Leha
Hi Nick, Nick Dokos ndo...@gmail.com writes: Andreas Leha andreas.l...@med.uni-goettingen.de writes: I forgot... Andreas Leha andreas.l...@med.uni-goettingen.de writes: Hi all, How can I make my toy sample file below export properly to github flavoured markdown (using ox-gfm

Re: [O] export (to gfm) with file local variables

2015-08-21 Thread Andreas Leha
Hi Nick, Nick Dokos ndo...@gmail.com writes: Andreas Leha andreas.l...@med.uni-goettingen.de writes: Hi Nick, Nick Dokos ndo...@gmail.com writes: Andreas Leha andreas.l...@med.uni-goettingen.de writes: I forgot... Andreas Leha andreas.l...@med.uni-goettingen.de writes: Hi all, How

Re: [O] user-error: No language for src block: (unnamed) when running `org-icalendar-combine-agenda-files`

2015-08-21 Thread Andreas Leha
Hi, Just a small comment. [ ... discussion of :caching of evaluation results ... ] For purely R-based work, Charles Berry’s ox-ravel package https://github.com/chasberry/orgmode-accessories/blob/master/ox-ravel.org is a very interesting approach, since it relies on the cache feature of

Re: [O] export (to gfm) with file local variables

2015-08-21 Thread Andreas Leha
Nick Dokos ndo...@gmail.com writes: Andreas Leha andreas.l...@med.uni-goettingen.de writes: Thanks for following that up! That is interesting. How did you see that file with the empty lines? I do not get anything exported -- neither md nor gfm. I looked in the *temp* buffer (which

Re: [O] export (to gfm) with file local variables

2015-08-21 Thread Andreas Leha
Hi Nicolas, Nicolas Goaziou m...@nicolasgoaziou.fr writes: Hello, Nick Dokos ndo...@gmail.com writes: That seems to be caused by the empty lines in the Local Variables: section of the md file: div id=table-of-contents h2Table of Contents/h2 div id=text-table-of-contents ul lia

[O] ox-gfm and toc

2015-08-21 Thread Andreas Leha
Hi all, I am confused about how tables of content are handled in ox-gfm. If I let org-mode do the default toc (#+OPTIONS: toc:t) then the TOC seems to work -- even without using the generated anchors for the headlines. Test file: --8---cut here---start-8---

Re: [O] outorg issue

2015-08-19 Thread Andreas Leha
Hi Kaushal, Kaushal kaushal.m...@gmail.com writes: I had submitted a pull request to solve this issue on that author's outshine package page a couple of months back but as Andreas noted, the author hasn't been able to maintain this stuff due to personal reasons. You can fix this issue by

Re: [O] outorg issue

2015-08-19 Thread Andreas Leha
Hi Pip, Pip Cet pip...@gmail.com writes: Hi, can you confirm the issue only appears when the first line of the buffer isn't an outline heading? I think it's easy enough to fix then, and if you like you might want to try the patch I've attached. It's bugged me for a while that

Re: [O] outorg issue

2015-08-18 Thread Andreas Leha
Hi Bastien, Bastien b...@gnu.org writes: Hi Andreas, Andreas Leha andreas.l...@med.uni-goettingen.de writes: For quite some time now, I have to disable outshine/outorg [1] as it does give me Before first heading (complete backtrace [2]) whenever I open an org file followed by more issues

Re: [O] 8.3 hangs

2015-08-15 Thread Andreas Leha
Hi all, Eric Abrahamsen e...@ericabrahamsen.net writes: Nicolas Goaziou m...@nicolasgoaziou.fr writes: Samuel Wales samolog...@gmail.com writes: i am still getting a lot of hangs in 8.3. most often, it is when i do a subtree sort. i keep trying element debug mode, but it has magical bug

Re: [O] named python session

2015-08-13 Thread Andreas Leha
Hi Ken, Ken Mankoff mank...@gmail.com writes: Hi Andreas, On 2015-08-12 at 08:06, Andreas Leha andreas.l...@med.uni-goettingen.de wrote: How do I associate that with the python process in *mypy*? I am asked to start python when I run python-shell-send-region. I have set up my system so

Re: [O] outorg issue

2015-08-13 Thread Andreas Leha
to the beginning of the buffer when outline-back-to-heading is called, which raises that error. I don't have time today to dig much further. I hope that helps get a solution though! I miss outshine! Andreas Leha writes: Hi all, For quite some time now, I have to disable outshine/outorg [1] as it does

[O] named python session

2015-08-12 Thread Andreas Leha
Hi python users, I have a simple question to all python users. I have a source block with a named python session, e.g. #+begin_src python :results output :session mypy x = 1 print x #+end_src Now I - execute that source block and then I - edit that block in its own buffer via C-c '.

[O] outorg issue

2015-08-12 Thread Andreas Leha
Hi all, For quite some time now, I have to disable outshine/outorg [1] as it does give me Before first heading (complete backtrace [2]) whenever I open an org file followed by more issues actually using org mode. I can even reproduce this with emacs -Q and a minimal configuration [3]. My system

Re: [O] Block level specification for tex code html export method

2015-08-12 Thread Andreas Leha
Hi Haochen, You can render svg from latex through org directly. Here is a complete example including a tikz diagram that that works on my system (once I tackle a bug in PGF [1]). It renders - png by default (and for inlining the image into the org document) - nothing for latex (directly include

Re: [O] Block level specification for tex code html export method

2015-08-12 Thread Andreas Leha
, 2015 at 5:50 PM, Andreas Leha andreas.l...@med.uni-goettingen.de wrote: Hi Haochen, You can render svg from latex through org directly. Here is a complete example including a tikz diagram that that works on my system (once I tackle a bug in PGF [1]). It renders - png by default

Re: [O] Block level specification for tex code html export method

2015-08-10 Thread Andreas Leha
Hi Haochen, Haochen Xie haoc...@xie.name writes: Hi, I'm trying to include a diagram drawn with tikz in a document, but couldn't find an elegant way to conditionally export it as png when generating HTML output and raw TeX code when generating PDF. It is possible to use #+OPTIONS:

Re: [O] org-html-use-unicode-chars breaks source code blocks

2015-08-08 Thread Andreas Leha
Hi, [ deleted: discussion on beatification ] My initial reaction was to kill it as well. But I might feel like this a bit to often (I feel the same way about headline keywords like COMMENT). There has been repeated 'bashing' of the COMMENT keyword lately on this list. Let me just raise a

Re: [O] Babel and R: Call code block and output plot

2015-07-27 Thread Andreas Leha
Hi Stefan, Stefan Nobis stefan...@snobis.de writes: Hi. I'm playing a little bit with R code blocks in babel and calling them in different parts of my document (e.g. showing output in the main part and the code in the appendix). With most code blocks (e.g. setting some variables or

Re: [O] bug: orgtbl-to-tsv: premature end of table

2015-07-23 Thread Andreas Leha
Hi all, Charles C. Berry ccbe...@ucsd.edu writes: On Wed, 22 Jul 2015, Nicolas Goaziou wrote: Hello, Charles C. Berry ccbe...@ucsd.edu writes: Not a bug IMO. Notwithstanding the R issue, I think trimming the output of a radio table is a bit aggressive. We cannot know if trailing (and

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

2015-06-20 Thread Andreas Leha
Rainer M Krug rai...@krugs.de writes: Andreas Leha andreas.l...@med.uni-goettingen.de writes: Hi Rainer, Hi Andreas, 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

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

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

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

2015-06-18 Thread Andreas Leha
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) that analyzes data, produces graphics, etc.

Re: [O] org-babel-lob-ingest and debug-init

2015-06-18 Thread Andreas Leha
Hi, Nicolas Goaziou m...@nicolasgoaziou.fr writes: Hello, Andreas Leha andreas.l...@med.uni-goettingen.de writes: Andreas Leha andreas.l...@med.uni-goettingen.de writes: Hi all, I have two lines like this in my .emacs: (org-babel-lob-ingest ~/path/to/library-of-babel.org) (org-babel

[O] org-babel-lob-ingest and debug-init

2015-06-17 Thread Andreas Leha
Hi all, I have two lines like this in my .emacs: --8---cut here---start-8--- (org-babel-lob-ingest ~/path/to/library-of-babel.org) (org-babel-lob-ingest ~/path/to/custom-library-of-babel.org) --8---cut here---end---8--- All

Re: [O] org-babel-lob-ingest and debug-init

2015-06-17 Thread Andreas Leha
Andreas Leha andreas.l...@med.uni-goettingen.de writes: Hi all, I have two lines like this in my .emacs: (org-babel-lob-ingest ~/path/to/library-of-babel.org) (org-babel-lob-ingest ~/path/to/custom-library-of-babel.org) All works fine usually. But when I start emacs using the --debug

Re: [O] Why navigating in Org mode is so slow in overview mode?

2015-06-17 Thread Andreas Leha
Hi Gregor, Gregor Zattler telegr...@gmx.net writes: Hi Nicolas, * Nicolas Goaziou m...@nicolasgoaziou.fr [17. Jun. 2015]: Hello, Q godbles...@gmail.com writes: I am view this file http://doc.norang.ca/org-mode.org It's a prettey long document, when it all folded up, navigating to

Re: [O] How to end a :session?

2015-05-28 Thread Andreas Leha
Hi Rainer, Rainer M Krug rai...@krugs.de writes: Christopher Witte ch...@witte.net.au writes: perhaps what you want is a named session, see http://orgmode.org/manual/session.html Sure - that's what I have. But how can I close the named session when I don't need it anymore, or want to

Re: [O] How to end a :session?

2015-05-28 Thread Andreas Leha
Hi Rainer, Rainer M Krug rai...@krugs.de writes: Andreas Leha andreas.l...@med.uni-goettingen.de writes: Hi Rainer, Hi Andreas, Rainer M Krug rai...@krugs.de writes: Christopher Witte ch...@witte.net.au writes: perhaps what you want is a named session, see http://orgmode.org/manual

Re: [O] How to end a :session?

2015-05-28 Thread Andreas Leha
Rainer M Krug rai...@krugs.de writes: Andreas Leha andreas.l...@med.uni-goettingen.de writes: Hi Rainer, Rainer M Krug rai...@krugs.de writes: Andreas Leha andreas.l...@med.uni-goettingen.de writes: Hi Rainer, Hi Andreas, Rainer M Krug rai...@krugs.de writes: Christopher Witte ch

Re: [O] [RFC] Org linting library

2015-05-27 Thread Andreas Leha
Hi Nicolas, some more spurious warnings I get: 1. Captions with short version: , | 1105 low Possible missing colon in keyword #+caption[Data ` 2. header arguments from ob-latex: , |451 high Unknown header argument packages |451 high Unknown header argument

Re: [O] ox-latex: includegraphics should quote filenames

2015-05-26 Thread Andreas Leha
Hi Vaidheeswaran, Vaidheeswaran C vaidheeswaran.chinnar...@gmail.com writes: In: [[./emacs-24.5.1-startup-screen-annotated.png]] Buggy Out: \includegraphics[width=.9\linewidth]{./emacs-24.5.1-startup-screen-annotated.png} Desired: Out:

Re: [O] [BUG] org-edit-src-auto-save-idle-delay no effect

2015-05-26 Thread Andreas Leha
Hi all, Andreas Leha andreas.l...@med.uni-goettingen.de writes: Hi all, Today I found out the hard way, that org-edit-src-auto-save-idle-delay does not have any effect for me any more. I'd say this is a serious regression. I have tested with emacs -Q. Turned out I have not tested

[O] [BUG] org-edit-src-auto-save-idle-delay no effect

2015-05-26 Thread Andreas Leha
Hi all, Today I found out the hard way, that org-edit-src-auto-save-idle-delay does not have any effect for me any more. I'd say this is a serious regression. I have tested with emacs -Q. My system: - GNU Emacs 24.4.50.1 (x86_64-apple-darwin13.3.0, NS appkit-1265.21 Version 10.9.4 (Build

Re: [O] [BUG] org-edit-src-auto-save-idle-delay no effect

2015-05-26 Thread Andreas Leha
Hi Nicolas, Nicolas Goaziou m...@nicolasgoaziou.fr writes: Hello, Andreas Leha andreas.l...@med.uni-goettingen.de writes: All my tests now show that (at least) in a fresh emacs session the auto-saving still works -- also repeatedly. But in longer running emacs sessions things stop working

Re: [O] [BUG] org-edit-src-auto-save-idle-delay no effect

2015-05-26 Thread Andreas Leha
Hi all, Here is now a more accurate but still vague bug description. All my tests now show that (at least) in a fresh emacs session the auto-saving still works -- also repeatedly. But in longer running emacs sessions things stop working: I edit the source buffer and wait but now auto-save will

Re: [O] position figures side by side in PDF output

2015-05-20 Thread Andreas Leha
Hi Zhihao, Rasmus ras...@gmx.us writes: Hi Zhihao, Zhihao Ding zhihao.d...@imm.ox.ac.uk writes: Could anyone give me some advice on how to position figures side by side in PDF output? I am trying to write a report, while my figures were all originally produced individually. I’d like

Re: [O] [RFC] Org linting library

2015-05-20 Thread Andreas Leha
Hi Rainer, Rainer M Krug rai...@krugs.de writes: Rainer M Krug rai...@krugs.de writes: Rainer M Krug rai...@krugs.de writes: Andreas Leha andreas.l...@med.uni-goettingen.de writes: Hi Rainer, Rainer M Krug rai...@krugs.de writes: Nicolas Goaziou m...@nicolasgoaziou.fr writes: Hello

Re: [O] [RFC] Org linting library

2015-05-19 Thread Andreas Leha
Nicolas Goaziou m...@nicolasgoaziou.fr writes: Hello, The following library implements linting for Org syntax. The sole public function is `org-lint', which see. Internally, the library defines a new structure: `org-lint-checker', with the following slots: - NAME: Unique check

[O] attachments in parent

2015-05-19 Thread Andreas Leha
Hi all, As it seems, attachments are not found when they are attached to a parental header. Is that on purpose? IMO, it would be nice if attachments would be searched for up the hierarchy as well. The attachment directory is not inherited, as it seems. Here is an example illustrating my

Re: [O] [RFC] Org linting library

2015-05-19 Thread Andreas Leha
Hi Rainer, Rainer M Krug rai...@krugs.de writes: Nicolas Goaziou m...@nicolasgoaziou.fr writes: Hello, The following library implements linting for Org syntax. The sole public function is `org-lint', which see. Internally, the library defines a new structure: `org-lint-checker', with the

Re: [O] [RFC] Org linting library

2015-05-19 Thread Andreas Leha
Hi Nicolas, Nicolas Goaziou m...@nicolasgoaziou.fr writes: I have finally made some time to test this. I get some unexpected warnings: 79 low Unknown value myfile.R for header :tangle 192 low Unknown value none for header :results Make sure you rebased the wip-lint branch on top

Re: [O] can't find src blocks

2015-05-19 Thread Andreas Leha
Hi Nicolas, Nicolas Goaziou m...@nicolasgoaziou.fr writes: Hello, Andreas Leha andreas.l...@med.uni-goettingen.de writes: Since some time (sorry, no bisect, I am afraid) I am having issues with `org-babel-goto-named-src-block'. I simply can not find any source block any more -- even

Re: [O] [RFC] Org linting library

2015-05-19 Thread Andreas Leha
Hi Nicolas, Nicolas Goaziou m...@nicolasgoaziou.fr writes: Andreas Leha andreas.l...@med.uni-goettingen.de writes: I just pulled and rebased again. The never-export issue is gone, indeed. The others are still there. What am I missing here? Nothing. I overlooked a typo. It should be fixed

[O] can't find src blocks

2015-05-19 Thread Andreas Leha
Hi all, Since some time (sorry, no bisect, I am afraid) I am having issues with `org-babel-goto-named-src-block'. I simply can not find any source block any more -- even with emacs -Q Here is the MWE: --8---cut here---start-8--- * Test code block names Try

Re: [O] [RFC] Org linting library

2015-05-19 Thread Andreas Leha
Hi Nicolas, Nicolas Goaziou m...@nicolasgoaziou.fr writes: Andreas Leha andreas.l...@med.uni-goettingen.de writes: But I still get 191 low Unknown value none for header :results Could you show an ECM? I cannot reproduce it. Sure: --8---cut here---start

Re: [O] [RFC] Org linting library

2015-05-19 Thread Andreas Leha
Hi Nicolas, Nicolas Goaziou m...@nicolasgoaziou.fr writes: Andreas Leha andreas.l...@med.uni-goettingen.de writes: * Test code block names #+name: test #+begin_src R :results none 1:10 #+end_src OK. It was a R-specific bug. It should now be fixed. Thank you! Fix confirmed. The last

Re: [O] attachments in parent

2015-05-19 Thread Andreas Leha
Hi all, Andreas Leha andreas.l...@med.uni-goettingen.de writes: As it seems, attachments are not found when they are attached to a parental header. Is that on purpose? IMO, it would be nice if attachments would be searched for up the hierarchy as well. The attachment directory

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