Re: [O] export of src block ignores :results

2016-10-02 Thread Thomas Alexander Gerds
your help and patience! Thomas "Charles C. Berry" <ccbe...@ucsd.edu> writes: > On Fri, 30 Sep 2016, Thomas Alexander Gerds wrote: > >> right, this is what changed and setting :eval never-export on a each >> block solves the problem. however, the new way breaks all

Re: [O] export of src block ignores :results

2016-09-30 Thread Thomas Alexander Gerds
gt; writes: > On Thu, 29 Sep 2016, Thomas Alexander Gerds wrote: > >> > [deleted] > > Follow the advice in the docstring for > `org-export-babel-evaluate'. Use `:eval never-export'. Set > org-export-babel-evaluate to t. > > Chuck > > -- sent from nil

Re: [O] export of src block ignores :results

2016-09-29 Thread Thomas Alexander Gerds
Berry wrote: > >> On Thu, 29 Sep 2016, Thomas Alexander Gerds wrote: >> >>> Hi Chuck >>> >>> thanks for checking. my org-version is the same >>> release_8.3.6-1178-g2b22d5 >>> >>> to get the date and time of the in the result

Re: [O] export of src block ignores :results

2016-09-29 Thread Thomas Alexander Gerds
in the export process where the :results option is interpreted? Thomas "Charles C. Berry" <ccbe...@ucsd.edu> writes: > On Thu, 29 Sep 2016, Thomas Alexander Gerds wrote: > >> Hi >> org's development version (I am using the one updated yesterday: >> 2b22d50 Nicolas Go

[O] export of src block ignores :results

2016-09-29 Thread Thomas Alexander Gerds
Hi org's development version (I am using the one updated yesterday: 2b22d50 Nicolas Go 2016-09-28) seems to ignore the :results setting of a src block. more specifically, the export of this #+BEGIN_SRC R :results output :exports code :session *R* :cache yes 2+2 #+END_SRC

[O] export of src block ignores :results

2016-09-29 Thread Thomas Alexander Gerds
Hi org's development version (I am using the one updated yesterday: 2b22d50 Nicolas Go 2016-09-28) seems to ignore the :results setting of a src block. more specifically, the export of this #+BEGIN_SRC R :results output :exports code :session *R* :cache yes 2+2 #+END_SRC

Re: [O] proposed change of org-gnus-store-link for nnir groups

2015-12-17 Thread Thomas Alexander Gerds
yes, I now found the "how to contribute" page :) the updated patch is attached. thanks! Nicolas Goaziou <m...@nicolasgoaziou.fr> writes: > Hello, > > Thomas Alexander Gerds <t...@biostat.ku.dk> writes: > >> great. the updated patch is attached. > &g

Re: [O] proposed change of org-gnus-store-link for nnir groups

2015-12-16 Thread Thomas Alexander Gerds
.fr> writes: > Hello, > > Thomas Alexander Gerds <t...@biostat.ku.dk> writes: > >> sometimes after searching for mail with notmuch, I want to save a >> link to one of the articles shown in the nnir summary. since nnir >> groups are temporary I would like o

[O] proposed change of org-gnus-store-link for nnir groups

2015-12-12 Thread Thomas Alexander Gerds
sometimes after searching for mail with notmuch, I want to save a link to one of the articles shown in the nnir summary. since nnir groups are temporary I would like org-gnus-store-link to treat nnir groups differently and to use the articles orginal group when creating the link. the following 3

Re: [O] Latex export of tables

2013-04-16 Thread Thomas Alexander Gerds
Hi Vikas I am not sure I understand the problem correctly, but how about this? Here is a table produced by a R-src block with some descriptive text in a minipage: ---snip-- #+BEGIN_SRC R :results output latex :exports results

Re: [O] minor bug in babel with silent output and remote R session

2013-04-15 Thread Thomas Alexander Gerds
the Babel source if the R session is remote? Thanks, Thomas Alexander Gerds t...@biostat.ku.dk writes: yes, I am using ESS. ess-remote allows me to evaluate R-code from the local emacs-session on a remote machine connected to via ssh. there are two problems: 1) the remote machine cannot

Re: [O] minor bug in babel with silent output and remote R session

2013-04-14 Thread Thomas Alexander Gerds
to avoid the endless loop when waiting for a file which never will generated. cheers thomas Eric Schulte schulte.e...@gmail.com writes: Bastien b...@gnu.org writes: Hi Thomas, thanks for the follow-up. Thomas Alexander Gerds t...@biostat.ku.dk writes: I think that I can describe

Re: [O] org babel problems with (org-babel-read *R*)

2013-04-10 Thread Thomas Alexander Gerds
works again. thanks very much for fixing this so quickly! Eric Schulte schulte.e...@gmail.com writes: Charles Berry ccbe...@ucsd.edu writes: Thomas Alexander Gerds tag at biostat.ku.dk writes: after upgrading to the latest bleeding edge version I have problems executing org-babel R

Re: [O] minor bug in babel with silent output and remote R session

2013-04-09 Thread Thomas Alexander Gerds
me note that there are at least two ways to start a remote R session in emacs: 1) M-x shell 2) M-x ssh via ssh.el (not part of emacs) Cheers Thomas Bastien b...@gnu.org writes: Hi Thomas, Thomas Alexander Gerds t...@biostat.ku.dk writes: Using the silent option together with a remote R

[O] org babel problems with (org-babel-read *R*)

2013-04-09 Thread Thomas Alexander Gerds
after upgrading to the latest bleeding edge version I have problems executing org-babel R blocks where the session is named *R*. the error is this: ELISP (org-babel-read *R*) *** Eval error *** Symbol's value as variable is void: *R* did I miss any conventions or is this a bug? cheers thomas

Re: [O] latex figure scaling question, backward compatibility and outdated manual

2013-03-22 Thread Thomas Alexander Gerds
Alexander Gerds t...@biostat.ku.dk writes: I was learning about this by guessing around for some time ... it is surprisingly hard to edebug the export process (any hints?). This is a bit vague. next, the following educated guess does not work: #+ATTR_LaTeX: :width 5cm :angle 90 This is because

Re: [O] latex figure scaling question, backward compatibility and outdated manual

2013-03-20 Thread Thomas Alexander Gerds
sorry for this post. I should have read the mailing list more carefully. looks as if a) the issue is already under discussion and b) that the manual is for latest release whereas I had problems with the pre-release. Thomas Alexander Gerds t...@biostat.ku.dk writes: the following page from

[O] latex figure scaling question, backward compatibility and outdated manual

2013-03-19 Thread Thomas Alexander Gerds
the following page from the official manual http://orgmode.org/manual/Images-in-LaTeX-export.html says #+ATTR_LaTeX: width=5cm,angle=90 however, the new exporter does not recognize this syntax. instead the following works: #+ATTR_LaTeX: :width 5cm I was learning about this by guessing

[O] minor bug in babel with silent output and remote R session

2013-03-13 Thread Thomas Alexander Gerds
Using the silent option together with a remote R session block (started via ssh.el and ess-remote), like this: #+BEGIN_SRC R :results silent :exports results :session *ssh gauss* :cache yes a=1 1 #+END_SRC produces: , |[1] 1 | Warning message: | In file.rename(tfile,

Re: [O] minor bug in babel with silent output and remote R session

2013-03-13 Thread Thomas Alexander Gerds
| ` cheers Thomas Eric Schulte schulte.e...@gmail.com writes: Thomas Alexander Gerds t...@biostat.ku.dk writes: Using the silent option together with a remote R session block (started via ssh.el and ess-remote), like this: #+BEGIN_SRC R :results silent :exports results :session *ssh gauss* :cache

[O] latex listings number-lines problems with new exporter

2013-03-05 Thread Thomas Alexander Gerds
Hi using org-mode 7.9.3f and the new exporter I was desperately trying to get line numbers back for exported R code blocks using the latex listing package. first I tried (setq org-latex-listings-options '((basicstyle \\small) (numbers left))) which gives , |

Re: [O] latex listings number-lines problems with new exporter

2013-03-05 Thread Thomas Alexander Gerds
thanks for the fast fix. now, I agree that there is no great need to put a link into the doc-string of org-latex-listings-options. Nicolas Goaziou n.goaz...@gmail.com writes: Hello, Thomas Alexander Gerds t...@biostat.ku.dk writes: using org-mode 7.9.3f and the new exporter I

Re: [O] can babel results show time of evaluation?

2013-01-30 Thread Thomas Alexander Gerds
will help to learn how caching works. Cheers Thomas Bastien b...@altern.org writes: Hi Thomas, Thomas Alexander Gerds t...@biostat.ku.dk writes: (when hash (concat [[hash][ (with-temp-buffer (org-insert-time-stamp (current-time) 'hm)) ]])) but, not sure if that is a good idea and what

Re: [O] can babel results show time of evaluation?

2013-01-30 Thread Thomas Alexander Gerds
Hi Eric yes, it is in line 178 the call to (defcustom org-babel-load-languages '((emacs-lisp . t)) ... which seems to need `org-ts-regexp' but, otherwise it works! Thank you very much for this option. Best Thomas Bastien b...@altern.org writes: Hi Eric, Eric Schulte

[O] can babel results show time of evaluation?

2013-01-28 Thread Thomas Alexander Gerds
hi I would like to overlay the hash info in results lines of this type #+RESULTS[6e22789c4866716ffb3d0966cbb07c80cacf2d3c]: [1] 1 by a description which shows the evaluation time, e.g. like this #+RESULTS[[6e22789c4866716ffb3d0966cbb07c80cacf2d3c][ evaluated 2013-01-28 Mon 09:33]]: as far

Re: [O] org agenda extensions

2013-01-12 Thread Thomas Alexander Gerds
-list'. Bastien b...@altern.org writes: Hi Thomas, Thomas Alexander Gerds t...@biostat.ku.dk writes: thanks for looking into this! I understand your general point of view. however, the proposed changes would only slow down agenda creating if org-agenda-property-list is set, right? Right

Re: [O] org agenda extensions

2013-01-12 Thread Thomas Alexander Gerds
Hi Bastien ok. will investigate. thanks for now. Best Thomas Bastien b...@altern.org writes: Hi Thomas, Thomas Alexander Gerds t...@biostat.ku.dk writes: I feel that your proposal to first create the agenda using the standard `org-agenda-format-item' function and then to replace all

[O] org agenda extensions

2013-01-11 Thread Thomas Alexander Gerds
Dear all with the aim to show properties in custom match views, I have been experimenting with new variables: org-agenda-overriding-agenda-format org-agenda-property-list then, tweaking the function org-scan-tags this enables custom format for the agenda lines, optionally showing properties

Re: [O] org agenda extensions

2013-01-11 Thread Thomas Alexander Gerds
? Bastien b...@altern.org writes: Hi Thomas, Thomas Alexander Gerds t...@biostat.ku.dk writes: with the aim to show properties in custom match views, I have been experimenting with new variables: org-agenda-overriding-agenda-format org-agenda-property-list then, tweaking the function org

Re: [O] org agenda extensions

2013-01-11 Thread Thomas Alexander Gerds
Hi Bastien thanks for looking into this! I understand your general point of view. however, the proposed changes would only slow down agenda creating if org-agenda-property-list is set, right? also, it certainly requires some insights to write org-agenda-overriding-agenda-format which could

[O] orgmode latex export: reference to label rather than section

2012-06-18 Thread Thomas Alexander Gerds
Hi I would be grateful if someone could help me sort out my confusion regarding references to headings (sections) in latex export. I am used to latex section labels and references via reftex, e.g. , | \section{This is a test} | \label{sec:testit} | | In Section \ref{sec:testit} ` To

Re: [O] issue with babel R evaluate session vs external process

2012-03-12 Thread Thomas Alexander Gerds
finally I found the problem: it was not at all related to org or babel, but due to a function in my ess-send-input-hook. sorry for bothering :) Thomas Alexander Gerds tagt...@sund.ku.dk writes: still a beginner, and maybe therefore, in my setup (release is: 7.8.03, emacs 23.2.1

Re: [O] \section*{}

2012-02-24 Thread Thomas Alexander Gerds
but, you can always do this: , | ** sec 1 | | bla | | #+LaTeX: \section*{sec2} ` Tomy Marvin Doyley marvin...@gmail.com writes: Thanks nick, Can I use this to suppress the numbering selectively For example, lets say I have * Intro * Results * Figures and Tables Can I use

[O] babel bugs??

2012-02-23 Thread Thomas Alexander Gerds
Dear Babel developers I may have found two bugs (org-mode: 7.8.03 release_7.8.03.330.gc804.dirty), emacs: 23.2.1): 1. when I have case-fold-search set to nil, I get problems with the begin/end src notation: , lower case works as expected | | #+begin_src emacs-lisp :results list |

[O] worg access source

2012-02-09 Thread Thomas Alexander Gerds
in worg it would be great if (as in emacs muse) there was a link to the underlying .org file which was used to generate the page. my naiive attempt to catch a glimpse of the source of http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.html was to browse-url

[O] issue with babel R evaluate session vs external process

2012-02-09 Thread Thomas Alexander Gerds
still a beginner, and maybe therefore, in my setup (release is: 7.8.03, emacs 23.2.1) the following occurs -org.snip--- * here it works: org-ctrl-c-ctrl-c and export #+begin_src R :results output :exports results foo=matrix(1:2) foo #+end_src #+RESULTS: :

Re: [O] worg access source

2012-02-09 Thread Thomas Alexander Gerds
jasondunsm...@gmail.com writes: On Thu, Feb 09 2012, Thomas Alexander Gerds wrote: in worg it would be great if (as in emacs muse) there was a link to the underlying .org file which was used to generate the page. my naiive attempt to catch a glimpse of the source of http://orgmode.org/worg/org

Re: [O] orgmode and auctex

2012-02-09 Thread Thomas Alexander Gerds
Hi Chris, maybe I cannot follow exactly what you are trying to do, but when I start emacs -q and evaluate (setq-default TeX-master nil) and then open a new file test.tex, then I get the same prompt Master file:. so maybe, if you do not want to get prompted, you could try setting (setq-default

Re: [O] help regarding babel to set in-buffer specific keybinding

2012-02-08 Thread Thomas Alexander Gerds
this works. thanks for the hint! Eric Schulte eric.schu...@gmx.com writes: Thomas Alexander Gerds tagt...@sund.ku.dk writes: here is a (beginner) question regarding the following org-file with buffer-local function and keybinding: , | | * Lisp header (C-c C-c to activate

[O] help regarding babel to set in-buffer specific keybinding

2012-02-07 Thread Thomas Alexander Gerds
here is a (beginner) question regarding the following org-file with buffer-local function and keybinding: , | | * Lisp header (C-c C-c to activate) | #+BEGIN_SRC emacs-lisp | (defun blue-file () | (interactive) | (org-table-insert-row 'below) | (org-table-goto-column 1) |