[O] HOWTO?: export without (re)eval-ing src blocks (was? disable automatic source block evaluation but allow manual)

2011-09-16 Thread Cook, Malcolm
I would like to be able to export a buffer as HTML, LaTex, what-have-you without having to re-evaluate any source blocks, and without having to modify the :eval tag in any source header blocks. Is there any way to accomplish this via hooks, flags, appropriate function calls? I think my

Re: [O] HOWTO?: export without (re)eval-ing src blocks (was? disable automatic source block evaluation but allow manual)

2011-09-16 Thread Cook, Malcolm
, September 16, 2011 12:01 PM To: Cook, Malcolm Cc: 'emacs-orgmode@gnu.org'; 'andreas.l...@med.uni-goettingen.de'; nicholas.do...@hp.com Subject: Re: [O] HOWTO?: export without (re)eval-ing src blocks (was? disable automatic source block evaluation but allow manual) [forgot to cc: the list] Cook

Re: [O] [PATCH] WAS Re: Bug: problem w/ R code blocks [8.3beta (release_8.3beta-362-ga92789 at /usr/local/share/emacs/site-lisp/org/)]

2014-09-17 Thread Cook, Malcolm
Hiya, Likewise - same problem here is fixed with injection of patch. Thanks! ~ malcolm_cook -Original Message- From: emacs-orgmode-bounces+mec=stowers@gnu.org [mailto:emacs-orgmode-bounces+mec=stowers@gnu.org] On Behalf Of Rainer M Krug Sent: Wednesday, September 17,

Re: [O] [PATCH] WAS Re: Bug: problem w/ R code blocks [8.3beta (release_8.3beta-362-ga92789 at /usr/local/share/emacs/site-lisp/org/)]

2014-09-18 Thread Cook, Malcolm
going to wait till things settle down before trying to upgrade ESS again. Thanks for the patch anyway. Cheers, Malcolm -Original Message- From: Cook, Malcolm Sent: Wednesday, September 17, 2014 6:14 PM To: 'Rainer M Krug'; 'Charles Berry' Cc: 'emacs-orgmode@gnu.org' Subject: RE: [O

Re: [O] sortable columns in html tables

2014-09-30 Thread Cook, Malcolm
Hi, The syntax for much of this has changed since that post. Instead of #+style: you will want #+HTML_HEAD: And, attaching a class to an exported html table is handled differently too. Instead of #+attr_html: class=sortable you want #+attr_html: :class sortable Such

Re: [O] Switch for exported file types when evaluating code blocks

2013-07-17 Thread Cook, Malcolm
: :file (by-backend (html graph.png) (latex graph.pdf) (t graph.svg)) #+header: :export results #+begin_src dot digraph Name { tail - head; } #+end_src [Cook, Malcolm] Brett, Thanks for posting your findings. They almost help me. I am looking for a solution to a similar problem

Re: [O] Switch for exported file types when evaluating code blocks

2013-07-18 Thread Cook, Malcolm
...@gmail.com writes: Hello again Malcolm, On Thu, Jul 18, 2013 at 12:45:36AM +, Cook, Malcolm wrote: I tend to work with org-export-babel-evaluate set to nil. Thus, my code blocks are not evaled in the context of an export. Thus at eval time there is no way of knowing what the eventual

Re: [O] Switch for exported file types when evaluating code blocks

2013-07-19 Thread Cook, Malcolm
, July 18, 2013 8:02 PM To: emacs-orgmode@gnu.org Subject: Re: [O] Switch for exported file types when evaluating code blocks Cook, Malcolm m...@stowers.org writes: Hi Nick, I'm not sure how to use this ctan package in concert with orgmode's export to tex-pdf. Here's a simplfied example of what I

Re: [O] Switch for exported file types when evaluating code blocks

2013-07-19 Thread Cook, Malcolm
Suvayu, This is splendid news! I will try it immediately upon return from gone fishin in a week... (erhm, that is, right after I figure out haw to migrate my orgmode SETUPFILE to comport with new export backend I just upgraded to my fancy TOC and org-export-html-table-tag javascript

Re: [O] import R data frame into org-mode table

2013-07-29 Thread Cook, Malcolm
Hi Andreas, On 17 July 2013 23:09, Andreas Leha andreas.l...@med.uni-goettingen.de wrote: Definitely there is: --8---cut here---start-8--- #+begin_src R :results table :colnames yes read.csv('test.csv') #+end_src #+results: | X |

Re: [O] import R data frame into org-mode table

2013-07-29 Thread Cook, Malcolm
-Original Message- From: John Hendy [mailto:jw.he...@gmail.com] Sent: Monday, July 29, 2013 11:03 AM To: Cook, Malcolm Cc: Rob Stewart; Andreas Leha; emacs-orgmode@gnu.org Subject: Re: [O] import R data frame into org-mode table On Mon, Jul 29, 2013 at 10:35 AM, Cook, Malcolm m

Re: [O] import R data frame into org-mode table

2013-07-30 Thread Cook, Malcolm
Indeed, thanks, and, my worked out example follows using emacs 2.18.9 and org-mode version 8.0.6 2.18.9? oops, that was the GTK_ Version number. My emacs is 24.3.1. #+LATEX: \listoftables #+LaTeX_HEADER: \usepackage{longtable} #+name: longtabletest #+CAPTION: test of longtable

Re: [O] how to handle svg files when exporting orgmode to html and pdf?

2013-08-08 Thread Cook, Malcolm
In case of difficulties like this, I produce the tex file (C-c C-e l l) and then I process it by hand: pdflatex --shell-escape foo.tex Separates concerns nicely. I will try your approach - thanks - I agree Sleuthing, I see the output .tex file includes the following lines:

Re: [O] how to handle svg files when exporting orgmode to html and pdf?

2013-08-10 Thread Cook, Malcolm
Thomas, Suvayu, Aaron, Nick, Eric, Carsten, Phil, et al, Thanks for all your help. I am now satisfied with approach for exporting images to inline html and inline latex=pdf. In my hands, the following code block will produce in-line images in html and be included in exported pdf.

Re: [O] example filter for code blocks?

2013-09-26 Thread Cook, Malcolm
Check out `org-export-filter-src-block-functions'. It shouldn't be too hard to add a custom filter to that list which may be used to process all code block bodies during latex export. Somewhat off-topic, but, thanks for pointing out this variable Eric I've been wanting an approach that

Re: [O] how to handle svg files when exporting orgmode to html and pdf?

2013-10-28 Thread Cook, Malcolm
=stowers@gnu.org] On Behalf Of Cook, Malcolm Sent: Friday, August 09, 2013 4:01 PM To: 'Malcolm Cook'; 'emacs-orgmode@gnu.org'; 'Nick Dokos'; 'Suvayu Ali'; 'Eric Schulte'; 'Vincent Beffara'; 'Thomas S. Dye'; 'phil...@cern.ch'; 'Charles Berry'; 'Aaron Ecay' Subject: Re: [O] how to handle svg

Re: [O] how to handle svg files when exporting orgmode to html and pdf?

2013-10-29 Thread Cook, Malcolm
Hi Aaron, Can I re-open this thread to discuss two new issues I now experience with emacs 24.3.1 and orgmode version 8.2.1 in the handling of svg = tex = pdf ? Here goes: 1) If the plot has text in it which contains a percent character (%), then we fail due to

Re: [O] make new links show as figures?

2013-10-31 Thread Cook, Malcolm
know if this works for you and i will apply to master when i get home and have git push access. I tried it on some files with images as links, and it works great. Thanks a lot! [Cook, Malcolm] Hi - I'm trying to follow this thread but having a challenge. Can you please summarize/repeat

[O] HowTo? have R :sessions in org mode invoke a specific R

2013-11-04 Thread Cook, Malcolm
I wish to lock an org buffer to a particular installation of R so that all code blocks use it. I found that I could not, for instance, write `:session R-3.0.1`. Is there some best way for me to accomplish this? Perhaps some way of setting inferior-R-program-name to a buffer local value?

[O] BUG? table output despite #+begin_src sh :results verbatim

2013-01-25 Thread Cook, Malcolm
Hi, In org 7.9.3d, under Gnu emacs 24.2.1 / linux: I find that org-mode is tablizing shell output despite require 'verbatim' results. #+begin_src sh :results verbatim echo 1 echo 2 echo 3 #+end_src #+results: | 1 | | 2 | | 3 | The same happens if I used 'scalar' in place of verbatim.

Re: [O] BUG? table output despite #+begin_src sh :results verbatim

2013-01-25 Thread Cook, Malcolm
Thomas, Thanks for checking. What does meta-x org-version tell you ?? ~Malcolm .-Original Message- .From: Thomas S. Dye [mailto:t...@tsdye.com] .Sent: Friday, January 25, 2013 1:44 PM .To: Cook, Malcolm .Cc: 'emacs-orgmode@gnu.org' .Subject: Re: BUG? table output despite

Re: [O] BUG? table output despite #+begin_src sh :results verbatim

2013-01-25 Thread Cook, Malcolm
...@tsdye.com] .Sent: Friday, January 25, 2013 2:31 PM .To: Cook, Malcolm .Cc: 'emacs-orgmode@gnu.org' .Subject: Re: BUG? table output despite #+begin_src sh :results verbatim . .Cook, Malcolm m...@stowers.org writes: . . Thomas, . . Thanks for checking. . . What does . . meta-x org-version

Re: [O] BUG? table output despite #+begin_src sh :results verbatim

2013-01-28 Thread Cook, Malcolm
, January 26, 2013 1:37 PM .To: Cook, Malcolm .Cc: 'Thomas S. Dye'; Blanchette, Marco; 'emacs-orgmode@gnu.org' .Subject: Re: [O] BUG? table output despite #+begin_src sh :results verbatim . .Cook, Malcolm m...@stowers.org writes: . . THanks Thomas, I see we are running same version of org

SOLVED? [Orgmode] org-babel-tangle-lang-exts must be initialized? how to get syntax coloring?

2010-09-08 Thread Cook, Malcolm
I am following up with a workaround for this old issue (from July). This problem persists with latest `git pull` on orgmode version 7.01 This minimal init file will cause it: (require 'org-install) ;(require 'org) (require 'ob-perl) uncomment the 2nd line, and the problem goes away. Cheers,

RE: SOLVED? [Orgmode] org-babel-tangle-lang-exts must be initialized? how to get syntax coloring?

2010-09-08 Thread Cook, Malcolm
fix confirmed. thanks! Malcolm Cook Stowers Institute for Medical Research - Bioinformatics Kansas City, Missouri USA -Original Message- From: Eric Schulte [mailto:schulte.e...@gmail.com] Sent: Wednesday, September 08, 2010 12:35 PM To: Cook, Malcolm Cc: 'emacs-orgmode@gnu.org

[Orgmode] HOWTO?: make install contrib

2010-09-09 Thread Cook, Malcolm
Is there a blessed mantra for installing the contents of contrib something perhapls like sudo make install-contrib prefix=/my/prefix Thanks! Malcolm Cook Stowers Institute for Medical Research - Bioinformatics Kansas City, Missouri USA ___

RE: [Orgmode] HOWTO?: make install contrib

2010-09-09 Thread Cook, Malcolm
of is a necessity. Ideas? Other guidance? Malcolm Cook Stowers Institute for Medical Research - Bioinformatics Kansas City, Missouri USA From: John Hendy [mailto:jw.he...@gmail.com] Sent: Thursday, September 09, 2010 9:17 AM To: Cook, Malcolm Cc: emacs-orgmode

[Orgmode] link export confused when URL parameter is another URL

2010-09-30 Thread Cook, Malcolm
If find that this orgtext [[http://www.foo.com/foo?URL=http://www.bar.com][test]] exports to html incorrectly as [[http://www.foo.com/foo?URL=[[http://www.bar.com][test][http://www.bar.com][test]]] using today's fresh git pull make install Any pointers? Thanks Malcolm Cook

RE: [Orgmode] link export confused when URL parameter is another URL

2010-10-21 Thread Cook, Malcolm
a thought perhaps expressible as a context-free-grammar. Cheers back, Malcolm -Original Message- From: David Maus [mailto:dm...@ictsoc.de] Sent: Wednesday, October 20, 2010 11:36 PM To: Cook, Malcolm Cc: 'emacs-orgmode@gnu.org' Subject: Re: [Orgmode] link export confused when URL parameter

[Orgmode] exporting a html table with gridlines - is it possible

2010-10-22 Thread Cook, Malcolm
I don't see any hooks for this. Malcolm Cook Stowers Institute for Medical Research - Bioinformatics Kansas City, Missouri USA ___ Emacs-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org

Re: [O] [PATCH] WAS Re: Bug: problem w/ R code blocks [8.3beta (release_8.3beta-362-ga92789 at /usr/local/share/emacs/site-lisp/org/)]

2014-12-09 Thread Cook, Malcolm
Hi, On this old subject, I too finally confirm the pushed patch addresses the issue - and - thanks. -Original Message- From: emacs-orgmode-bounces+mec=stowers@gnu.org [mailto:emacs-orgmode-bounces+mec=stowers@gnu.org] On Behalf Of Aaron Ecay Sent: Friday, October 10, 2014

Re: [O] Recently emacs hangs on startup due to ESS

2015-05-28 Thread Cook, Malcolm
On Thu, May 28, 2015 at 5:07 PM, Cook, Malcolm m...@stowers.org wrote: I would install latest ess fresh. I wondered about that as well, so I tried that prior to posting here. Sorry, I should have listed my version, which is now 15.03-1. What version of emacs? The package manager

Re: [O] Recently emacs hangs on startup due to ESS

2015-05-28 Thread Cook, Malcolm
I would install latest ess fresh. What version of emacs? The package manager is a moving target these days. Try to use the package manager to interactively install the latest - emacs -Q following: http://melpa.org/?utm_source=dlvr.itutm_medium=twitter#/getting-started - putting this in

Re: [O] Recently emacs hangs on startup due to ESS

2015-05-28 Thread Cook, Malcolm
John, still recommend you try fresh ess, compiled via package manager. Also, update any packages needing updated. Maybe speedbar? I'm dry, Best, Malcolm -Original Message- From: John Hendy [mailto:jw.he...@gmail.com] Sent: Thursday, May 28, 2015 6:24 PM To: Cook, Malcolm Cc

Re: [O] Recently emacs hangs on startup due to ESS

2015-05-28 Thread Cook, Malcolm
...@stowers.org From: John Hendy jw.he...@gmail.com Sent: Thursday, May 28, 2015 11:15 PM To: Cook, Malcolm Cc: emacs-orgmode Subject: Re: [O] Recently emacs hangs on startup due to ESS On Thu, May 28, 2015 at 6:34 PM, Cook, Malcolm m...@stowers.org wrote: John, still

Re: [O] capture htmlwidgets for export - a pattern in search of a new :results type???

2015-07-28 Thread Cook, Malcolm
On Tue, 28 Jul 2015, Cook, Malcolm wrote: I have been playing with exporting htmlwidgets [1] generated in R code- blocks. [snip: proposal for new :results format to accomodate repetitive codes] Perhaps there is a better or more useful abstraction. Or a better workaround

[O] capture htmlwidgets for export - a pattern in search of a new :results type???

2015-07-28 Thread Cook, Malcolm
I have been playing with exporting htmlwidgets [1] generated in R code-blocks. [1] http://www.htmlwidgets.org/ and Here is a worked example that exports to html #+BEGIN_SRC R :session *R* :exports both :results html library(htmlwidgets) library(d3heatmap)

Re: [O] orgmode and R?

2015-08-03 Thread Cook, Malcolm
It is possible to send a org table to R as a data.frame, which could edit it, add columns, and produce a new data.frame which, with :results value, will be understood by org as an table. -Original Message- From: emacs-orgmode-bounces+mec=stowers@gnu.org [mailto:emacs-

Re: [O] remote R session

2015-08-11 Thread Cook, Malcolm
Using ESS, If you are editing a org file file via tramp, editing an R src code block should “just work” to start the attached R session remotely. I do it all the time. Try this: make sure you do NOT have a local R session already and edit your source block…. From:

Re: [O] eval source blocks in a subtree when opening file

2015-08-07 Thread Cook, Malcolm
...) \ # (org-babel-execute-subtree)) didn't work. [Cook, Malcolm] Ditch the line continuation character. This works in my hands with emacs 24.4.1 to set foo to bar: # Local Variables: # eval: (setq foo # bar) # End: Best, Tamas

Re: [O] Babel error on init with 8.3.1

2015-08-10 Thread Cook, Malcolm
When you “ updated org through the package manager in Emacs,” I believe you need to make sure org has not been loaded at all. My practice is to exec `emacs –Q`, immediately update with package manager, then quit and restart emacs without the –Q. Let us know…. From:

[O] Link to http://orgmode.org/build-org-pkg.txt is 404 in http://orgmode.org/elpa.html

2015-08-10 Thread Cook, Malcolm
Link to http://orgmode.org/build-org-pkg.txt is 404 in http://orgmode.org/elpa.html ~Malcolm

Re: [O] Babel error on init with 8.3.1

2015-08-10 Thread Cook, Malcolm
@gnu.org [mailto:emacs-orgmode-bounces+mec=stowers@gnu.org] On Behalf Of Cook, Malcolm Sent: Monday, August 10, 2015 9:32 AM To: 'Ryan Schuetzler' rsch...@gmail.com; emacs-orgmode@gnu.org Subject: Re: [O] Babel error on init with 8.3.1 When you “ updated org through the package manager in Emacs

Re: [O] Capture-like browser plugin?

2015-07-23 Thread Cook, Malcolm
Frequently when I'm doing a Web search and find pages I like, I want to save a link to the page, along with the title and perhaps a few notes. Something like org-mode's capture would be great, but I'd like to initiate it from a browser. I imaging hitting a plugin button on the the browser's

Re: [O] ox-html HOWTO? exporting #+RESULTS inside div

2015-10-22 Thread Cook, Malcolm
From: Charles C. Berry <ccbe...@ucsd.edu> Sent: Wednesday, October 21, 2015 9:18 PM To: Cook, Malcolm Cc: emacs-orgmode@gnu.org Subject: Re: ox-html HOWTO? exporting #+RESULTS inside div On Wed, 21 Oct 2015, Cook, Malcolm wrote: > Hi, > &g

Re: [O] pdflatex not found?

2015-10-27 Thread Cook, Malcolm
> > John Kitchin writes: > > > This reminds me that I think I have this problem unless I open Emacs from a > > command line. > > Yup - this is one way of circumvent the problem: by starting emacs from > the command line. And, just to chime in late in the

[O] ox-html HOWTO? exporting #+RESULTS inside div

2015-10-21 Thread Cook, Malcolm
Hi, I would like to contrive for the contents of results blocks to be embedded in a new div with a common class of org-results-container. Can this be accomplished through configuring ox-html somehow? Or must I contrive to modify ox-html.el source? Or is this "Just A Bad Idea" (tm). My use

Re: [O] BUG: emacs orgmode ob-R.el function org-babel-R-evaluate-session over aggressively performs "; ; cleanup extra prompts left in output" and a possible workaround

2015-11-09 Thread Cook, Malcolm
> [...] > > > > > > > [...] > > > > > > > > I've wondered if there is not a better way for Babel to share an > > > > interactive session with the user. For instance, if we wanted to > > > > support a new form of results processing on addition to value and > > > > output Namely,

Re: [O] BUG: emacs orgmode ob-R.el function org-babel-R-evaluate-session over aggressively performs "; ; cleanup extra prompts left in output" and a possible workaround

2015-11-09 Thread Cook, Malcolm
> -Original Message- > From: Charles C. Berry [mailto:ccbe...@ucsd.edu] > Sent: Saturday, November 07, 2015 6:33 PM > To: Cook, Malcolm <m...@stowers.org> > Cc: emacs-orgmode@gnu.org > Subject: Re: BUG: emacs orgmode ob-R.el function org-babel-R-e

Re: [O] ox-html HOWTO? exporting #+RESULTS inside div

2015-11-04 Thread Cook, Malcolm
rgmode-bounces+mec=stowers....@gnu.org] On Behalf Of Cook, Malcolm > Sent: Thursday, October 22, 2015 1:14 AM > To: Charles C. Berry <ccbe...@ucsd.edu> > Cc: emacs-orgmode@gnu.org > Subject: Re: [O] ox-html HOWTO? exporting #+RESULTS inside div > > Charles, > > Exc

Re: [O] BUG: emacs orgmode ob-R.el function org-babel-R-evaluate-session over aggressively performs "; ; cleanup extra prompts left in output" and a possible workaround

2015-11-07 Thread Cook, Malcolm
Thanks Chuck for setting this through. I've never been happy at how Babel arranged the inter process communication with R including the need for cleaning up the output with scary regular expressions like this. Also there are some of uses of temp files that sometime cause of bugs especially

Re: [O] ox-html HOWTO? exporting #+RESULTS inside div

2015-11-06 Thread Cook, Malcolm
> > Charles, Thanks again for you suggestion. Alas, using 'header-args > >:wrap org-results-container' has the unforeseen (by me) side effect > >of masking my use of `#+ATTR_HTML :class dataTable` on selected > >exported tables (which I use to allow for search/sortable/scrollable > >tables).

Re: [O] HowTo? have R :sessions in org mode invoke a specific R

2015-10-16 Thread Cook, Malcolm
Replying on an old thread: > >>On Mon, Nov 4, 2013 at 11:22 AM, Cook, Malcolm <m...@stowers.org> > wrote: > > >> I wish to lock an org buffer to a particular installation of R so that > > all > code blocks use it. > > >> > > >

Re: [O] BUG: emacs orgmode ob-R.el function org-babel-R-evaluate-session over aggressively performs "; ; cleanup extra prompts left in output" and a possible workaround

2015-10-08 Thread Cook, Malcolm
> On Thu, 1 Oct 2015, Cook, Malcolm wrote: > > >>> I am not sure what the best solution is, but, in my hands using > > > > Org-mode version 8.3.2-elpa org-20150929 the reg-expt used to > > > > "cleanup extra prompts left in output" is ov

[O] BUG: emacs orgmode ob-R.el function org-babel-R-evaluate-session over aggressively performs "; ; cleanup extra prompts left in output" and a possible workaround

2015-10-01 Thread Cook, Malcolm
Hello , I am not sure what the best solution is, but, in my hands using Org-mode version 8.3.2-elpa org-20150929 the reg-expt used to "cleanup extra prompts left in output" is over-aggressive and will trim session :output at lines consisting exclusively of blanks and periods such as produced

Re: [O] BUG: emacs orgmode ob-R.el function org-babel-R-evaluate-session over aggressively performs "; ; cleanup extra prompts left in output" and a possible workaround

2015-10-01 Thread Cook, Malcolm
> > I am not sure what the best solution is, but, in my hands using > > Org-mode version 8.3.2-elpa org-20150929 the reg-expt used to "cleanup > > extra prompts left in output" is over-aggressive and will trim session > > :output at lines consisting exclusively of blanks and periods such as >

Re: [O] html export list of figures

2015-09-24 Thread Cook, Malcolm
anks, I will see what I can add. Is this package part of any library available via that package manager? > > Cook, Malcolm writes: > > > Hi, > > > > I see know what to generate a list of figures to appear in my html > > export in addition to my current >

[O] html export list of figures

2015-09-23 Thread Cook, Malcolm
Hi, I see know what to generate a list of figures to appear in my html export in addition to my current #+TOC: listings #+TOC: tables Exporting latex provides #+LATEX: \listoffigures To complement #+LATEX: \tableofcontents #+LATEX: \listoftables But

Re: [O] Table formula bug? (TBLFM line populated, but C-c = prompt is empty)

2015-11-24 Thread Cook, Malcolm
> > I just noticed that upon editing a table formula, C-u C-c C-c was updating > > all > but the first instance of formula (all but the first row). > > > > Org-mode version 8.3.2 > > > > Could this be related issue? > > If it was, I can't reproduce it with the latest pull that fixed my >

Re: [O] Table formula bug? (TBLFM line populated, but C-c = prompt is empty)

2015-11-23 Thread Cook, Malcolm
I just noticed that upon editing a table formula, C-u C-c C-c was updating all but the first instance of formula (all but the first row). Org-mode version 8.3.2 Could this be related issue? > -Original Message- > From: emacs-orgmode-bounces+mec=stowers@gnu.org [mailto:emacs- >

Re: [O] Using tramp to run R source code blocks on remote server

2016-04-22 Thread Cook, Malcolm
> On Fri, 22 Apr 2016, Nick Dokos wrote: > > > Vikas Rawal writes: > > > >> I am trying to run R source code blocks on a remote server > >> (defined in > my ~/.ssh/config as > >> cesp). > >> > >> I am facing several problems. >

Re: [O] Using tramp to run R source code blocks on remote server

2016-04-21 Thread Cook, Malcolm
I believe some of the inter-process communication magic depends upon i/o through a file that exists in /tmp on the remote host If the remote server shares a file system with localhost (does it?), you could contrive for that temp file to live there (~/.emacs.d/ESS.IPC.HACK) instead. I've been

Re: [O] seeking good practices for writing about org using org

2016-08-03 Thread Cook, Malcolm
Hi, Additionally, if I change to #+BEGIN_SRC org :exports both :results value html I do not want the html rendered in the browser when I export to html. Rather, I want to see the html that was created. Actually, having the option to see BOTH would be ideal. Similarly, if I change to

Re: [O] seeking good practices for writing about org using org

2016-08-03 Thread Cook, Malcolm
o:ccbe...@ucsd.edu] > Sent: Wednesday, August 03, 2016 9:16 PM > To: Cook, Malcolm <m...@stowers.org> > Cc: 'emacs-orgmode@gnu.org' <emacs-orgmode@gnu.org> > Subject: Re: seeking good practices for writing about org using org > > On Wed, 3 Aug 2016, Cook, Malco

Re: [O] seeking good practices for writing about org using org

2016-08-04 Thread Cook, Malcolm
Hi Charles, > On Wed, 3 Aug 2016, Cook, Malcolm wrote: > > > Thanks. Much closer. Still some issues. Mind taking another > > gander (hoping the attached jpeg of the webpage rendered comes > > through as an attachment) > >

[O] org-html-list-of-tables ODD BEHAVIOR in producing in html export a hyperlinked table of figures to result tables

2016-08-03 Thread Cook, Malcolm
Hi, I understand that Including in my org file: #+TOC: tables Produces a list of all captioned tables in my document. If the table lacks a caption, it does not appear in the list of tables. Alas, they are not hyperlinked to the table unless I add a #+NAME directive. Oddly, the #+NAME: may

[O] seeking good practices for writing about org using org

2016-08-03 Thread Cook, Malcolm
Hi, I am seeking good practices for writing about org using , erhm, well, org itself. (doh!) I'd use these practices, for example, when writing examples of using org, or lessons in using org, or bug reports about org. I reached of ob-org thinking this is what it was for, and wrote the

Re: [O] How to safely update from ver. 8.2.10 to 8.3.x

2016-08-15 Thread Cook, Malcolm
> this weekend I got through lots of troubles, because I updated my > orgmode version with "manage emacs packages" menu command and > somehow > got mixed preferences. > > Now, after a clean install, I have org mode 8.2.10 and would like to > update to version 8.3.x (20160808) which is shown

Re: [O] org-annotate/collaboration?

2017-02-10 Thread Cook, Malcolm
Alan, just wondering, what operating system and file system are you using now?

Re: [O] How to safely update from ver. 8.2.10 to 8.3.x

2016-08-22 Thread Cook, Malcolm
> > I would not trust the result from failing to drop the -Q since the -Q is > > what > prevents your init file from loading, which we are explicitly trying to avoid > for the sake of compiling org in a fresh environment. > > > According to [[info:emacs#Initial Options]], --batch implies -q.

Re: [O] How to safely update from ver. 8.2.10 to 8.3.x

2016-08-22 Thread Cook, Malcolm
ent. ~Malcolm > > On 22 August 2016 at 12:25, Jorge <jorge13...@gmail.com> wrote: > > On 15 August 2016 at 14:29, Cook, Malcolm <m...@stowers.org> wrote: > >> emacs -Q -batch -eval "(progn (require 'package) (add-to-list > 'package-ar

Re: [O] heading specific fast keys?

2016-12-21 Thread Cook, Malcolm
> -Original Message- > From: Emacs-orgmode [mailto:emacs-orgmode- > bounces+mec=stowers@gnu.org] On Behalf Of John Kitchin > Sent: Wednesday, December 21, 2016 2:18 PM > To: emacs-orgmode@gnu.org > Subject: [O] heading specific fast keys? > > I wondered if anyone know a

Re: [O] is it bad to have both org and org-plus-contrib installed?

2017-04-11 Thread Cook, Malcolm
Hi, Coming late to this fray and responding to original Subject If you (require 'use-package) Then you might find the following to work, as I do: (use-package org :ensure org-plus-contrib ; following

Re: [O] Release 9.1.2

2017-10-05 Thread Cook, Malcolm
> Hi all, Yay! Thanks for org! Always a game changer. Should we expect to find release notes at http://orgmode.org/Changes.html or somewhere else? > > Org 9.1.2 is out. > > Enjoy! > > -- > Bastien >

Re: [O] Release 9.1.2

2017-10-05 Thread Cook, Malcolm
> "Cook, Malcolm" <m...@stowers.org> writes: > > > Should we expect to find release notes at > > http://orgmode.org/Changes.html or somewhere else? > > Yes, that's the place for human readable changelogs, which we update > for major and m

Re: [O] [POLL] Should Org tempo be enabled by default? (expand templates thru e.g. "<s[TAB]")

2018-04-30 Thread Cook, Malcolm
If the poll is still open, I vote don’t change the default. Unless I missed a prior good argument for changing it… Or, unless, upon first invocation, org-mode guided you through or prompted you to changing your defaults, or at the very least, offered/insisted upon your reading ORG-NEWS.

Re: [O] [POLL] Should Org tempo be enabled by default? (expand templates thru e.g. "<s[TAB]")

2018-05-01 Thread Cook, Malcolm
Thanks for the re-cap. I'm changing my vote. Make the change! Change the default! And make lots of noise advertising it (make more prominent https://orgmode.org/Changes.html , etc). Someone suggested going to v10.x Is there a case for this? Thx of org! > -Original Message- >

[O] info-js hijacks clicks disallowing integration with other custom click handlers

2018-03-02 Thread Cook, Malcolm
Hello, I am using infojs_opt while exporting to html from org-mode I find that it “hijacks” all clicks. This is interfering with some custom click handlers I’ve coded up for toggling the display of code listings when clicking on their caption. Does anyone have a suggestion for me to get the

[O] BUG: org-archive-subtree LOSES DATA when run on unsaved buffer

2019-04-09 Thread Cook, Malcolm
Hi, I never use org's archiving capabilities. So imaging my surprise when I accidently invoked org-archive-subtree from its key-binding and I lost a whole subtree of a new buffer which (alas) I had not yet saved to disk Further alas, I was so alarmed not knowing where my content disappeared

[O] sql code block #+BEGIN_SRC sql :tangle qry/testthis.sql :cmdline "-v this=\\'asdf\\'"

2019-09-03 Thread Cook, Malcolm
I am surprised by the level of quoting seemingly required by org-mode to pass a variable to psql in :cmdline The following works: #+PROPERTY: header-args:sql :engine postgresql :dbhost my.host :database mydb :dbuser me #+PROPERTY: header-args:sql+ :tangle no :results table :exports

RE: org 9.2.6 and org 9.1.9

2019-11-26 Thread Cook, Malcolm
Tim, Yes, it is a bit of dependency hell. Quoting myself from Re: [O] How to safely update from ver. 8.2.10 to 8.3.x : Here's what I do, at the shell: emacs -Q -batch -eval "(progn

RE: org 9.2.6 and org 9.1.9

2019-11-27 Thread Cook, Malcolm
Hi Stefan, I don’t think I’ve ever seen a root-cause analysis, but I’ve seen many problems that are resolved by some version of a “clean build” of org. Here are some: - [[https://lists.defectivebydesign.org/archive/html/emacs-orgmode/2012-09/msg01365.html][Installing Org through the new

RE: TMIO Pre-release, request for feedback

2021-06-12 Thread Cook, Malcolm
Agreed, +1, yes yes, much appreciated, I look forward to your summaries, I always learn something useful…. ~Malcolm

RE: org-babel not finding executables when using direnv [Was: Re: ob-sql is not finding psql when using direnv+guix]

2021-05-13 Thread Cook, Malcolm
> > > > >I am using Guix with direnv. > > > > > > > > What is your shell? > > > > > > > > > > My shell is bash, originally I was using zsh and I thought that was the > > > problem, so I switched to bash and still not working. > > > > > > > How/When do you "hook direnv into your shell"

RE: ob-sql is not finding psql when using direnv+guix

2021-05-12 Thread Cook, Malcolm
> > >I am using Guix with direnv. > > > > What is your shell? > > > > My shell is bash, originally I was using zsh and I thought that was the > problem, so I switched to bash and still not working. > > > How/When do you "hook direnv into your shell" (https://direnv.net/)? > > > > In the

RE: ob-sql is not finding psql when using direnv+guix

2021-05-10 Thread Cook, Malcolm
>I am using Guix with direnv. What is your shell? How/When do you "hook direnv into your shell" (https://direnv.net/)? > In an specific folder I am installing and using psql and postgresql using > direnv+guix as follows: >use guix --manifest=cdpp-manifest.scm > >export PGUSER=food_user >export

RE: Sharing variables between source blocks without session

2021-03-18 Thread Cook, Malcolm
Eric S Fraga writes: > >> On Tuesday, 16 Mar 2021 at 09:56, Loris Bennett wrote: >>> How can I avoid having to declare the variable 'user' for both blocks? >> >> I imagine you could use a property, as in >> >> #+property: header-args :var user=loris >> >> or even make it

RE: state of the art in org-mode tables e.g. join, etc

2021-02-21 Thread Cook, Malcolm
John, Checkout what R sqldf package makes easy: ** aggregation example Examples from https://github.com/tbanel/orgaggregate #+NAME: original | Day | Color | Level | Quantity | |---+---+---+--| | Monday| Red |30 | 11 | | Monday| Blue |25

RE: state of the art in org-mode tables e.g. join, etc

2021-02-22 Thread Cook, Malcolm
02:13 To: Cook, Malcolm Cc: John Kitchin ; Tim Cross ; org-mode-email Subject: Re: state of the art in org-mode tables e.g. join, etc ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails. Malcolm, > Check

RE: Unable to get current or via use-package

2022-02-09 Thread Cook, Malcolm
>(use-package org >:ensure org-contrib) I believe `:ensure org-contrib` is no longer needed. I tend to use the org-mode from the package manager, but do not do it interactively from within emacs. Instead, which when I want to refresh org, I do from the command line: emacs -Q -batch

RE: Unable to get current or via use-package

2022-02-10 Thread Cook, Malcolm
Hi Loris, > > I tend to use the org-mode from the package manager, but do not do it > > interactively from within emacs. Instead, which when I want to refresh org, > > I do from the command line: > > > > emacs -Q -batch -eval "(progn (require 'package) (package-initialize) > >

RE: [BUG] org-mode #+SETUPFILE not working with properties [9.5.2 (release_9.5.2-378-g98588e @ /home/eros/src/org-mode/lisp/)]

2022-04-29 Thread Cook, Malcolm
I agree. There is no reason to think this should not work. I have been down this road myself in wished it did. From: Emacs-orgmode On Behalf Of Ihor Radchenko Sent: Thursday, April 28, 2022 9:41 AM To: Eros Zaupa Cc: emacs-orgmode@gnu.org Subject: Re: [BUG] org-mode #+SETUPFILE not working

RE: R code blocks in org version 9.5

2022-10-19 Thread Cook, Malcolm
> My R code blocks work fine in org 9.5. When I plot graph using base graphics > in session, it works fine. The problem is with lattice graphs. With below > header variables, code block works fine. > > #+begin_src R :session *R* :results graphics file :file test.png > library(lattice) >

RE: org-assert-version considered harmful

2022-10-31 Thread Cook, Malcolm
Hello, I found this recent thread researching why my strategy for staying abreast with org head had started failing with invalid-function "org-assert-version" My strategy had been to build org initially with ` cd ~/.emacs.d && git clone https://git.savannah.gnu.org/git/emacs/org-mode.git &&

RE: You can now support Org-mode through https://liberapay.com/org-mode/

2022-09-20 Thread Cook, Malcolm
Thanks for all you do – donation forthcoming! From: Emacs-orgmode On Behalf Of Bastien Sent: Saturday, September 17, 2022 3:32 AM To: emacs-orgmode@gnu.org Subject: You can now support Org-mode through https://liberapay.com/org-mode/ CAUTION: This email is from an External Source. Please use

RE: [BUG] ob-R: session evaluation returns empty ouputs with Org 9.6 [9.6 ( @ /home/fsantos/.emacs.d/elpa/org-9.6/)]

2022-12-07 Thread Cook, Malcolm
>"Cook, Malcolm" <mailto:m...@stowers.org> writes: > >> I tried applying just the change in >> https://git.savannah.gnu.org/cgit/emacs/org-mode.git/commit/?id=456462741 to >> released Org 9.6 and find that when using `:session *R*` the #+RESULTS are

RE: Multiple versions of Org in load-path problem

2022-12-09 Thread Cook, Malcolm
t; > I'm not sure this is related to your problem, or whether that helps > > (but I hope it does)... > > I think it does. > > Side note: > > In my testing, I found a strange case where, in *scratch*, I get: > > (message "%s" org-version) > ;; Error un

RE: bug#59882: Multiple versions of Org in load-path problem

2022-12-09 Thread Cook, Malcolm
> Eli Zaretskii writes: > > >> Cc: emacs-orgmode@gnu.org, 59...@debbugs.gnu.org > >> From: David Masterson > >> Date: Thu, 08 Dec 2022 13:56:03 -0800 > >> > >> In my testing, I found a strange case where, in *scratch*, I get: > >> > >> (message "%s" org-version) > >> ;; Error undefined > >> ;;

RE: [BUG] ob-R: session evaluation returns empty ouputs with Org 9.6 [9.6 ( @ /home/fsantos/.emacs.d/elpa/org-9.6/)]

2022-12-06 Thread Cook, Malcolm
Hi, I tried applying just the change in https://git.savannah.gnu.org/cgit/emacs/org-mode.git/commit/?id=456462741 to released Org 9.6 and find that when using `:session *R*` the #+RESULTS are still empty, but when running without :session the results are provided. Is there any diagnostic or

RE: bug#59882: Multiple versions of Org in load-path problem

2022-12-14 Thread Cook, Malcolm
>On a related note, is it normal that package like org-mouse.el gets >loaded upon calling C-h f org-mouse- completion prompt? >org-mouse.el does not contain a single autoload cookie. There need not be which is apparently by design: The autoload happens as a consequence of emacs' documented

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