[O] [babel] [bug] inline src_R breaks downstream src block

2011-08-09 Thread Charles C. Berry
results Also, placing a dummy example like this: , | #+begin_example | #+end_example ` after the src_R line produces correct results. Chuck Charles C. BerryDept of Family/Preventive Medicine cbe...@tajo.ucsd.eduUC San Diego http

Re: [O] [babel] [bug] inline src_R breaks downstream src block

2011-08-21 Thread Charles C. Berry
of days before I have sufficient time to address these issues, but rest assured it is only my TODO list. Thanks -- Eric Charles C. Berry ccbe...@ucsd.edu writes: , | | * inline code block example | | | AAA | blah blah src_R[:results output]{cat(rnorm(2

Re: [O] [babel] [bug] inline src_R breaks downstream src block

2011-08-22 Thread Charles C. Berry
on the example. Thanks, Chuck Thanks -- Eric Charles C. Berry ccbe...@ucsd.edu writes: On Sun, 21 Aug 2011, Eric Schulte wrote: I've just pushed up a change to org-exp-blocks which should fix Charles' original problem related to conflict between inline and regular code blocks. Please let me know

Re: [O] Fwd: Mac OS Alias file links

2014-04-14 Thread Charles C. Berry
On Mon, 14 Apr 2014, Ivan Andrus wrote: On Apr 14, 2014, at 12:36 PM, Ken Mankoff mank...@gmail.com wrote: On 2014-04-14 at 13:42, Charles Berry wrote: For this to work as you fantasize, you would need to enable the Finder application to modify the part of the *.org file that encodes the

Re: [O] [babel][PATCHES] ob-R patches for review

2014-04-30 Thread Charles C. Berry
On Wed, 30 Apr 2014, Rainer M Krug wrote: Charles Berry ccbe...@ucsd.edu writes: Rainer M Krug Rainer at krugs.de writes: Hi Attached please find seven patches for review to implement the storing of org variables in their own environment and to make the org-issued R code look nicer in the

Re: [O] [babel][PATCHES] ob-R patches for review

2014-05-12 Thread Charles C. Berry
elisp. But maybe there is a way of doing both... noweb will do it. Quote the chunk like this: #+BEGIN_SRC emacs-lisp :noweb yes :tangle elisp-R.el (setq rlines r-code) #+END_SRC HTH, Chuck Charles C. BerryDept of Family/Preventive Medicine cberry at ucsd edu

Re: [O] [babel][PATCHES] ob-R patches for review

2014-05-16 Thread Charles C. Berry
till June. Comments inline below. Chuck Charles C. Berry ccbe...@ucsd.edu writes: On Mon, 12 May 2014, Rainer M Krug wrote: Eric Schulte schulte.e...@gmail.com writes: [...] [Rainer writes] My idea is to have all R code in one directory and to let ESS load it upon initialization of ESS

Re: [O] bug in exporter (org-babel-exp-process-buffer)

2014-06-10 Thread Charles C. Berry
On Tue, 10 Jun 2014, Nicolas Goaziou wrote: Hello, Charles Berry ccbe...@ucsd.edu writes: The use of `org-confirm-babel-evaluate' as a function breaks inline src blocks just as was described in this thread from last year: http://lists.gnu.org/archive/html/emacs-orgmode/2013-11/msg00669.html

Re: [O] [bug][babel] noweb gotcha

2014-06-12 Thread Charles C. Berry
On Thu, 12 Jun 2014, Eric Schulte wrote: Charles Berry ccbe...@ucsd.edu writes: The following , | #+PROPERTY: tangle yes | | #+NAME: print-abc | #+BEGIN_SRC emacs-lisp | (format | %s abc) | #+END_SRC | | #+NAME: print-def | #+BEGIN_SRC emacs-lisp | (concat | def ) | #+END_SRC | |

Re: [O] navigation broken - occur, org-babel-goto-named-src-block, etc fail

2014-06-15 Thread Charles C. Berry
On Sun, 15 Jun 2014, Nicolas Richard wrote: Charles Berry ccbe...@ucsd.edu writes: Start with emacs -q, then load today's org-mode. A glitch in 30220ff was quickly fixed in feca87b (three hours ago). Maybe that's what you see ? The ECM still fails. Did it work for you? FWIW, this has

Re: [O] [PATCH] -for review- Tangling with variable transfer of variables

2014-06-21 Thread Charles C. Berry
On Fri, 20 Jun 2014, Rainer M Krug wrote: Attached please find =the reworked patch. 1) uses local() and closes connection 2) does not leave a variable cal;led file behind Seems to work on a few test cases. I'd move the strings to defconsts. Putting a newline before each `%S' will outdent

Re: [O] [PATCH] -for review- Tangling with variable transfer of variables

2014-06-23 Thread Charles C. Berry
On Mon, 23 Jun 2014, Rainer M Krug wrote: One more question concerning the variable transfer of tables: , | (let ((file (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field))) | (header (if (or (eq (nth 1 value) 'hline) colnames-p) | TRUE

Re: [O] [PATCH] -for review- Tangling with variable transfer of variables

2014-06-23 Thread Charles C. Berry
On Mon, 23 Jun 2014, Rainer M Krug wrote: Charles C. Berry ccbe...@ucsd.edu writes: V On Fri, 20 Jun 2014, Rainer M Krug wrote: Attached please find =the reworked patch. 1) uses local() and closes connection 2) does not leave a variable cal;led file behind [deleted] OK - attached

Re: [O] R code block produces only partial output

2014-08-05 Thread Charles C. Berry
On Tue, 5 Aug 2014, John Hendy wrote: On Tue, Aug 5, 2014 at 2:02 PM, Eric Schulte schulte.e...@gmail.com wrote: Charles Berry ccbe...@ucsd.edu writes: Eric Schulte schulte.eric at gmail.com writes: [snip] Eric, As noted by Andreas and John this is a problem for session output.

Re: [O] R code block produces only partial output

2014-08-05 Thread Charles C. Berry
On Tue, 5 Aug 2014, Andreas Kiermeier wrote: ​ On 6 August 2014 03:35, Charles Berry ccbe...@ucsd.edu wrote: ​[snip]​ org-babel-R-evaluate-session uses (string-match ^\\([ ]*[+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\) line) to find the start of R output in the session. [snip] ​ Thanks Charles

Re: [O] R code block produces only partial output

2014-08-06 Thread Charles C. Berry
On Tue, 5 Aug 2014, Aaron Ecay wrote: Hi Chuck, 2014ko abuztuak 5an, Charles C. Berry-ek idatzi zuen: [...] Here is the docstring from ESS's inferior-S-prompt: inferior-S-prompt is a variable defined in `ess-custom.el'. Its value is []a-zA-Z0-9.[]*\\([+.] \\)* [snip] Note

Re: [O] R code block produces only partial output

2014-08-07 Thread Charles C. Berry
On Wed, 6 Aug 2014, Aaron Ecay wrote: Hi Eric, 2014ko abuztuak 6an, Eric Schulte-ek idatzi zuen: [...] Perhaps you could begin with a patch for the regexp issue in this thread? I have pushed a patch which allows us to avoid the regex issue entirely by using a native R method to capture

Re: [O] R code block produces only partial output

2014-08-07 Thread Charles C. Berry
On Thu, 7 Aug 2014, Aaron Ecay wrote: Hi Chuck, Thanks for your feedback. 2014ko abuztuak 7an, Charles C. Berry-ek idatzi zuen: Hi Aaron, I like what you are trying to do, but ... 1) The change has at least one bug: Remote sessions are broken by this change. 2) The behavior of :results

Re: [O] R code block produces only partial output

2014-08-16 Thread Charles C. Berry
On Fri, 15 Aug 2014, Aaron Ecay wrote: Hi Chuck, hi all, Attached to this message is a draft patch to complete this idea. It should address the issue of including warnings, errors, and messages in output. It uses the “evaluate” R package, originally created for the knitr literate programming

Re: [O] R code block produces only partial output

2014-08-23 Thread Charles C. Berry
for your feedback. 2014ko abuztuak 16an, Charles C. Berry-ek idatzi zuen: Aaron, I think doing something along these lines makes sense. evaluate() obviates the need for tryCatch() and capture.output(), and it makes customizing error/warning/message stuff clean. Its use might also lead to cleaner

Re: [O] R code block produces only partial output

2014-09-01 Thread Charles C. Berry
On Sun, 31 Aug 2014, Aaron Ecay wrote: Hi Chuck, Attached is a new version of the patch, including a few more tests. I have one question: 2014ko abuztuak 28an, Aaron Ecay-ek idatzi zuen: but the patch here uses on.exit(file.create(...)) to ensure that that file is created. One hiccup (not

Re: [O] Tangling from code block and header arguments WAS: Format output of org-babel-tangle for exported file

2014-09-03 Thread Charles C. Berry
On Wed, 3 Sep 2014, Rainer M Krug wrote: Charles Berry ccbe...@ucsd.edu writes: Rainer M Krug Rainer at krugs.de writes: Hi I am calling (org-bable-tangle) in a code block in an org file and I would show the files resulting from the tangling in a nice format. [original question nd

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 Charles C. Berry
On Wed, 17 Sep 2014, Aaron Ecay wrote: Hi all, I have pushed the patch to the master branch, thanks to Chuck and to Rainer and Malcom for testing it. Chuck, it looks like you have already provided another “preliminary patch” for org back in 2012 (commit 578a7f5a). If it’s possible for you,

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 Charles C. Berry
On Thu, 18 Sep 2014, Cook, Malcolm wrote: Hi, Hmm, I spoke too soon the problem is only partially fixed by this patch... Trying to work with in org-mode with R code blocks attached to persistent sessions (i.e. adding ':session myRsession' to the code block header ) makes things start

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 Charles C. Berry
On Thu, 18 Sep 2014, Charles C. Berry wrote: On Thu, 18 Sep 2014, Cook, Malcolm wrote: Hi, Hmm, I spoke too soon the problem is only partially fixed by this patch... Trying to work with in org-mode with R code blocks attached to persistent sessions (i.e. adding ':session myRsession

Re: [O] Exporter dispatcher bug?

2014-09-25 Thread Charles C. Berry
On Thu, 25 Sep 2014, Charles Millar wrote: Brady and Charles and all, Thanks for your suggestions. The following is rather long-winded. Charles Berry wrote: Brady Trainor algebrat at uw.edu writes: Charles Millar millarc at verizon.net writes: Brady Trainor wrote: Charles Millar

Re: [O] [PATCH] read.table in variable transfer caused sometimes function not found error - small change

2014-10-07 Thread Charles C. Berry
On Mon, 6 Oct 2014, Rainer M Krug wrote: Hi The variable transfer of tables from org to R caused sometimes 'could not find function read.table' errors (e.g. when the file was tangled into a ./data directory which was loaded by the function devtools::load_all(./)). This can easily be fixed by

Re: [O] [PATCH] read.table in variable transfer caused sometimes function not found error - small change

2014-10-08 Thread Charles C. Berry
On Wed, 8 Oct 2014, Rainer M Krug wrote: Charles C. Berry ccbe...@ucsd.edu writes: On Mon, 6 Oct 2014, Rainer M Krug wrote: Hi The variable transfer of tables from org to R caused sometimes 'could not find function read.table' errors (e.g. when the file was tangled into a ./data directory

Re: [O] [PATCH] read.table in variable transfer caused sometimes function not found error - small change

2014-10-08 Thread Charles C. Berry
On Wed, 8 Oct 2014, Rainer M Krug wrote: Charles C. Berry ccbe...@ucsd.edu writes: On Wed, 8 Oct 2014, Rainer M Krug wrote: Charles C. Berry ccbe...@ucsd.edu writes: On Mon, 6 Oct 2014, Rainer M Krug wrote: Hi The variable transfer of tables from org to R caused sometimes 'could

Re: [O] Text above first headline is being exported, despite :export: tag being used.

2014-10-18 Thread Charles C. Berry
On Sat, 18 Oct 2014, Brady Trainor wrote: Charles Berry ccbe...@ucsd.edu writes: Brady Trainor algebrat at uw.edu writes: But I have trees tagged for export, while text above first headline is being exported. Can anyone confirm? It works for me. Can you provide an ECM[1]? I have in a

Re: [O] Adding `sort' in R makes the output fail

2014-10-23 Thread Charles C. Berry
On Thu, 23 Oct 2014, Sebastien Vauban wrote: Charles C. Berry wrote: On Thu, 23 Oct 2014, Sebastien Vauban wrote: The following code does return a corrupted answer, while it's supposed to return a sorted dataframe. Not so. See below. So, that's RStudio that's wrong, in some way

Re: [O] Stack overflow in regexp matcher

2014-10-25 Thread Charles C. Berry
On Fri, 24 Oct 2014, Gregor Zattler wrote: Hi Charles, org-mode developers * Charles Berry ccbe...@ucsd.edu [24. Oct. 2014]: I do. Try this. Start emacs 24.4.1. 1) Copy this line: CLOCK: [2013-07-22 Mon 12:29]--[2013-07-22 Mon 15:26] = 2:57 into a new *.org file. 2) Save and close the

Re: [O] Stack overflow in regexp matcher

2014-10-25 Thread Charles C. Berry
On Sat, 25 Oct 2014, Charles C. Berry wrote: On Fri, 24 Oct 2014, Gregor Zattler wrote: Hi Charles, org-mode developers * Charles Berry ccbe...@ucsd.edu [24. Oct. 2014]: I do. Try this. Start emacs 24.4.1. 1) Copy this line: CLOCK: [2013-07-22 Mon 12:29]--[2013-07-22 Mon 15:26] = 2:57

Re: [O] R code blocks and 'could not find function .ess.eval'

2014-10-28 Thread Charles C. Berry
On Tue, 28 Oct 2014, William Denton wrote: This problem was reported last month and then again earlier this month, for example here: https://lists.gnu.org/archive/html/emacs-orgmode/2014-10/msg00178.html I'm running Emacs 25.0.50.2, Org 8.2.10 and ESS 14.1x. I'm getting a lot of

Re: [O] [bug] org-edit-src-code auto-save glitch

2013-04-09 Thread Charles C. Berry
On Sun, 7 Apr 2013, Bastien wrote: Hi Charles, Charles Berry ccbe...@ucsd.edu writes: IIUC the problem is that this part of the function , | (setq buffer-file-name nil | buffer-auto-save-file-name | (concat (make-temp-name org-src-) | (format-time-string

Re: [O] [bug] org-edit-src-code auto-save glitch

2013-04-09 Thread Charles C. Berry
On Tue, 9 Apr 2013, Bastien wrote: hi Charles, can you provide a patch for this? http://orgmode.org/worg/org-contribute.html#sec-5 Thanks, -- Bastien Attached. HTH, Chuck From 48de75ed0a78573a5beb32138608ae3784d0f47b Mon Sep 17 00:00:00 2001 From: cberry ccbe...@ucsd.edu Date: Tue, 9

Re: [O] [Patch] don't add indent for empty line when exiting, a code edit

2014-03-13 Thread Charles C. Berry
On Thu, 13 Mar 2014, Bastien wrote: Charles Berry ccbe...@ucsd.edu writes: Bastien bzg at gnu.org writes: Charles Berry ccberry at ucsd.edu writes: Time to failure seems longer. But now I get an infinite loop. Er, sorry for the confusion; should be fixed again. It is not. I am now

[Orgmode] avoiding source block prompts

2010-07-26 Thread Charles C. Berry
? If this is a bug, is there a simple patch to fix it? #+begin_src R :session :results output ### create x x - rnorm(1) ### now print the result x #+end_src #+results: : : [1] 2.186783 What I would have liked is to have something that looks like this: #+results: : [1] 2.186783 Thanks, Chuck Charles C

Prompts again WAS Re: [Orgmode] avoiding source block prompts

2010-07-27 Thread Charles C. Berry
-0.2938296 : 2 1.1095136 0.1769425 On Tue, 27 Jul 2010, Charles C. Berry wrote: On Tue, 27 Jul 2010, Eric Schulte wrote: Hi Charles, I just pushed up a fix for the extra prompts in your output. You will still have a blank line (the output from x - rnorm(1)), however you can suppress

Re: Prompts again WAS Re: [Orgmode] avoiding source block prompts

2010-07-27 Thread Charles C. Berry
source blocks and it seems to work OK, but I worry that there may be case where it will fail. Chuck On Tue, 27 Jul 2010, Charles C. Berry wrote: Eric, I spoke too soon. Have a look at the following. You'll see that the prompts show up there. :-( Chuck #+begin_src R :session :results

Re: Prompts again WAS Re: [Orgmode] avoiding source block prompts

2010-08-04 Thread Charles C. Berry
) invisible(1+1) #+end_src #+results: : 2 Charles C. Berry cbe...@tajo.ucsd.edu writes: Eric, In ob-R.el, changing this (if (string-match ^\\([ ]+\\)\\[[0-9]+\\] line) to this (if (string-match ^\\([ ]*[+][ ]?\\)+\\([[0-9]+\\|[ ]\\) line) seems to fix things (note I

Re: [Orgmode] R code not producing expected results

2010-08-13 Thread Charles C. Berry
list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:cbe

Re: [Orgmode] table, moving cells

2010-09-25 Thread Charles C. Berry
Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:cbe...@tajo.ucsd.edu

Re: [Orgmode] Re: [babel] Writing R-packages the org way?

2010-10-07 Thread Charles C. Berry
http://lists.gnu.org/mailman/listinfo/emacs-orgmode Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:cbe...@tajo.ucsd.edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La

[Orgmode] Babel ':session ' bug?

2010-11-20 Thread Charles C. Berry
. ) (:cache . no) (:noweb . no) (:tangle . no) (:exports . code) (:results . output replace) (:session . *R*) ...) nil 0) Chuck Charles C. BerryDept of Family/Preventive Medicine cbe...@tajo.ucsd.eduUC San Diego http://famprevmed.ucsd.edu/faculty

Re: [Orgmode] Babel ':session ' bug?

2010-11-20 Thread Charles C. Berry
Correction in line below. CCB On Sat, 20 Nov 2010, Charles C. Berry wrote: I think :session without passing a string used to start a session, but now it does not. I think this is a bug. Details: Just did git pull and now with this: , | #+BEGIN_SRC R :session :results output xyz

Re: [Orgmode] Babel ':session ' bug?

2010-11-21 Thread Charles C. Berry
On Sat, 20 Nov 2010, Nick Dokos wrote: Charles C. Berry cbe...@tajo.ucsd.edu wrote: Correction in line below. CCB On Sat, 20 Nov 2010, Charles C. Berry wrote: I think :session without passing a string used to start a session, but now it does not. I think this is a bug. Details: I ran

Re: [Orgmode] Babel ':session ' bug?

2010-11-22 Thread Charles C. Berry
-- Eric Charles C. Berry cbe...@tajo.ucsd.edu writes: Correction in line below. CCB On Sat, 20 Nov 2010, Charles C. Berry wrote: I think :session without passing a string used to start a session, but now it does not. I think this is a bug. Details: Just did git pull and now

Re: [Orgmode] Babel ':session ' bug?

2010-11-22 Thread Charles C. Berry
output replace) (:result-type . output) (:comments . ) (:shebang . ) (:cache . no) (:noweb . no) (:tangle . no) (:exports . code) (:results . output replace) (:session\ \ ) ...) nil 0) Deleting the extra blanks gives the same result you have. Chuck Thanks -- Eric Charles C. Berry cbe

Re: [Orgmode] [Babel] Reporting 2 problems of code execution

2010-11-28 Thread Charles C. Berry
-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode Charles C. BerryDept of Family/Preventive Medicine cbe...@tajo.ucsd.eduUC San Diego http

Re: [Orgmode] Re: [Babel] Reporting 2 problems of code execution

2010-11-29 Thread Charles C. Berry
On Mon, 29 Nov 2010, Sébastien Vauban wrote: Hi Charles, Thanks a lot for taking a look at this, too... Charles C. Berry wrote: On Sun, 28 Nov 2010, Sébastien Vauban wrote: Hi Eric and Dan, * Abstract Reporting two problems: Did you mean to include :results output in the headers

Re: [Orgmode] Re: Org-mode Code Blocks Manuscript: Request For Comments

2010-12-06 Thread Charles C. Berry
://lists.gnu.org/mailman/listinfo/emacs-orgmode ___ Emacs-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode Charles C. BerryDept

Re: [Orgmode] Re: Org-mode Code Blocks Manuscript: Request For Comments

2010-12-06 Thread Charles C. Berry
you in advance. Best Regards, S. On Mon, Dec 6, 2010 at 2:52 PM, Charles C. Berry cbe...@tajo.ucsd.eduwrote: On Sat, 4 Dec 2010, Thomas S. Dye wrote: Aloha Detlef On Dec 2, 2010, at 9:58 PM, Detlef Steuer wrote: Hi! [rest deleted] Charles C. BerryDept

Re: [Orgmode] Re: Org-mode Code Blocks Manuscript: Request For Comments

2010-12-07 Thread Charles C. Berry
On Tue, 7 Dec 2010, Thomas S. Dye wrote: Aloha Chuck, On Dec 6, 2010, at 6:48 PM, Charles C. Berry wrote: On Mon, 6 Dec 2010, Sunny Srivastava wrote: {snip] I posted the vanilla version of the file at http://famprevmed.ucsd.edu/faculty/cberry/org-mode/RpkgExample.org It has the src

Re: [Orgmode] Re: Org-mode Code Blocks Manuscript: Request For Comments

2010-12-09 Thread Charles C. Berry
On Tue, 7 Dec 2010, Thomas S. Dye wrote: Aloha Chuck, On Dec 6, 2010, at 6:48 PM, Charles C. Berry wrote: [stuff deleted] Thanks for sharing this. It looks useful. Would you consider putting it on Worg with the other babel source block examples? OK, I've put up a fresh version

Re: [Orgmode] Re: Release 7.4

2010-12-10 Thread Charles C. Berry
-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode - Carsten ___ Emacs-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode Charles C

Re: [Orgmode] Reproducible Research Template

2011-01-05 Thread Charles C. Berry
Charles C. BerryDept of Family/Preventive Medicine cbe...@tajo.ucsd.eduUC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 ___ Emacs-orgmode mailing list Please

Re: [Orgmode] [BABEL] Tangling to a hierarchy of files?

2011-01-18 Thread Charles C. Berry
`Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode Charles C. BerryDept of Family/Preventive Medicine cbe...@tajo.ucsd.eduUC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La

Re: [Orgmode] [BABEL] Tangling to a hierarchy of files?

2011-01-19 Thread Charles C. Berry
. Eric's embedded Lisp code trick will do the job, but I can imagine that it would get cumbersome for more complex projects. Thanks for all the help, everyone! Chris Charles C. BerryDept of Family/Preventive Medicine cbe...@tajo.ucsd.eduUC San

Re: [O] Anyone using or interested in an org to Rmarkdown exporter?

2014-11-01 Thread Charles C. Berry
On Sat, 1 Nov 2014, Rasmus wrote: Hello, Grant Rettke g...@wisdomandwonder.com writes: • Does one exist and I missed it? Are you aware of this project? https://github.com/chasberry/orgmode-accessories —Rasmus Thanks for this, Rasmus. Grant, If ox-ravel is something you are

Re: [O] Fwd: Anyone using or interested in an org to Rmarkdown exporter?

2014-11-01 Thread Charles C. Berry
On Sat, 1 Nov 2014, John Hendy wrote: [snip] From: John Hendy jw.he...@gmail.com Date: Fri, Oct 31, 2014 at 7:32 PM Subject: Re: [O] Anyone using or interested in an org to Rmarkdown exporter? To: Grant Rettke g...@wisdomandwonder.com On Thu, Oct 30, 2014 at 11:37 AM, Grant Rettke

[O] [PATCH] md backend needs to add blank line before some lists

2014-11-02 Thread Charles C. Berry
John Hendy pointed out [1] that list - item1 - item2 Isn't the same as this: list - item1 - item2 when exported using the `md' backend (or its derivatives). But it needs to be to generate a proper document (at least with engines like pandoc.) The attached patch enables this by adding a

Re: [O] Inline code :results replace not working

2014-11-10 Thread Charles C. Berry
On Mon, 10 Nov 2014, Andreas Leha wrote: Hi Sebastien, Sebastien Vauban sva-n...@mygooglest.com writes: Andreas Leha wrote: Sebastien Vauban sva-n...@mygooglest.com writes: Andreas Leha wrote: For me, that's the correct behavior, as inline code blocks are *only expected to be evaluated

[O] [PATCH] inline src block results can be removed

2014-11-11 Thread Charles C. Berry
Inline src blocks cannot update their results --- causing some of us heaadaches [1]. These patches fix that by placing the result of an inline src block in an export snippet with a faux :back-end called 'babel'. So C-c C-c with point on src_R{1+2} will insert `@@babel:3@@'. Updating the

Re: [O] [PATCH] inline src block results can be removed

2014-11-11 Thread Charles C. Berry
On Wed, 12 Nov 2014, Andreas Leha wrote: Hi Chuck, Charles C. Berry ccbe...@ucsd.edu writes: Inline src blocks cannot update their results --- causing some of us heaadaches [1]. [deleted announcement of fix] First of all: Thanks a lot! I'll (try to find time to) test these patches

Re: [O] pdf images in html export

2014-11-12 Thread Charles C. Berry
On Wed, 12 Nov 2014, Andreas Leha wrote: Hi Rainer, Rainer M Krug rai...@krugs.de writes: Andreas Leha andreas.l...@med.uni-goettingen.de writes: Hi Marco, Marco Wahl marcowahls...@gmail.com writes: Andreas Leha andreas.l...@med.uni-goettingen.de writes: how would I export an org file

Re: [O] [PATCH] inline src block results can be removed

2014-11-12 Thread Charles C. Berry
On Wed, 12 Nov 2014, Aaron Ecay wrote: Hi Chuck, 2014ko azaroak 12an, Charles C. Berry-ek idatzi zuen: Inline src blocks cannot update their results --- causing some of us heaadaches [1]. These patches fix that by placing the result of an inline src block in an export snippet with a faux

Re: [O] [PATCH] inline src block results can be removed

2014-11-14 Thread Charles C. Berry
Nicolas, More patches (as you can see). Now ox.el, ob-core.el, and ob-exp.el are patched. A few examples of how they render various src_lang[headers]{code} setups are also attached. Discussion inline below. On Thu, 13 Nov 2014, Nicolas Goaziou wrote: Hello, Charles C. Berry ccbe

Re: [O] [PATCH] inline src block results can be removed

2014-11-15 Thread Charles C. Berry
On Fri, 14 Nov 2014, Nicolas Goaziou wrote: Charles C. Berry ccbe...@ucsd.edu writes: More patches (as you can see). Now ox.el, ob-core.el, and ob-exp.el are patched. Thanks. [skipping to the bottom - omitting useful critiques of code and opinions about strategy and tactics from Nicolas

Re: [O] #+CALL get the first row of output table lost when using latex export

2014-11-17 Thread Charles C. Berry
On Mon, 17 Nov 2014, iem...@gmail.com wrote: Thank you, Charles. And =:colnames yes= does work here. But the results are the same when I evaluate t1 and t2 with `org-babel-execute-maybe'. When I take another try, new problem seems to occur. The test file is: #+BEGIN_EXAMPLE #+NAME: t1

Re: [O] possible bug in adding properties to headlines with no properties

2014-11-28 Thread Charles C. Berry
On Fri, 28 Nov 2014, John Kitchin wrote: I noticed an undesirable behavior in setting a property on a headline with no properties, but which contains a code block that generates headlines with properties. When I try to set a property with C-c C-x p, the property gets put in the wrong place

Re: [O] Apply a patch with a single key press from Gnus

2015-01-23 Thread Charles C. Berry
On Fri, 23 Jan 2015, Sebastien Vauban wrote: Hello, I've seen some code to apply Git patches from Gnus [1]. That code should be updated to work for Org-mode, not to say for the correct paths to my local repo. Has someone done this already, or are you aware of a standard approach in Gnus to

Re: [O] How to override :eval no in call lines?

2015-01-23 Thread Charles C. Berry
On Fri, 23 Jan 2015, Sebastien Vauban wrote: Charles C. Berry wrote: Sebastien Vauban wrote: In a long document, I must have :eval no at file level, as this is the common setting for most code blocks. However, how do I unset that for some call lines. [snip] I don't get why one has to add

Re: [O] New patches WAS Re: [PATCH] inline src block results can be removed

2015-01-24 Thread Charles C. Berry
On Thu, 22 Jan 2015, Nicolas Goaziou wrote: Charles C. Berry ccbe...@ucsd.edu writes: I attach 3 patches and a file of usage examples. Thanks. [delete - numerous pointers to small issues] This looks good. I think you can push them into master once the minor issues above are fixed

Re: [O] [RFC] removing all results WAS: Re: idempotency ... org-babel-remove-inline-result

2015-02-03 Thread Charles C. Berry
Further Daniele's response to '[bug] Removing the Babel results': http://article.gmane.org/gmane.emacs.orgmode/94604 See below. On Sat, 31 Jan 2015, Charles C. Berry wrote: On Sat, 31 Jan 2015, Daniele Pizzolli wrote: [discussing the RFC, now] Hello Charles, Charles C. Berry writes

Re: [O] export subtree from the command line

2015-02-05 Thread Charles C. Berry
On Thu, 5 Feb 2015, Alan Schmitt wrote: Hello, I'm teaching a class where I have a big monolithic file for all the lectures. Right now I export each lecture as a subtree from the file itself, but I would like to do it from a Makefile. Is it possible to export a subtree from the command line?

Re: [O] [bug] Wrong type argument, computation and layout of inline Babel calls

2015-01-15 Thread Charles C. Berry
On Thu, 15 Jan 2015, Sebastien Vauban wrote: Hello Charles, Charles C. Berry wrote: On Wed, 14 Jan 2015, Sebastien Vauban wrote: Charles C. Berry wrote: On Wed, 14 Jan 2015, Sebastien Vauban wrote: This ECM exhibits wrong type argument. Carré de 7 : call_square(x=7)[:results raw]. Looks

Re: [O] New patches WAS Re: [PATCH] inline src block results can be removed

2015-01-18 Thread Charles C. Berry
On Fri, 16 Jan 2015, Nicolas Goaziou wrote: Charles C. Berry ccbe...@ucsd.edu writes: I've attached three patches and two files that show the behavior under the current master (12 Jan 2015, e0879b03d08bb4acc663084076370482f61e8698) and under the patched version. Thank you. Some comments

Re: [O] How to extract header arguments of a special block?

2015-01-20 Thread Charles C. Berry
On Tue, 20 Jan 2015, Marcin Borkowski wrote: Hello Orgers, assume that I have this in my Org file: #+BEGIN_FOO :bar baz qux whatever #+END_FOO and I want to extract the value of the header argument bar (i.e., the string baz qux in this case). How do I do it? (I'm writing – still – the

Re: [O] New patches WAS Re: [PATCH] inline src block results can be removed

2015-01-21 Thread Charles C. Berry
On Tue, 20 Jan 2015, Nicolas Goaziou wrote: Charles C. Berry ccbe...@ucsd.edu writes: This is probably the shortest path. I'd apprecaite it if you would refactor that part. I implemented `org-macro-escape-arguments' which can replace your initial snippet: Nicolas, Thank you! I attach 3

Re: [O] New patches WAS Re: [PATCH] inline src block results can be removed

2015-01-19 Thread Charles C. Berry
On Mon, 19 Jan 2015, Nicolas Goaziou wrote: Charles C. Berry ccbe...@ucsd.edu writes: Thanks for the patches. Here's another round of comments. OK. Now those cases (and some others) insert `*Inline error:' and a comment as to what the error is and ignore the actual value. Based on my own

Re: [O] [bug] Wrong type argument, computation and layout of inline Babel calls

2015-01-14 Thread Charles C. Berry
On Wed, 14 Jan 2015, Sebastien Vauban wrote: Hello Charles, Charles C. Berry wrote: On Wed, 14 Jan 2015, Sebastien Vauban wrote: This ECM exhibits different troubles: [snip] Carré de 7 : call_square(x=7)[:results raw]. --8---cut here---end---8

Re: [O] [bug] Wrong type argument, computation and layout of inline Babel calls

2015-01-14 Thread Charles C. Berry
Sebastien, See below. On Wed, 14 Jan 2015, Sebastien Vauban wrote: Hello, This ECM exhibits different troubles: - error when exporting to HTML - bad layout - bad computation --8---cut here---start-8--- * Square #+name: square #+begin_src emacs-lisp

Re: [O] How to override :eval no in call lines?

2015-01-22 Thread Charles C. Berry
On Thu, 22 Jan 2015, Sebastien Vauban wrote: Hello, May I bump up this thread? Sebastien Vauban wrote: In a long document, I must have :eval no at file level, as this is the common setting for most code blocks. However, how do I unset that for some call lines. See (info (org) Evaluating

Re: [O] Latex code before maketitle

2015-02-11 Thread Charles C. Berry
On Wed, 11 Feb 2015, Jacob Gerlach wrote: Hi List, I am using a custom Latex class that requires some code between \begin{document} and \maketitle. It seems from looking at ox-latex.el that there is nothing between document start and title command available for me to customize. I suppose I

Re: [O] [PATCH]: Add header-args property to source block info

2015-02-10 Thread Charles C. Berry
On Tue, 10 Feb 2015, Rainer M Krug wrote: Hi Following a recent discussion (based on me forgetting a : when setting the property :header-args), I added the output of the property header-args to the output of org-babel-get-src-block-info to make debugging easier. [snip] Using the patched

Re: [O] [PATCH]: BUG fix and Add header-args property to source block info

2015-02-12 Thread Charles C. Berry
On Thu, 12 Feb 2015, Rainer M Krug wrote: Rainer M Krug rai...@krugs.de writes: Nicolas Goaziou m...@nicolasgoaziou.fr writes: Hello, Rainer M Krug rai...@krugs.de writes: Please find attached the below described patch including the fix for the error reported - function raises error

Re: [O] How to get a column correctly formatted in Babel + R (w/ or w/o name)?

2015-02-19 Thread Charles C. Berry
On Thu, 19 Feb 2015, Sebastien Vauban wrote: #+PROPERTY: session *R* * Source #+name: table | ID | User1 | User2 | |-+---+---| | 26/0163 | lrp | nil | | 37/0001 | nil | nil | | 37/0003 | nil | nil | [snip] * First column (with name) When I try to get

[O] Buffer positions from `org-element-map'?

2015-01-27 Thread Charles C. Berry
I'd like to be able to determine the buffer position of (say) inline src blocks as in the following and operate on them using `org-element-map'. This might enable modification and replacement of a few objects in a large buffer. What I would like is to have the same values of :begin as would be

Re: [O] idempotency and inconsistency for org-babel-remove-inline-result

2015-01-30 Thread Charles C. Berry
On Fri, 30 Jan 2015, Daniele Pizzolli wrote: Hello, I really like the new inline results. Thanks for this new cool feature. I have only a few problems with it. Thanks for your feedback. Is there a way to evaluate a buffer an then remove inline results or better, to get the very same

[O] [RFC] removing all results WAS: Re: idempotency ... org-babel-remove-inline-result

2015-01-30 Thread Charles C. Berry
RFC: the patch to `org-babel-remove-inline-result-one-or-many' removes inline results, too. Do you see any bad consequences? On Fri, 30 Jan 2015, Daniele Pizzolli wrote: Hello Charles, Charles C. Berry writes: On Fri, 30 Jan 2015, Daniele Pizzolli wrote: [discussion of extra

Re: [O] traling whitespace inconsistency for inline babel

2015-01-31 Thread Charles C. Berry
On Sat, 31 Jan 2015, Daniele Pizzolli wrote: Hello Charles, Thanks for fixing the leading whitespace issue. I found another, more impacting, inconsistency involving trailing whitespace during export in release_8.3beta-780-g37fc86: The following line in org: 1 + 4 in R is src_R[:exports

Re: [O] [RFC] removing all results WAS: Re: idempotency ... org-babel-remove-inline-result

2015-01-31 Thread Charles C. Berry
On Sat, 31 Jan 2015, Nicolas Goaziou wrote: Charles C. Berry ccbe...@ucsd.edu writes: [discussion of extra whitespace bug deleted] There is now a bugfix on master. I've also added 'interactive' to `org-babel-remove-inline-result'. Thanks. Would you mind providing a test case for this? I

Re: [O] [RFC] removing all results WAS: Re: idempotency ... org-babel-remove-inline-result

2015-01-31 Thread Charles C. Berry
On Sat, 31 Jan 2015, Daniele Pizzolli wrote: [discussing the RFC, now] Hello Charles, Charles C. Berry writes: RFC: the patch to `org-babel-remove-inline-result-one-or-many' removes inline results, too. Do you see any bad consequences? On Fri, 30 Jan 2015, Daniele Pizzolli wrote: Hello

Re: [O] New patches WAS Re: [PATCH] inline src block results can be removed

2015-01-24 Thread Charles C. Berry
On Sat, 24 Jan 2015, Aaron Ecay wrote: Hi Chuck, 2015ko urtarrilak 24an, Charles C. Berry-ek idatzi zuen: All tests passed (modulo a few shell and fortran issues unique to my setup which also failed for master). Then I did an update and `git merge master' and got a pile of errors due

Re: [O] Tabs in export of code

2015-01-11 Thread Charles C. Berry
On Sun, 11 Jan 2015, Giuseppe Lipari wrote: Dear all, I am preparing a set of slides with examples of java code. I am using the beamer exporter, configured for using minted with the following options: [snip] Ok, now the problem.I want to export a slide with this snippet: #+BEGIN_SRC

[O] New patches WAS Re: [PATCH] inline src block results can be removed

2015-01-12 Thread Charles C. Berry
On Sun, 16 Nov 2014, Nicolas Goaziou wrote: Charles C. Berry ccbe...@ucsd.edu writes: For now, I'd be willing to make patches that will allow removal of the inline src block results that do *not* involve these header args: - :file fn - :wrap wrapper - :results latex html drawer org code

Re: [O] How to override :eval no in call lines?

2015-02-09 Thread Charles C. Berry
On Mon, 9 Feb 2015, Sebastien Vauban wrote: Charles C. Berry wrote: On Fri, 23 Jan 2015, Sebastien Vauban wrote: Charles C. Berry wrote: Sebastien Vauban wrote: In a long document, I must have :eval no at file level, as this is the common setting for most code blocks. However, how do I

Re: [O] export code with backslashes

2015-03-18 Thread Charles C. Berry
On Wed, 18 Mar 2015, hy...@lactose.homelinux.net wrote: Charles C. Berry writes: (defun org-export-ascii-filter-code (text back-end info) Replace `\\n' with `\\' in ascii code. (if (eq back-end 'ascii) (replace-regexp-in-string \n \\\n (org-babel-chomp

Re: [O] export code with backslashes

2015-03-16 Thread Charles C. Berry
On Mon, 16 Mar 2015, hymie! wrote: Greetings. I'm only asking this question because it seems that Orgmode can do anything, although I admit that what I'm asking for is probably outside the normal scope. I have snips of code in my org files, denoted as ~code~. I prefer ~code~ to BEGIN_SRC

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