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" 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 and if

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&

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 ap

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] 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" 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 at

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 c

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" 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

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" 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 f

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 :

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

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 :ta

[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" 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 - :wrap - :results latex html drawer org code which

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 jav

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 (insi

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 #+BEGI

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" 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 Nicol

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_[headers]{code} setups are also attached. Discussion inline below. On Thu, 13 Nov 2014, Nicolas Goaziou wrote: Hello, "Charles C. Berry&quo

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 w

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 writes: Andreas Leha writes: Hi Marco, Marco Wahl writes: Andreas Leha writes: how would I export an org file containing [[file:./myimage.pdf]] to html so that a say png version myimage.pdf is inlined in the html w

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" 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.

[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 co

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 writes: Andreas Leha wrote: Sebastien Vauban writes: Andreas Leha wrote: For me, that's the correct behavior, as inline code blocks are *only expected to be evaluated during export*. I disagree here. [snip] N

[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 bl

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 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 On Thu, Oct 30, 2014 at 11:37 AM, Grant Rettke wrote: Good morning, Last week I started learning a

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 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 interested, I recommend that yo

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] 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 [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

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 [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 file and reopen

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&

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 writes: Brady Trainor 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 file simply: --8<--

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" writes: On Wed, 8 Oct 2014, Rainer M Krug wrote: "Charles C. Berry" writes: On Mon, 6 Oct 2014, Rainer M Krug wrote: Hi The variable transfer of tables from org to R caused sometimes 'could not

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" 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 int

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 b

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 uw.edu> writes: Charles Millar verizon.net> writes: Brady Trainor wrote: Charles Millar verizon.net> writes: T

Re: [O] [PATCH] WAS Re: Bug: problem w/ R code blocks [8.3beta (release_8.3beta-362-ga92789 /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 myRse

Re: [O] [PATCH] WAS Re: Bug: problem w/ R code blocks [8.3beta (release_8.3beta-362-ga92789 /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 t

Re: [O] [PATCH] WAS Re: Bug: problem w/ R code blocks [8.3beta (release_8.3beta-362-ga92789 /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, it

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 writes: Rainer M Krug 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 answer deleted] Thanks - t

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 su

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

2014-08-23 Thread Charles C. Berry
hanks 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 mig

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

2014-08-07 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 o

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 the

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.[]*\\([>+.]

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 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 for finding this

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 wrote: Charles Berry writes: Eric Schulte gmail.com> writes: [snip] Eric, As noted by Andreas and John this is a problem for session output. org-babel-R-evaluate-session uses (string-match "^\\([ ]*[

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" 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 - attache

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" "FALS

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 t

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 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 been around for a

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

2014-06-12 Thread Charles C. Berry
On Thu, 12 Jun 2014, Eric Schulte wrote: Charles Berry 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 | | #+BEG

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 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 [...] I bel

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" writes: On Mon, 12 May 2014, Rainer M Krug wrote: Eric Schulte writes: [...] [Rainer writes] My idea is to have all R code in one directory and to let ESS load it upon initialization of ESS (which is a dependency of

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

2014-05-12 Thread Charles C. Berry
g to thin about 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 " <>") #+END_SRC HTH, Chuck Charles C. BerryDept of Family/Preventive

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 writes: Rainer M Krug 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 R session. Rainer,

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 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 alias when you chang

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 writes: Bastien gnu.org> writes: Charles Berry 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 back to getting the 'End of Buffe

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 Date: Tue, 9 Apr 2013 19:05:17

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 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 "-%Y-%d-%m") ".txt")) `

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

2011-08-22 Thread Charles C. Berry
example. Thanks, Chuck Thanks -- Eric "Charles C. Berry" 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

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

2011-08-21 Thread Charles C. Berry
cient time to address these issues, but rest assured it is only my TODO list. Thanks -- Eric "Charles C. Berry" writes: , | | * inline code block example | | | AAA | blah blah src_R[:results output]{cat(rnorm(2))} | CC

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

2011-08-09 Thread Charles C. Berry
; seems to give correct 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.edu

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

2011-01-19 Thread Charles C. Berry
ember the outcome? This would be a great feature to have. 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/Preventiv

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

2011-01-18 Thread Charles C. Berry
advance for any help. ___ 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 of Family/Preven

Re: [Orgmode] Reproducible Research Template

2011-01-05 Thread Charles C. Berry
example code in a template? I certainly appreciate any thoughts. --andy 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 _

Re: [Orgmode] Re: Release 7.4

2010-12-10 Thread Charles C. Berry
d replies to the list. Emacs-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/li

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 versi

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

2010-12-06 Thread Charles C. Berry
Thank you in advance. Best Regards, S. On Mon, Dec 6, 2010 at 2:52 PM, Charles C. Berry wrote: 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 of Family/Preve

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

2010-12-06 Thread Charles C. Berry
man/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 _________

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&

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

2010-11-28 Thread Charles C. Berry
#+results: : "He said \"I'll do it\" : but that cannot be echo'ed!" Best regards, Seb -- Sébastien Vauban ___ Emacs-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/em

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

2010-11-22 Thread Charles C. Berry
t;") (: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 --

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

2010-11-22 Thread Charles C. Berry
:tangle . "no") (:exports . "code") (:results . "output replace") (:session\ \ ) ...) "" nil 0) Chuck Thanks for the report -- Eric "Charles C. Berry" writes: Correction in line below. CCB On Sat, 20 Nov 2010, Charles C. Berry wrote: I

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

2010-11-21 Thread Charles C. Berry
On Sat, 20 Nov 2010, Nick Dokos wrote: Charles C. Berry 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 into this too: see

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

[Orgmode] Babel ':session ' bug?

2010-11-20 Thread Charles C. Berry
in the second block leads to ("R" "xyz " ((:colname-names) (:rowname-names) (:result-params "output" "replace") (:result-type . output) (:comments . "") (:shebang . "") (:cache . "no") (:noweb . "no&qu

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

2010-10-07 Thread Charles C. Berry
______ 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. Berry(858) 534-2098

Re: [Orgmode] table, moving cells

2010-09-25 Thread Charles C. Berry
macs-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. Berry(858) 534-2098 Dept of Family/Preventive Medicine E ma

Re: [Orgmode] R code not producing expected results

2010-08-13 Thread Charles C. Berry
Investigator Stowers Institute for Medical Research 1000 East 50th St. Kansas City, MO 64110 Tel: 816-926-4071 Cell: 816-726-8419 Fax: 816-926-2018 ___ Emacs-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/e

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

2010-08-04 Thread Charles C. Berry
" ) x <- rnorm(3) x y <- as.data.frame(diag(2)) y+x cat(" >end of block< ") # no newline #+end_src #+results: : > start of block < : [1] -1.4569661 0.1888919 -0.3685594 : V1 V2 : 1 -0.4569661 -0.3685594 : 2 0.188

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

2010-07-27 Thread Charles C. Berry
I tried it on a bunch of varied 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

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

2010-07-27 Thread Charles C. Berry
b : 1 0.2702748 -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(

Re: [Orgmode] avoiding source block prompts

2010-07-27 Thread Charles C. Berry
ous code block in the same session. Eric, Thanks. That works for me. Chuck Best -- Eric "Charles C. Berry" writes: I think this is a new feature or perhaps a bug, which I noticed when upgrading to version 7.01. The newline and the two prompts '> >' in the results

[Orgmode] avoiding source block prompts

2010-07-26 Thread Charles C. Berry
lts: : [1] 2.186783 Thanks, Chuck 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/cber

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