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
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&
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
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
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
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
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
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
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 :
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
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
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
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
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
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
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
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
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
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
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.
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
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
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
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
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
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
...
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
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
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&
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<--
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
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
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
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
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
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
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
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
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
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
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
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
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
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.[]*\\([>+.]
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
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 "^\\([ ]*[
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
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
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
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
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
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
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
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
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,
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
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
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
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"))
`
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
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
; 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
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
advance for any help.
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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
_
d replies to the list.
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- Carsten
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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
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
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
man/listinfo/emacs-orgmode
>
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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&
#+results:
: "He said \"I'll do it\"
: but that cannot be echo'ed!"
Best regards,
Seb
--
Sébastien Vauban
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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 --
: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
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
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
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
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Charles C. Berry(858) 534-2098
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Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E ma
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
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" )
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
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
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(
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
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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