From: Rainer M Krug <Rainer@krugs.de>
To: Eric Schulte <schulte.eric@gmail.com>
Cc: emacs-orgmode@gnu.org, Charles Berry <ccberry@ucsd.edu>
Subject: Re: [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?
Date: Mon, 07 Apr 2014 09:59:29 +0200 [thread overview]
Message-ID: <m2zjjxzi1q.fsf@krugs.de> (raw)
In-Reply-To: <87bnwio5x4.fsf@gmail.com> (Eric Schulte's message of "Wed, 02 Apr 2014 17:09:37 -0600")
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Eric Schulte <schulte.eric@gmail.com> writes:
> Rainer M Krug <Rainer@krugs.de> writes:
>
>> Eric Schulte <schulte.eric@gmail.com> writes:
>>
>>>>
>>>> Apologies - I am still struggling with encryption......
>>>>
>>>> So here is my example:
>>>>
>>>> --8<---------------cut here---------------start------------->8---
>>>> #+TITLE: single_to_multi
>>>> #+DATE: <2013-10-15 Tue>
>>>> #+AUTHOR: Rainer M. Krug
>>>> #+EMAIL: Rainer@krugs.de
>>>>
>>>> ≈* Load R packages and data
>>>> #+BEGIN_SRC R
>>>> cat("Loading Data\n")
>>>> #+END_SRC
>>>> --8<---------------cut here---------------end--------------->8---
>>>>
>>>> I am using only org loaded and R enabled.
>>>>
>>>> C-c C-c on the block produces the error
>>>>
>>>> emacs version:
>>>> GNU Emacs 24.3.1 (x86_64-apple-darwin13.0.0, Carbon Version 1.6.0
>>>> AppKit 1265) of 2014-02-13 on Rainers-MacBook-Pro-2.local
>>>>
>>>> org version:
>>>> Org-mode version 8.2.5h (release_8.2.5h-837-gb296cc @
>>>> /Users/rainerkrug/.emacs.d/org-mode/lisp/)
>>>>
>>>
>>> Thanks, a fixed version of the patch is attached. If this works please
>>> let me know and I'll apply.
>>
>> Still the same error:
>>
>
> Your previous example works as expected for me with the latest patch.
>
> * Load R packages and data
>
> #+BEGIN_SRC R :results output
> cat("Loading Data\n")
> #+END_SRC
>
> #+RESULTS:
> : Loading Data
>
> Please double check that you applied the patch and reloaded Org-mode,
> and if the bug persists provide another minimal example.
Sorry - no idea what went wrong, but I assumed I applied the old
patch.
I applied the patch and it is working.
Cheers,
Rainer
>
> Thanks,
>
>>
>> ,----
>> | Debugger entered--Lisp error: (wrong-type-argument sequencep 99)
>> | Mapconcat(identity "cat(\"YEAR\")" "\n")
>> | Org-babel-execute:R("cat(\"YEAR\")" ((:comments . "") (:shebang
>> | . "") (:cache . "no") (:padline . "") (:noweb . "no") (:tangle
>> | . "no") (:exports . "code") (:results . "replace output") (:session
>> | . "none") (:hlines . "no") (:result-type . output) (:result-params
>> | "output" "replace") (:rowname-names) (:colname-names)))
>> | org-babel-execute-src-block(nil)
>> | org-babel-execute-src-block-maybe()
>> | org-babel-execute-maybe()
>> | org-babel-execute-safely-maybe()
>> | run-hook-with-args-until-success(org-babel-execute-safely-maybe)
>> | org-ctrl-c-ctrl-c(nil)
>> | call-interactively(org-ctrl-c-ctrl-c nil nil)
>> `----
>>
>> Cheers,
>>
>> Rainer
>>
>>
>>>
>>> Best,
>>>
>>>
>>> From d67248db79faf19e1bdcac0230c37670b6115bdd Mon Sep 17 00:00:00 2001
>>> From: Eric Schulte <schulte.eric@gmail.com>
>>> Date: Sun, 23 Mar 2014 20:01:37 -0600
>>> Subject: [PATCH] only wrap R code graphics-file on execution
>>>
>>> Move this out of the expand-body function so that it is *never*
>>> applied to tangled code.
>>> ---
>>> lisp/ob-R.el | 40 +++++++++++++++++++++-------------------
>>> 1 file changed, 21 insertions(+), 19 deletions(-)
>>>
>>> diff --git a/lisp/ob-R.el b/lisp/ob-R.el
>>> index 62aa7f2..780d99f 100644
>>> --- a/lisp/ob-R.el
>>> +++ b/lisp/ob-R.el
>>> @@ -97,24 +97,15 @@ this variable.")
>>> "Expand BODY according to PARAMS, return the expanded body."
>>> (let ((graphics-file
>>> (or graphics-file (org-babel-R-graphical-output-file params))))
>>> - (mapconcat
>>> - #'identity
>>> - (let ((inside
>>> - (append
>>> - (when (cdr (assoc :prologue params))
>>> - (list (cdr (assoc :prologue params))))
>>> - (org-babel-variable-assignments:R params)
>>> - (list body)
>>> - (when (cdr (assoc :epilogue params))
>>> - (list (cdr (assoc :epilogue params)))))))
>>> - (if graphics-file
>>> - (append
>>> - (list (org-babel-R-construct-graphics-device-call
>>> - graphics-file params))
>>> - inside
>>> - (list "},error=function(e){plot(x=-1:1, y=-1:1, type='n', xlab='', ylab='', axes=FALSE); text(x=0, y=0, labels=e$message, col='red'); paste('ERROR', e$message, sep=' : ')}); dev.off()"))
>>> - inside))
>>> - "\n")))
>>> + (mapconcat #'identity
>>> + (append
>>> + (when (cdr (assoc :prologue params))
>>> + (list (cdr (assoc :prologue params))))
>>> + (org-babel-variable-assignments:R params)
>>> + (list body)
>>> + (when (cdr (assoc :epilogue params))
>>> + (list (cdr (assoc :epilogue params)))))
>>> + "\n")))
>>>
>>> (defun org-babel-execute:R (body params)
>>> "Execute a block of R code.
>>> @@ -127,7 +118,18 @@ This function is called by `org-babel-execute-src-block'."
>>> (colnames-p (cdr (assoc :colnames params)))
>>> (rownames-p (cdr (assoc :rownames params)))
>>> (graphics-file (org-babel-R-graphical-output-file params))
>>> - (full-body (org-babel-expand-body:R body params graphics-file))
>>> + (full-body
>>> + (let ((inside
>>> + (list (org-babel-expand-body:R body params graphics-file))))
>>> + (mapconcat #'identity
>>> + (if graphics-file
>>> + (append
>>> + (list (org-babel-R-construct-graphics-device-call
>>> + graphics-file params))
>>> + inside
>>> + (list "},error=function(e){plot(x=-1:1, y=-1:1, type='n', xlab='', ylab='', axes=FALSE); text(x=0, y=0, labels=e$message, col='red'); paste('ERROR', e$message, sep=' : ')}); dev.off()"))
>>> + inside)
>>> + "\n")))
>>> (result
>>> (org-babel-R-evaluate
>>> session full-body result-type result-params
>>> --
>>> 1.9.1
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa
Tel : +33 - (0)9 53 10 27 44
Cell: +33 - (0)6 85 62 59 98
Fax : +33 - (0)9 58 10 27 44
Fax (D): +49 - (0)3 21 21 25 22 44
email: Rainer@krugs.de
Skype: RMkrug
PGP: 0x0F52F982
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next prev parent reply other threads:[~2014-04-07 7:59 UTC|newest]
Thread overview: 25+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-02-07 6:18 Omitting try/catch blocks from tangled R code? John Hendy
2014-02-07 8:26 ` [BABEL] BUG " Rainer M Krug
2014-02-07 16:47 ` Eric Schulte
2014-02-07 19:22 ` Rainer M Krug
2014-03-12 1:13 ` John Hendy
2014-03-17 15:00 ` Eric Schulte
2014-03-17 17:11 ` John Hendy
2014-03-17 17:44 ` Eric Schulte
2014-03-18 8:44 ` Rainer M Krug
2014-03-18 21:56 ` John Hendy
2014-03-19 19:07 ` Charles Berry
2014-03-20 4:57 ` Eric Schulte
2014-03-20 9:22 ` Rainer M Krug
2014-03-24 2:03 ` Eric Schulte
2014-03-24 10:22 ` Rainer M Krug
2014-03-24 13:16 ` Eric Schulte
2014-03-25 9:37 ` Rainer M Krug
2014-03-26 20:17 ` Eric Schulte
2014-03-28 8:32 ` Rainer M Krug
2014-03-28 8:51 ` Rainer M Krug
2014-03-30 14:19 ` Eric Schulte
2014-03-31 7:52 ` Rainer M Krug
2014-04-02 23:09 ` Eric Schulte
2014-04-07 7:59 ` Rainer M Krug [this message]
2014-04-11 2:35 ` Eric Schulte
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