emacs-orgmode@gnu.org archives
 help / color / mirror / code / Atom feed
* [babel] [bug] bug in R-specific header argument for graphics driver
@ 2012-03-19  8:55 Rainer M Krug
  2012-03-19 14:17 ` Eric Schulte
  0 siblings, 1 reply; 5+ messages in thread
From: Rainer M Krug @ 2012-03-19  8:55 UTC (permalink / raw)
  To: emacs-orgmode; +Cc: Eric Schulte

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

I did not get any response so far, so I hope that the email did not went out...

Rainer


- -----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

When giving the header argument :title: the graph is not produced in a file:

* This works
  Display boxplot of spread of Mff over time for each release strategy
  :PROPERTIES:
  :results: graphics
  :file: SpreadOverTime.pdf
  :width: 4
  :height: 8
  :pointsize: 8
  :END:
  #+begin_src R
    plot(runif(100))
  #+end_src

* This doesn't
  Display boxplot of spread of Mff over time for each release strategy
  :PROPERTIES:
  :results: graphics
  :file: test.pdf
  :width: 4
  :height: 8
  :pointsize: 8
  :title: "test"
  :END:
  #+begin_src R
    plot(runif(100))
  #+end_src

Error message:

Error in pdf(file = "test.pdf", width = 4, height = 8, pointsize = 8,  :
  object 'test' not found
Calls: <Anonymous> -> <Anonymous> -> pdf
Execution halted

Cheers,

Rainer

- - --
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
- -----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.11 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iEYEARECAAYFAk9h34AACgkQoYgNqgF2egpEAgCfWUPrimW6av6/m7PU+KgBnNu+
BegAn2ZWnAhWvflhDKw8225qt9vCkqJg
=4gNf
- -----END PGP SIGNATURE-----
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.11 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iEYEARECAAYFAk9m9IgACgkQoYgNqgF2egr3AgCdG1kEDQLSEuACtvhm8bnQNdhh
3FQAnjbMtLBd4nSOD5MNokTYb+YoiOic
=xSBq
-----END PGP SIGNATURE-----

^ permalink raw reply	[flat|nested] 5+ messages in thread

* Re: [babel] [bug] bug in R-specific header argument for graphics driver
  2012-03-19  8:55 [babel] [bug] bug in R-specific header argument for graphics driver Rainer M Krug
@ 2012-03-19 14:17 ` Eric Schulte
  2012-03-19 14:35   ` Rainer M Krug
  0 siblings, 1 reply; 5+ messages in thread
From: Eric Schulte @ 2012-03-19 14:17 UTC (permalink / raw)
  To: R.M.Krug; +Cc: emacs-orgmode

Hi Rainer,

I see you CC'd me on this email.  I personally do not know anything
about how the graphics header argument to R code blocks works.  I would
recommend looking deeper into the behavior using the following tools

- Look at the expanded code block body using org-babel-expand-src-block
- Run the code block in a session, and then look into the session buffer
  to see what R code is being generated by Babel, then try to debug the
  R as you would normally
- look into the temporary R scripts generated during execution, which
  will live in a directory with a name like /tmp/babel-XXXXXX

If you are able to isolate a bug in Babel then I can help fix that bug
in the elisp code.

Thanks and sorry I can't be of more immediate,

Rainer M Krug <r.m.krug@gmail.com> writes:

> I did not get any response so far, so I hope that the email did not went out...
>
> Rainer
>
>
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> When giving the header argument :title: the graph is not produced in a file:
>
> * This works
>   Display boxplot of spread of Mff over time for each release strategy
>   :PROPERTIES:
>   :results: graphics
>   :file: SpreadOverTime.pdf
>   :width: 4
>   :height: 8
>   :pointsize: 8
>   :END:
>   #+begin_src R
>     plot(runif(100))
>   #+end_src
>
> * This doesn't
>   Display boxplot of spread of Mff over time for each release strategy
>   :PROPERTIES:
>   :results: graphics
>   :file: test.pdf
>   :width: 4
>   :height: 8
>   :pointsize: 8
>   :title: "test"
>   :END:
>   #+begin_src R
>     plot(runif(100))
>   #+end_src
>
> Error message:
>
> Error in pdf(file = "test.pdf", width = 4, height = 8, pointsize = 8,  :
>   object 'test' not found
> Calls: <Anonymous> -> <Anonymous> -> pdf
> Execution halted
>
> Cheers,
>
> Rainer
>
> - --
> 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
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.11 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>
> iEYEARECAAYFAk9h34AACgkQoYgNqgF2egpEAgCfWUPrimW6av6/m7PU+KgBnNu+
> BegAn2ZWnAhWvflhDKw8225qt9vCkqJg
> =4gNf
> -----END PGP SIGNATURE-----

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

^ permalink raw reply	[flat|nested] 5+ messages in thread

* Re: [babel] [bug] bug in R-specific header argument for graphics driver
  2012-03-19 14:17 ` Eric Schulte
@ 2012-03-19 14:35   ` Rainer M Krug
  2012-03-19 14:48     ` Eric Schulte
  0 siblings, 1 reply; 5+ messages in thread
From: Rainer M Krug @ 2012-03-19 14:35 UTC (permalink / raw)
  To: Eric Schulte; +Cc: emacs-orgmode

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

On 19/03/12 15:17, Eric Schulte wrote:
> Hi Rainer,
> 
> I see you CC'd me on this email.  I personally do not know anything about how the graphics
> header argument to R code blocks works.

Sorry - I thought it was part of babel, and when I hear "babel", I think "eric knows it"...


> I would recommend looking deeper into the behavior using the following tools
> 
> - Look at the expanded code block body using org-babel-expand-src-block - Run the code block in
> a session, and then look into the session buffer to see what R code is being generated by
> Babel, then try to debug the R as you would normally - look into the temporary R scripts
> generated during execution, which will live in a directory with a name like /tmp/babel-XXXXXX

Good idea - I'll look into it and give you feedback.

> 
> If you are able to isolate a bug in Babel then I can help fix that bug in the elisp code.

Thanks - I still haven't managed to get into (e)lisp...

> 
> Thanks and sorry I can't be of more immediate,

No problem,

Cheers,

Rainer

> 
> Rainer M Krug <r.m.krug@gmail.com> writes:
> 
>> I did not get any response so far, so I hope that the email did not went out...
>> 
>> Rainer
>> 
>> 
> When giving the header argument :title: the graph is not produced in a file:
> 
> * This works Display boxplot of spread of Mff over time for each release strategy :PROPERTIES: 
> :results: graphics :file: SpreadOverTime.pdf :width: 4 :height: 8 :pointsize: 8 :END: 
> #+begin_src R plot(runif(100)) #+end_src
> 
> * This doesn't Display boxplot of spread of Mff over time for each release strategy 
> :PROPERTIES: :results: graphics :file: test.pdf :width: 4 :height: 8 :pointsize: 8 :title:
> "test" :END: #+begin_src R plot(runif(100)) #+end_src
> 
> Error message:
> 
> Error in pdf(file = "test.pdf", width = 4, height = 8, pointsize = 8,  : object 'test' not
> found Calls: <Anonymous> -> <Anonymous> -> pdf Execution halted
> 
> Cheers,
> 
> Rainer
> 
> 

- -- 
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
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.11 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iEYEARECAAYFAk9nRBsACgkQoYgNqgF2egqjLgCffCgBTR1Eo03E2au/ocUfSAWK
f3UAn2zw0o9ApDpAuxScN3kRrWLWIUYc
=Y5d+
-----END PGP SIGNATURE-----

^ permalink raw reply	[flat|nested] 5+ messages in thread

* Re: [babel] [bug] bug in R-specific header argument for graphics driver
  2012-03-19 14:35   ` Rainer M Krug
@ 2012-03-19 14:48     ` Eric Schulte
  0 siblings, 0 replies; 5+ messages in thread
From: Eric Schulte @ 2012-03-19 14:48 UTC (permalink / raw)
  To: R.M.Krug; +Cc: emacs-orgmode

Rainer M Krug <r.m.krug@gmail.com> writes:

> On 19/03/12 15:17, Eric Schulte wrote:
>> Hi Rainer,
>> 
>> I see you CC'd me on this email.  I personally do not know anything about how the graphics
>> header argument to R code blocks works.
>
> Sorry - I thought it was part of babel, and when I hear "babel", I think "eric knows it"...
>

It is part of Babel, but Dan Davison is the author of much of the R
code, and in general there are increasingly language-specific authors
who know more about support particular to a specific language than do I.

>
>
>> I would recommend looking deeper into the behavior using the following tools
>> 
>> - Look at the expanded code block body using org-babel-expand-src-block - Run the code block in
>> a session, and then look into the session buffer to see what R code is being generated by
>> Babel, then try to debug the R as you would normally - look into the temporary R scripts
>> generated during execution, which will live in a directory with a name like /tmp/babel-XXXXXX
>
> Good idea - I'll look into it and give you feedback.
>

Great, Thanks,

>
>> 
>> If you are able to isolate a bug in Babel then I can help fix that bug in the elisp code.
>
> Thanks - I still haven't managed to get into (e)lisp...
>
>> 
>> Thanks and sorry I can't be of more immediate,
>
> No problem,
>
> Cheers,
>
> Rainer
>
>> 
>> Rainer M Krug <r.m.krug@gmail.com> writes:
>> 
>>> I did not get any response so far, so I hope that the email did not went out...
>>> 
>>> Rainer
>>> 
>>> 
>> When giving the header argument :title: the graph is not produced in a file:
>> 
>> * This works Display boxplot of spread of Mff over time for each release strategy :PROPERTIES: 
>> :results: graphics :file: SpreadOverTime.pdf :width: 4 :height: 8 :pointsize: 8 :END: 
>> #+begin_src R plot(runif(100)) #+end_src
>> 
>> * This doesn't Display boxplot of spread of Mff over time for each release strategy 
>> :PROPERTIES: :results: graphics :file: test.pdf :width: 4 :height: 8 :pointsize: 8 :title:
>> "test" :END: #+begin_src R plot(runif(100)) #+end_src
>> 
>> Error message:
>> 
>> Error in pdf(file = "test.pdf", width = 4, height = 8, pointsize = 8,  : object 'test' not
>> found Calls: <Anonymous> -> <Anonymous> -> pdf Execution halted
>> 
>> Cheers,
>> 
>> Rainer
>> 
>> 

-- 
Eric Schulte
http://cs.unm.edu/~eschulte/

^ permalink raw reply	[flat|nested] 5+ messages in thread

* [babel] [bug] bug in R-specific header argument for graphics driver
@ 2012-03-15 12:24 Rainer M Krug
  0 siblings, 0 replies; 5+ messages in thread
From: Rainer M Krug @ 2012-03-15 12:24 UTC (permalink / raw)
  To: emacs-orgmode; +Cc: Eric Schulte

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

When giving the header argument :title: the graph is not produced in a file:

* This works
  Display boxplot of spread of Mff over time for each release strategy
  :PROPERTIES:
  :results: graphics
  :file: SpreadOverTime.pdf
  :width: 4
  :height: 8
  :pointsize: 8
  :END:
  #+begin_src R
    plot(runif(100))
  #+end_src

* This doesn't
  Display boxplot of spread of Mff over time for each release strategy
  :PROPERTIES:
  :results: graphics
  :file: test.pdf
  :width: 4
  :height: 8
  :pointsize: 8
  :title: "test"
  :END:
  #+begin_src R
    plot(runif(100))
  #+end_src

Error message:

Error in pdf(file = "test.pdf", width = 4, height = 8, pointsize = 8,  :
  object 'test' not found
Calls: <Anonymous> -> <Anonymous> -> pdf
Execution halted

Cheers,

Rainer

- -- 
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
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.11 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iEYEARECAAYFAk9h34AACgkQoYgNqgF2egpEAgCfWUPrimW6av6/m7PU+KgBnNu+
BegAn2ZWnAhWvflhDKw8225qt9vCkqJg
=4gNf
-----END PGP SIGNATURE-----

^ permalink raw reply	[flat|nested] 5+ messages in thread

end of thread, other threads:[~2012-03-19 14:48 UTC | newest]

Thread overview: 5+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2012-03-19  8:55 [babel] [bug] bug in R-specific header argument for graphics driver Rainer M Krug
2012-03-19 14:17 ` Eric Schulte
2012-03-19 14:35   ` Rainer M Krug
2012-03-19 14:48     ` Eric Schulte
  -- strict thread matches above, loose matches on Subject: below --
2012-03-15 12:24 Rainer M Krug

Code repositories for project(s) associated with this inbox:

	https://git.savannah.gnu.org/cgit/emacs/org-mode.git

This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).