[O] [babel] [bug] bug in R-specific header argument for graphics driver

2012-03-19 Thread Rainer M Krug
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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:  rai...@krugs.de

Skype:  RMkrug
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Re: [O] [babel] [bug] bug in R-specific header argument for graphics driver

2012-03-19 Thread Eric Schulte
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-XX

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.k...@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:  rai...@krugs.de

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

 iEYEARECAAYFAk9h34AACgkQoYgNqgF2egpEAgCfWUPrimW6av6/m7PU+KgBnNu+
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 =4gNf
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-- 
Eric Schulte
http://cs.unm.edu/~eschulte/



Re: [O] [babel] [bug] bug in R-specific header argument for graphics driver

2012-03-19 Thread Rainer M Krug
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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-XX

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.k...@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:  rai...@krugs.de

Skype:  RMkrug
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Re: [O] [babel] [bug] bug in R-specific header argument for graphics driver

2012-03-19 Thread Eric Schulte
Rainer M Krug r.m.k...@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-XX

 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.k...@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/



[O] [babel] [bug] bug in R-specific header argument for graphics driver

2012-03-15 Thread Rainer M Krug
-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:  rai...@krugs.de

Skype:  RMkrug
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