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