Re: [O] [babel] [bug] bug in R-specific header argument for graphics driver
Rainer M Krug 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 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: -> -> pdf Execution halted >> >> Cheers, >> >> Rainer >> >> -- 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 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: -> -> 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
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 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: -> -> 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/
[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: -> -> 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-
[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: -> -> 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-
