* R and babel on Windows problem @ 2012-06-28 17:46 John Hendy 2012-06-29 14:59 ` Alexander Vorobiev 2012-06-29 18:26 ` Achim Gratz 0 siblings, 2 replies; 27+ messages in thread From: John Hendy @ 2012-06-28 17:46 UTC (permalink / raw) To: emacs-orgmode I typically use orgmode + babel on Linux and have no problems. Trying to run on Windows 7 and having issues... The pertinent bits from .emacs: ---------- ;; setup babel (add-to-list 'load-path "~/.emacs.d/ess-12.04/lisp") (require 'ess-site) (setq org-babel-R-command "C:/Program\ Files/R/R-2.15.0/bin/R") (org-babel-do-load-languages 'org-babel-load-languages '((latex . t) (R . t))) ---------- When I try to execute a simple R src block, I get: "The system cannot find the path specified." I get the same with or without setting the org-babel-R-command path and with or without using R.exe instead of just R. There's an *ESS* buffer that /appears/ to be finding the versions of R on my machine: ---------- [ess-site.el]: ess-customize-alist=nil [ess-site.el _2_]: ess-customize-alist=nil (R): ess-r-versions-create making M-x defuns for R-2.15.0-64bit R-2.14.1-64bit ---------- Any suggestions? Best regards, John ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-06-28 17:46 R and babel on Windows problem John Hendy @ 2012-06-29 14:59 ` Alexander Vorobiev 2012-06-29 15:24 ` John Hendy 2012-06-29 18:26 ` Achim Gratz 1 sibling, 1 reply; 27+ messages in thread From: Alexander Vorobiev @ 2012-06-29 14:59 UTC (permalink / raw) To: John Hendy; +Cc: emacs-orgmode [-- Attachment #1: Type: text/plain, Size: 1388 bytes --] John, Do you have native Windows emacs or cygwin emacs? I use native emacs on XP with the latest released ess and org-mode, and have no problems with calling R from babel. I do not set the org-babel-R-command which has its default value "R --slave --no-save" and let ess find path to R on my system. Regards, Alex On Thu, Jun 28, 2012 at 12:46 PM, John Hendy <jw.hendy@gmail.com> wrote: > I typically use orgmode + babel on Linux and have no problems. Trying > to run on Windows 7 and having issues... > > The pertinent bits from .emacs: > ---------- > ;; setup babel > (add-to-list 'load-path "~/.emacs.d/ess-12.04/lisp") > (require 'ess-site) > (setq org-babel-R-command "C:/Program\ Files/R/R-2.15.0/bin/R") > (org-babel-do-load-languages > 'org-babel-load-languages > '((latex . t) > (R . t))) > ---------- > > When I try to execute a simple R src block, I get: "The system cannot > find the path specified." I get the same with or without setting the > org-babel-R-command path and with or without using R.exe instead of > just R. > > There's an *ESS* buffer that /appears/ to be finding the versions of R > on my machine: > ---------- > [ess-site.el]: ess-customize-alist=nil > [ess-site.el _2_]: ess-customize-alist=nil > (R): ess-r-versions-create making M-x defuns for > R-2.15.0-64bit > R-2.14.1-64bit > ---------- > > Any suggestions? > > > Best regards, > John > > [-- Attachment #2: Type: text/html, Size: 1870 bytes --] ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-06-29 14:59 ` Alexander Vorobiev @ 2012-06-29 15:24 ` John Hendy 2012-06-29 17:12 ` Alexander Vorobiev 0 siblings, 1 reply; 27+ messages in thread From: John Hendy @ 2012-06-29 15:24 UTC (permalink / raw) To: Alexander Vorobiev; +Cc: emacs-orgmode On Fri, Jun 29, 2012 at 9:59 AM, Alexander Vorobiev <alexander.vorobiev@gmail.com> wrote: > John, > > Do you have native Windows emacs or cygwin emacs? I use native emacs on XP > with the latest released ess and org-mode, and have no problems with calling > R from babel. I do not set the org-babel-R-command which has its default > value "R --slave --no-save" and let ess find path to R on my system. > I installed native Windows and compile org-mode from git with that no compiler worg ditty. -- http://orgmode.org/worg/org-hacks.html#compiling-org-without-make Actually, in finding that page, it looks like it's been updated. I've been using that compile-org lisp code in .emacs and now it appears that functionality is included by default. Maybe I'll update via git and use the built in stuff to see if that helps? Like I said, setting org-babel-R-command makes no difference (commenting it out and re-loading .emacs still produces the error). Also, ess, as posted below, *does* seem to find my installed R versions, so it doesn't seem to be an ess issue? Any other suggestions to try? John > Regards, > Alex > > > On Thu, Jun 28, 2012 at 12:46 PM, John Hendy <jw.hendy@gmail.com> wrote: >> >> I typically use orgmode + babel on Linux and have no problems. Trying >> to run on Windows 7 and having issues... >> >> The pertinent bits from .emacs: >> ---------- >> ;; setup babel >> (add-to-list 'load-path "~/.emacs.d/ess-12.04/lisp") >> (require 'ess-site) >> (setq org-babel-R-command "C:/Program\ Files/R/R-2.15.0/bin/R") >> (org-babel-do-load-languages >> 'org-babel-load-languages >> '((latex . t) >> (R . t))) >> ---------- >> >> When I try to execute a simple R src block, I get: "The system cannot >> find the path specified." I get the same with or without setting the >> org-babel-R-command path and with or without using R.exe instead of >> just R. >> >> There's an *ESS* buffer that /appears/ to be finding the versions of R >> on my machine: >> ---------- >> [ess-site.el]: ess-customize-alist=nil >> [ess-site.el _2_]: ess-customize-alist=nil >> (R): ess-r-versions-create making M-x defuns for >> R-2.15.0-64bit >> R-2.14.1-64bit >> ---------- >> >> Any suggestions? >> >> >> Best regards, >> John >> > ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-06-29 15:24 ` John Hendy @ 2012-06-29 17:12 ` Alexander Vorobiev 0 siblings, 0 replies; 27+ messages in thread From: Alexander Vorobiev @ 2012-06-29 17:12 UTC (permalink / raw) To: John Hendy; +Cc: emacs-orgmode [-- Attachment #1: Type: text/plain, Size: 2717 bytes --] John, I have no experience with the development version of org-mode. Try activating 'enter debugger on error' flag to see where exactly it runs into problems. Also try launching R first in ess so that there is active R session available to babel. Regards, Alex On Fri, Jun 29, 2012 at 10:24 AM, John Hendy <jw.hendy@gmail.com> wrote: > On Fri, Jun 29, 2012 at 9:59 AM, Alexander Vorobiev > <alexander.vorobiev@gmail.com> wrote: > > John, > > > > Do you have native Windows emacs or cygwin emacs? I use native emacs on > XP > > with the latest released ess and org-mode, and have no problems with > calling > > R from babel. I do not set the org-babel-R-command which has its default > > value "R --slave --no-save" and let ess find path to R on my system. > > > > I installed native Windows and compile org-mode from git with that no > compiler worg ditty. > -- http://orgmode.org/worg/org-hacks.html#compiling-org-without-make > > Actually, in finding that page, it looks like it's been updated. I've > been using that compile-org lisp code in .emacs and now it appears > that functionality is included by default. Maybe I'll update via git > and use the built in stuff to see if that helps? > > Like I said, setting org-babel-R-command makes no difference > (commenting it out and re-loading .emacs still produces the error). > > Also, ess, as posted below, *does* seem to find my installed R > versions, so it doesn't seem to be an ess issue? > > > Any other suggestions to try? > John > > > Regards, > > Alex > > > > > > On Thu, Jun 28, 2012 at 12:46 PM, John Hendy <jw.hendy@gmail.com> wrote: > >> > >> I typically use orgmode + babel on Linux and have no problems. Trying > >> to run on Windows 7 and having issues... > >> > >> The pertinent bits from .emacs: > >> ---------- > >> ;; setup babel > >> (add-to-list 'load-path "~/.emacs.d/ess-12.04/lisp") > >> (require 'ess-site) > >> (setq org-babel-R-command "C:/Program\ Files/R/R-2.15.0/bin/R") > >> (org-babel-do-load-languages > >> 'org-babel-load-languages > >> '((latex . t) > >> (R . t))) > >> ---------- > >> > >> When I try to execute a simple R src block, I get: "The system cannot > >> find the path specified." I get the same with or without setting the > >> org-babel-R-command path and with or without using R.exe instead of > >> just R. > >> > >> There's an *ESS* buffer that /appears/ to be finding the versions of R > >> on my machine: > >> ---------- > >> [ess-site.el]: ess-customize-alist=nil > >> [ess-site.el _2_]: ess-customize-alist=nil > >> (R): ess-r-versions-create making M-x defuns for > >> R-2.15.0-64bit > >> R-2.14.1-64bit > >> ---------- > >> > >> Any suggestions? > >> > >> > >> Best regards, > >> John > >> > > > [-- Attachment #2: Type: text/html, Size: 3925 bytes --] ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-06-28 17:46 R and babel on Windows problem John Hendy 2012-06-29 14:59 ` Alexander Vorobiev @ 2012-06-29 18:26 ` Achim Gratz 2012-06-29 19:31 ` John Hendy 1 sibling, 1 reply; 27+ messages in thread From: Achim Gratz @ 2012-06-29 18:26 UTC (permalink / raw) To: emacs-orgmode [re-sent] John Hendy writes: > I typically use orgmode + babel on Linux and have no problems. Trying > to run on Windows 7 and having issues... > > (setq org-babel-R-command "C:/Program\ Files/R/R-2.15.0/bin/R") Try the 8.3 compatible name to avoid the space in the path. If it ever goes through more than one level of unquoting it will otherwise break. (setq org-babel-R-command "C:/Progra~1/R/R-2.15.0/bin/R") Regards, Achim. -- +<[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]>+ Factory and User Sound Singles for Waldorf Blofeld: http://Synth.Stromeko.net/Downloads.html#WaldorfSounds ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-06-29 18:26 ` Achim Gratz @ 2012-06-29 19:31 ` John Hendy 2012-06-29 19:37 ` Nick Dokos 2012-06-30 5:13 ` Achim Gratz 0 siblings, 2 replies; 27+ messages in thread From: John Hendy @ 2012-06-29 19:31 UTC (permalink / raw) To: Achim Gratz; +Cc: emacs-orgmode On Fri, Jun 29, 2012 at 1:26 PM, Achim Gratz <Stromeko@nexgo.de> wrote: > [re-sent] > > John Hendy writes: >> I typically use orgmode + babel on Linux and have no problems. Trying >> to run on Windows 7 and having issues... >> >> (setq org-babel-R-command "C:/Program\ Files/R/R-2.15.0/bin/R") > > Try the 8.3 compatible name to avoid the space in the path. If it ever > goes through more than one level of unquoting it will otherwise break. > > (setq org-babel-R-command "C:/Progra~1/R/R-2.15.0/bin/R") Same error. Also, curiously, =M-x customize-variable RET org-babel-R TAB= yields no results... is this the right variable? John > > > Regards, > Achim. > -- > +<[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]>+ > > Factory and User Sound Singles for Waldorf Blofeld: > http://Synth.Stromeko.net/Downloads.html#WaldorfSounds > > ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-06-29 19:31 ` John Hendy @ 2012-06-29 19:37 ` Nick Dokos 2012-06-29 20:00 ` John Hendy 2012-06-30 5:13 ` Achim Gratz 1 sibling, 1 reply; 27+ messages in thread From: Nick Dokos @ 2012-06-29 19:37 UTC (permalink / raw) To: John Hendy; +Cc: Achim Gratz, emacs-orgmode John Hendy <jw.hendy@gmail.com> wrote: > On Fri, Jun 29, 2012 at 1:26 PM, Achim Gratz <Stromeko@nexgo.de> wrote: > > [re-sent] > > > > John Hendy writes: > >> I typically use orgmode + babel on Linux and have no problems. Trying > >> to run on Windows 7 and having issues... > >> > >> (setq org-babel-R-command "C:/Program\ Files/R/R-2.15.0/bin/R") > > > > Try the 8.3 compatible name to avoid the space in the path. If it ever > > goes through more than one level of unquoting it will otherwise break. > > > > (setq org-babel-R-command "C:/Progra~1/R/R-2.15.0/bin/R") > > Same error. Also, curiously, =M-x customize-variable RET org-babel-R > TAB= yields no results... is this the right variable? > It is, but it seems not to have a customizable interface I guess: I get the same result you do with customize-variable. OTOH, C-h v org-babel-R-TAB brings it up with no problem. Nick ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-06-29 19:37 ` Nick Dokos @ 2012-06-29 20:00 ` John Hendy 2012-06-29 20:16 ` Nick Dokos 0 siblings, 1 reply; 27+ messages in thread From: John Hendy @ 2012-06-29 20:00 UTC (permalink / raw) To: nicholas.dokos; +Cc: Achim Gratz, emacs-orgmode On Fri, Jun 29, 2012 at 2:37 PM, Nick Dokos <nicholas.dokos@hp.com> wrote: > John Hendy <jw.hendy@gmail.com> wrote: > >> On Fri, Jun 29, 2012 at 1:26 PM, Achim Gratz <Stromeko@nexgo.de> wrote: >> > [re-sent] >> > >> > John Hendy writes: >> >> I typically use orgmode + babel on Linux and have no problems. Trying >> >> to run on Windows 7 and having issues... >> >> >> >> (setq org-babel-R-command "C:/Program\ Files/R/R-2.15.0/bin/R") >> > >> > Try the 8.3 compatible name to avoid the space in the path. If it ever >> > goes through more than one level of unquoting it will otherwise break. >> > >> > (setq org-babel-R-command "C:/Progra~1/R/R-2.15.0/bin/R") >> >> Same error. Also, curiously, =M-x customize-variable RET org-babel-R >> TAB= yields no results... is this the right variable? >> > It is, but it seems not to have a customizable interface I guess: I get > the same result you do with customize-variable. OTOH, C-h v > org-babel-R-TAB brings it up with no problem. Good call. It comes up with that and is set to the above (Progra~1 version) but is still saying command not found when I try C-c C-c on a babel block. Any debug methods? Using =M-x R= works find. ESS is finding R. I successfully loaded a .csv, ggplot2 and plotted. John John > > Nick > ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-06-29 20:00 ` John Hendy @ 2012-06-29 20:16 ` Nick Dokos 2012-07-02 20:15 ` John Hendy 0 siblings, 1 reply; 27+ messages in thread From: Nick Dokos @ 2012-06-29 20:16 UTC (permalink / raw) To: John Hendy; +Cc: Achim Gratz, emacs-orgmode John Hendy <jw.hendy@gmail.com> wrote: > On Fri, Jun 29, 2012 at 2:37 PM, Nick Dokos <nicholas.dokos@hp.com> wrote: > > John Hendy <jw.hendy@gmail.com> wrote: > > > >> On Fri, Jun 29, 2012 at 1:26 PM, Achim Gratz <Stromeko@nexgo.de> wrote: > >> > [re-sent] > >> > > >> > John Hendy writes: > >> >> I typically use orgmode + babel on Linux and have no problems. Trying > >> >> to run on Windows 7 and having issues... > >> >> > >> >> (setq org-babel-R-command "C:/Program\ Files/R/R-2.15.0/bin/R") > >> > > >> > Try the 8.3 compatible name to avoid the space in the path. If it ever > >> > goes through more than one level of unquoting it will otherwise break. > >> > > >> > (setq org-babel-R-command "C:/Progra~1/R/R-2.15.0/bin/R") > >> > >> Same error. Also, curiously, =M-x customize-variable RET org-babel-R > >> TAB= yields no results... is this the right variable? > >> > > > > It is, but it seems not to have a customizable interface I guess: I get > > the same result you do with customize-variable. OTOH, C-h v > > org-babel-R-TAB brings it up with no problem. > > Good call. It comes up with that and is set to the above (Progra~1 > version) but is still saying command not found when I try C-c C-c on a > babel block. > > Any debug methods? > edebug org-babel-R-evaluate-external-process and single step through it perhaps? I would clean up .elc files and start a new emacs before trying that just to makee sure that I have a clean slate. You might have to go down to org-babel-eval as well and single step through that. Nick > Using =M-x R= works find. ESS is finding R. I successfully loaded a > .csv, ggplot2 and plotted. > > > John > > John > > > > > Nick > > > ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-06-29 20:16 ` Nick Dokos @ 2012-07-02 20:15 ` John Hendy 2012-07-02 21:26 ` Nick Dokos 0 siblings, 1 reply; 27+ messages in thread From: John Hendy @ 2012-07-02 20:15 UTC (permalink / raw) To: nicholas.dokos; +Cc: Achim Gratz, emacs-orgmode On Fri, Jun 29, 2012 at 3:16 PM, Nick Dokos <nicholas.dokos@hp.com> wrote: > John Hendy <jw.hendy@gmail.com> wrote: > >> On Fri, Jun 29, 2012 at 2:37 PM, Nick Dokos <nicholas.dokos@hp.com> wrote: >> > John Hendy <jw.hendy@gmail.com> wrote: >> > >> >> On Fri, Jun 29, 2012 at 1:26 PM, Achim Gratz <Stromeko@nexgo.de> wrote: >> >> > [re-sent] >> >> > >> >> > John Hendy writes: >> >> >> I typically use orgmode + babel on Linux and have no problems. Trying >> >> >> to run on Windows 7 and having issues... >> >> >> >> >> >> (setq org-babel-R-command "C:/Program\ Files/R/R-2.15.0/bin/R") >> >> > >> >> > Try the 8.3 compatible name to avoid the space in the path. If it ever >> >> > goes through more than one level of unquoting it will otherwise break. >> >> > >> >> > (setq org-babel-R-command "C:/Progra~1/R/R-2.15.0/bin/R") >> >> >> >> Same error. Also, curiously, =M-x customize-variable RET org-babel-R >> >> TAB= yields no results... is this the right variable? >> >> >> >> >> > It is, but it seems not to have a customizable interface I guess: I get >> > the same result you do with customize-variable. OTOH, C-h v >> > org-babel-R-TAB brings it up with no problem. >> >> Good call. It comes up with that and is set to the above (Progra~1 >> version) but is still saying command not found when I try C-c C-c on a >> babel block. >> >> Any debug methods? >> > > edebug org-babel-R-evaluate-external-process and single step through it > perhaps? I would clean up .elc files and start a new emacs before trying > that just to makee sure that I have a clean slate. You might have to go > down to org-babel-eval as well and single step through that. Just did a fresh git clone and make via the updated non-gnu-tools method on worg. The above = `M-x edebug org-babel-R-evaluate-external-process`? I've never done this. When I do `M-x edebug TAB` I get various edebug completions but not it as a standalone command. John > > Nick > >> Using =M-x R= works find. ESS is finding R. I successfully loaded a >> .csv, ggplot2 and plotted. >> >> >> John >> >> John >> >> > >> > Nick >> > >> ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-07-02 20:15 ` John Hendy @ 2012-07-02 21:26 ` Nick Dokos 2012-07-02 21:47 ` John Hendy 0 siblings, 1 reply; 27+ messages in thread From: Nick Dokos @ 2012-07-02 21:26 UTC (permalink / raw) To: John Hendy; +Cc: Achim Gratz, emacs-orgmode John Hendy <jw.hendy@gmail.com> wrote: > On Fri, Jun 29, 2012 at 3:16 PM, Nick Dokos <nicholas.dokos@hp.com> wrote: > > John Hendy <jw.hendy@gmail.com> wrote: > > > >> On Fri, Jun 29, 2012 at 2:37 PM, Nick Dokos <nicholas.dokos@hp.com> wrote: > >> > John Hendy <jw.hendy@gmail.com> wrote: > >> > > >> >> On Fri, Jun 29, 2012 at 1:26 PM, Achim Gratz <Stromeko@nexgo.de> wrote: > >> >> > [re-sent] > >> >> > > >> >> > John Hendy writes: > >> >> >> I typically use orgmode + babel on Linux and have no problems. Trying > >> >> >> to run on Windows 7 and having issues... > >> >> >> > >> >> >> (setq org-babel-R-command "C:/Program\ Files/R/R-2.15.0/bin/R") > >> >> > > >> >> > Try the 8.3 compatible name to avoid the space in the path. If it ever > >> >> > goes through more than one level of unquoting it will otherwise break. > >> >> > > >> >> > (setq org-babel-R-command "C:/Progra~1/R/R-2.15.0/bin/R") > >> >> > >> >> Same error. Also, curiously, =M-x customize-variable RET org-babel-R > >> >> TAB= yields no results... is this the right variable? > >> >> > >> > >> > >> > It is, but it seems not to have a customizable interface I guess: I get > >> > the same result you do with customize-variable. OTOH, C-h v > >> > org-babel-R-TAB brings it up with no problem. > >> > >> Good call. It comes up with that and is set to the above (Progra~1 > >> version) but is still saying command not found when I try C-c C-c on a > >> babel block. > >> > >> Any debug methods? > >> > > > > edebug org-babel-R-evaluate-external-process and single step through it > > perhaps? I would clean up .elc files and start a new emacs before trying > > that just to makee sure that I have a clean slate. You might have to go > > down to org-babel-eval as well and single step through that. > > Just did a fresh git clone and make via the updated non-gnu-tools > method on worg. > > The above = `M-x edebug org-babel-R-evaluate-external-process`? > > I've never done this. When I do `M-x edebug TAB` I get various edebug > completions but not it as a standalone command. > Oh, sorry: edebug is described in (info "(elisp) Edebug") The basics: visit ob-R.el, go to the org-babel-R-evaluate-external-process definition and press C-u C-M-x. Then do whatever you were doing to get the problem. It should stop at the function and you can single-step by pressing SPACE. At strategic points, you can evaluate things with "e". If you mess it up (and you probably will a few times), no problem: just try again. And be patient! Good luck, Nick > > John > > > > > > Nick > > > >> Using =M-x R= works find. ESS is finding R. I successfully loaded a > >> .csv, ggplot2 and plotted. > >> > >> > >> John > >> > >> John > >> > >> > > >> > Nick > >> > > >> > ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-07-02 21:26 ` Nick Dokos @ 2012-07-02 21:47 ` John Hendy 2012-07-02 22:15 ` Nick Dokos 2012-07-02 22:16 ` John Hendy 0 siblings, 2 replies; 27+ messages in thread From: John Hendy @ 2012-07-02 21:47 UTC (permalink / raw) To: nicholas.dokos; +Cc: Achim Gratz, emacs-orgmode On Mon, Jul 2, 2012 at 4:26 PM, Nick Dokos <nicholas.dokos@hp.com> wrote: > John Hendy <jw.hendy@gmail.com> wrote: > >> On Fri, Jun 29, 2012 at 3:16 PM, Nick Dokos <nicholas.dokos@hp.com> wrote: >> > John Hendy <jw.hendy@gmail.com> wrote: >> > >> >> On Fri, Jun 29, 2012 at 2:37 PM, Nick Dokos <nicholas.dokos@hp.com> wrote: >> >> > John Hendy <jw.hendy@gmail.com> wrote: >> >> > >> >> >> On Fri, Jun 29, 2012 at 1:26 PM, Achim Gratz <Stromeko@nexgo.de> wrote: >> >> >> > [re-sent] >> >> >> > >> >> >> > John Hendy writes: >> >> >> >> I typically use orgmode + babel on Linux and have no problems. Trying >> >> >> >> to run on Windows 7 and having issues... >> >> >> >> >> >> >> >> (setq org-babel-R-command "C:/Program\ Files/R/R-2.15.0/bin/R") >> >> >> > >> >> >> > Try the 8.3 compatible name to avoid the space in the path. If it ever >> >> >> > goes through more than one level of unquoting it will otherwise break. >> >> >> > >> >> >> > (setq org-babel-R-command "C:/Progra~1/R/R-2.15.0/bin/R") >> >> >> >> >> >> Same error. Also, curiously, =M-x customize-variable RET org-babel-R >> >> >> TAB= yields no results... is this the right variable? >> >> >> >> >> >> >> >> >> > It is, but it seems not to have a customizable interface I guess: I get >> >> > the same result you do with customize-variable. OTOH, C-h v >> >> > org-babel-R-TAB brings it up with no problem. >> >> >> >> Good call. It comes up with that and is set to the above (Progra~1 >> >> version) but is still saying command not found when I try C-c C-c on a >> >> babel block. >> >> >> >> Any debug methods? >> >> >> > >> > edebug org-babel-R-evaluate-external-process and single step through it >> > perhaps? I would clean up .elc files and start a new emacs before trying >> > that just to makee sure that I have a clean slate. You might have to go >> > down to org-babel-eval as well and single step through that. >> >> Just did a fresh git clone and make via the updated non-gnu-tools >> method on worg. >> >> The above = `M-x edebug org-babel-R-evaluate-external-process`? >> >> I've never done this. When I do `M-x edebug TAB` I get various edebug >> completions but not it as a standalone command. >> > > Oh, sorry: edebug is described in > > (info "(elisp) Edebug") > > The basics: visit ob-R.el, go to the org-babel-R-evaluate-external-process > definition and press C-u C-M-x. Then do whatever you were doing to get the > problem. It should stop at the function and you can single-step by pressing > SPACE. At strategic points, you can evaluate things with "e". Eeks. Is the fact that I learned emacs only for org-mode showing. I don't even know how to =(info "(elisp) Edebug")= -- do I put an =M-x= in front of that? =M-x info= seems to bring me to a help page for info! Anyway... I just googled edebug and it says about the same as you did (except for appending "eval-defun with a prefix argument" onto =C-u C-M-x=. - http://www.gnu.org/software/emacs/manual/html_node/elisp/Using-Edebug.html Anyway: - Visited ob-R.el in emacs - Found org-babel-R-evaluate-external-process - Put the cursor on the line =(defun org-babel-R-evaluate-external-process= - Did =M-x C-M-x= and the minibuffer echoed the name of the function - Visited my file, test.org and did =C-c C-c= on the R babel block - Nothing different occurred; I just got "The system cannot find the path specified" I tried the above again with regular 'ol org-babel-R-evaluate just in case and had the same results. I'm clearly goofing something but have no idea what it is. John > > If you mess it up (and you probably will a few times), no problem: just try > again. And be patient! > > Good luck, > Nick > > > >> >> John >> >> >> > >> > Nick >> > >> >> Using =M-x R= works find. ESS is finding R. I successfully loaded a >> >> .csv, ggplot2 and plotted. >> >> >> >> >> >> John >> >> >> >> John >> >> >> >> > >> >> > Nick >> >> > >> >> >> ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-07-02 21:47 ` John Hendy @ 2012-07-02 22:15 ` Nick Dokos 2012-07-02 22:16 ` John Hendy 1 sibling, 0 replies; 27+ messages in thread From: Nick Dokos @ 2012-07-02 22:15 UTC (permalink / raw) To: John Hendy; +Cc: Achim Gratz, emacs-orgmode John Hendy <jw.hendy@gmail.com> wrote: ... > > > > Oh, sorry: edebug is described in > > > > (info "(elisp) Edebug") > > > > The basics: visit ob-R.el, go to the org-babel-R-evaluate-external-process > > definition and press C-u C-M-x. Then do whatever you were doing to get the > > problem. It should stop at the function and you can single-step by pressing > > SPACE. At strategic points, you can evaluate things with "e". > > Eeks. Is the fact that I learned emacs only for org-mode showing. I > don't even know how to =(info "(elisp) Edebug")= -- do I put an =M-x= > in front of that? =M-x info= seems to bring me to a help page for > info! > You have to evaluate it somehow. If you are reading your mail in emacs, just place the cursor after the closing paren and press C-x C-e. If not, just go to emacs and "C-h i elisp RET i edebug RET" or equivalently, type ESC ESC : (info "(elisp) Edebug") RET. Underlying assumption: you have the Emacs Lisp info files installed. > Anyway... I just googled edebug and it says about the same as you did > (except for appending "eval-defun with a prefix argument" onto =C-u > C-M-x=. > - http://www.gnu.org/software/emacs/manual/html_node/elisp/Using-Edebug.html > > Anyway: > - Visited ob-R.el in emacs > - Found org-babel-R-evaluate-external-process > - Put the cursor on the line =(defun org-babel-R-evaluate-external-process= > - Did =M-x C-M-x= and the minibuffer echoed the name of the function C-u C-M-x please: and the echo area should say "Edebug: org-babel-R-evaluate-external-process" afterwards. Nick > - Visited my file, test.org and did =C-c C-c= on the R babel block > - Nothing different occurred; I just got "The system cannot find the > path specified" > > I tried the above again with regular 'ol org-babel-R-evaluate just in > case and had the same results. > > I'm clearly goofing something but have no idea what it is. > > > John > > > > > > If you mess it up (and you probably will a few times), no problem: just try > > again. And be patient! > > > > Good luck, > > Nick > > > > > > > >> > >> John > >> > >> > >> > > >> > Nick > >> > > >> >> Using =M-x R= works find. ESS is finding R. I successfully loaded a > >> >> .csv, ggplot2 and plotted. > >> >> > >> >> > >> >> John > >> >> > >> >> John > >> >> > >> >> > > >> >> > Nick > >> >> > > >> >> > >> > ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-07-02 21:47 ` John Hendy 2012-07-02 22:15 ` Nick Dokos @ 2012-07-02 22:16 ` John Hendy 2012-07-06 16:58 ` John Hendy 1 sibling, 1 reply; 27+ messages in thread From: John Hendy @ 2012-07-02 22:16 UTC (permalink / raw) To: nicholas.dokos; +Cc: Achim Gratz, emacs-orgmode > > Anyway: > - Visited ob-R.el in emacs > - Found org-babel-R-evaluate-external-process > - Put the cursor on the line =(defun org-babel-R-evaluate-external-process= > - Did =M-x C-M-x= and the minibuffer echoed the name of the function > - Visited my file, test.org and did =C-c C-c= on the R babel block > - Nothing different occurred; I just got "The system cannot find the > path specified" > > I tried the above again with regular 'ol org-babel-R-evaluate just in > case and had the same results. > > I'm clearly goofing something but have no idea what it is. > Okay. I think I may have triggered =edebug-all-defs= when I was tinkering around earlier and from the page about "instrumenting" edebug it seemed like that could tweak some things undesirably. I got that fixed and turned on edebug for org-babel-R-evaluate-external-process and am getting nothing. The modeline in my test file has turned to "Org *Debugging* Fill" but still produces none of the incremental evaluation pauses I would have expected. I tried the same with org-babel-execute-src-block in ob.el since that's what's called first and am still getting no new activity from edebug. Just the same message about the path. John > > John > > >> >> If you mess it up (and you probably will a few times), no problem: just try >> again. And be patient! >> >> Good luck, >> Nick >> >> >> >>> >>> John >>> >>> >>> > >>> > Nick >>> > >>> >> Using =M-x R= works find. ESS is finding R. I successfully loaded a >>> >> .csv, ggplot2 and plotted. >>> >> >>> >> >>> >> John >>> >> >>> >> John >>> >> >>> >> > >>> >> > Nick >>> >> > >>> >> >>> ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-07-02 22:16 ` John Hendy @ 2012-07-06 16:58 ` John Hendy 2012-07-06 17:12 ` Nick Dokos 0 siblings, 1 reply; 27+ messages in thread From: John Hendy @ 2012-07-06 16:58 UTC (permalink / raw) To: nicholas.dokos; +Cc: Achim Gratz, emacs-orgmode On Mon, Jul 2, 2012 at 5:16 PM, John Hendy <jw.hendy@gmail.com> wrote: >> >> Anyway: >> - Visited ob-R.el in emacs >> - Found org-babel-R-evaluate-external-process >> - Put the cursor on the line =(defun org-babel-R-evaluate-external-process= >> - Did =M-x C-M-x= and the minibuffer echoed the name of the function >> - Visited my file, test.org and did =C-c C-c= on the R babel block >> - Nothing different occurred; I just got "The system cannot find the >> path specified" >> >> I tried the above again with regular 'ol org-babel-R-evaluate just in >> case and had the same results. >> >> I'm clearly goofing something but have no idea what it is. >> > > Okay. I think I may have triggered =edebug-all-defs= when I was > tinkering around earlier and from the page about "instrumenting" > edebug it seemed like that could tweak some things undesirably. I got > that fixed and turned on edebug for > org-babel-R-evaluate-external-process and am getting nothing. The > modeline in my test file has turned to "Org *Debugging* Fill" but > still produces none of the incremental evaluation pauses I would have > expected. > > I tried the same with org-babel-execute-src-block in ob.el since > that's what's called first and am still getting no new activity from > edebug. Just the same message about the path. Any updates on this? Could someone provide a minimal example I could try? Or verify that my steps above are correct. I'm not sure why it's not triggering the step by step function execution described. Thanks! John ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-07-06 16:58 ` John Hendy @ 2012-07-06 17:12 ` Nick Dokos 2012-07-06 17:46 ` John Hendy 0 siblings, 1 reply; 27+ messages in thread From: Nick Dokos @ 2012-07-06 17:12 UTC (permalink / raw) To: John Hendy; +Cc: Achim Gratz, emacs-orgmode John Hendy <jw.hendy@gmail.com> wrote: > Any updates on this? Could someone provide a minimal example I could > try? Or verify that my steps above are correct. I'm not sure why it's > not triggering the step by step function execution described. > I had sent out a note about C-u C-M-x and what you should see in the echo area after that, but I don't think I've seen a reply: did you try that and did it work as expected? Either gmane is or I am being stupid right now and cannot find the message (maybe it never made it, but gmane cannot seem to find the thread at all right now), so I append a copy of that message. Nick John Hendy <jw.hendy@gmail.com> wrote: ... > > > > Oh, sorry: edebug is described in > > > > (info "(elisp) Edebug") > > > > The basics: visit ob-R.el, go to the org-babel-R-evaluate-external-process > > definition and press C-u C-M-x. Then do whatever you were doing to get the > > problem. It should stop at the function and you can single-step by pressing > > SPACE. At strategic points, you can evaluate things with "e". > > Eeks. Is the fact that I learned emacs only for org-mode showing. I > don't even know how to =(info "(elisp) Edebug")= -- do I put an =M-x= > in front of that? =M-x info= seems to bring me to a help page for > info! > You have to evaluate it somehow. If you are reading your mail in emacs, just place the cursor after the closing paren and press C-x C-e. If not, just go to emacs and "C-h i elisp RET i edebug RET" or equivalently, type ESC ESC : (info "(elisp) Edebug") RET. Underlying assumption: you have the Emacs Lisp info files installed. > Anyway... I just googled edebug and it says about the same as you did > (except for appending "eval-defun with a prefix argument" onto =C-u > C-M-x=. > - http://www.gnu.org/software/emacs/manual/html_node/elisp/Using-Edebug.html > > Anyway: > - Visited ob-R.el in emacs > - Found org-babel-R-evaluate-external-process > - Put the cursor on the line =(defun org-babel-R-evaluate-external-process= > - Did =M-x C-M-x= and the minibuffer echoed the name of the function C-u C-M-x please: and the echo area should say "Edebug: org-babel-R-evaluate-external-process" afterwards. Nick > - Visited my file, test.org and did =C-c C-c= on the R babel block > - Nothing different occurred; I just got "The system cannot find the > path specified" > > I tried the above again with regular 'ol org-babel-R-evaluate just in > case and had the same results. > > I'm clearly goofing something but have no idea what it is. > > > John > > > > > > If you mess it up (and you probably will a few times), no problem: just try > > again. And be patient! > > > > Good luck, > > Nick > > > > > > > >> > >> John > >> > >> > >> > > >> > Nick > >> > > >> >> Using =M-x R= works find. ESS is finding R. I successfully loaded a > >> >> .csv, ggplot2 and plotted. > >> >> > >> >> > >> >> John > >> >> > >> >> John > >> >> > >> >> > > >> >> > Nick > >> >> > > >> >> > >> > ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-07-06 17:12 ` Nick Dokos @ 2012-07-06 17:46 ` John Hendy 2012-07-06 18:41 ` Eric Schulte 2012-07-06 18:45 ` Nick Dokos 0 siblings, 2 replies; 27+ messages in thread From: John Hendy @ 2012-07-06 17:46 UTC (permalink / raw) To: nicholas.dokos; +Cc: Achim Gratz, emacs-orgmode On Fri, Jul 6, 2012 at 12:12 PM, Nick Dokos <nicholas.dokos@hp.com> wrote: > John Hendy <jw.hendy@gmail.com> wrote: > >> Any updates on this? Could someone provide a minimal example I could >> try? Or verify that my steps above are correct. I'm not sure why it's >> not triggering the step by step function execution described. >> > > I had sent out a note about C-u C-M-x and what you should see in the > echo area after that, but I don't think I've seen a reply: did you try > that and did it work as expected? > > Either gmane is or I am being stupid right now and cannot find the message > (maybe it never made it, but gmane cannot seem to find the thread at all > right now), so I append a copy of that message. Yes. I guess I didn't explicitly say, but I mentioned that I had triggered something goofy by accident in my earlier hunt for edebug. I'll walkthrough right now: - Got to ob-R.el in emacs - C-s to find org-babel-R-evaluate-external-process - C-u C-M-x - Minibuffer: "Edebug: org-babel-R-evaluate-external-process" - Visit file test.org - C-c C-c on the src block - Well... of course it works now. Not sure what I was doing wrong before. I pressed space continually until failure, then again to verify the failing line. It's this one (line 313): ,--- | (output (org-babel-eval org-babel-R-command body)))) `--- When I run this line: ,--- | (org-babel-eval org-babel-R-command `--- I get this in the minibuffer: ,--- | Result: "C:/Progra~1/R/R-2.15.0/bin/R" `--- Should I be able to run this from the Windows cmd prompt successfully? I think this is my problem. Even using tab completion to ensure the path is correct, I get the same error message "The system cannot find the path specified" when I run this from cmd! I guess I honed in on my problem. I can run R from my Start Menu shortcut fine. Update: I'm on 64bit and just now realized there's another set of R cmds in ../R-2.15.0/bin/x64/. This is what I needed. Now my problem is that using R along doesn't produce any output. With the above modification, I get: ,--- | Fatal error: you must specify '--save', '--no-save' or '--vanilla' `--- I'm quite close! If I add --no-save, I get exported results but they include all of the R preamble text from when it starts. Here's my block for reference: #+begin_src R :results output org :exports results x <- c(1:10) summary(x) #+end_src Thanks, John > > Nick > > > John Hendy <jw.hendy@gmail.com> wrote: > ... >> > >> > Oh, sorry: edebug is described in >> > >> > (info "(elisp) Edebug") >> > >> > The basics: visit ob-R.el, go to the org-babel-R-evaluate-external-process >> > definition and press C-u C-M-x. Then do whatever you were doing to get the >> > problem. It should stop at the function and you can single-step by pressing >> > SPACE. At strategic points, you can evaluate things with "e". >> >> Eeks. Is the fact that I learned emacs only for org-mode showing. I >> don't even know how to =(info "(elisp) Edebug")= -- do I put an =M-x= >> in front of that? =M-x info= seems to bring me to a help page for >> info! >> > > You have to evaluate it somehow. If you are reading your mail in emacs, > just place the cursor after the closing paren and press C-x C-e. If not, > just go to emacs and "C-h i elisp RET i edebug RET" or equivalently, > type ESC ESC : (info "(elisp) Edebug") RET. Underlying assumption: you > have the Emacs Lisp info files installed. > >> Anyway... I just googled edebug and it says about the same as you did >> (except for appending "eval-defun with a prefix argument" onto =C-u >> C-M-x=. >> - http://www.gnu.org/software/emacs/manual/html_node/elisp/Using-Edebug.html >> >> Anyway: >> - Visited ob-R.el in emacs >> - Found org-babel-R-evaluate-external-process >> - Put the cursor on the line =(defun org-babel-R-evaluate-external-process= >> - Did =M-x C-M-x= and the minibuffer echoed the name of the function > > C-u C-M-x please: and the echo area should say "Edebug: > org-babel-R-evaluate-external-process" afterwards. > > Nick > >> - Visited my file, test.org and did =C-c C-c= on the R babel block >> - Nothing different occurred; I just got "The system cannot find the >> path specified" >> >> I tried the above again with regular 'ol org-babel-R-evaluate just in >> case and had the same results. >> >> I'm clearly goofing something but have no idea what it is. >> >> >> John >> >> >> > >> > If you mess it up (and you probably will a few times), no problem: just try >> > again. And be patient! >> > >> > Good luck, >> > Nick >> > >> > >> > >> >> >> >> John >> >> >> >> >> >> > >> >> > Nick >> >> > >> >> >> Using =M-x R= works find. ESS is finding R. I successfully loaded a >> >> >> .csv, ggplot2 and plotted. >> >> >> >> >> >> >> >> >> John >> >> >> >> >> >> John >> >> >> >> >> >> > >> >> >> > Nick >> >> >> > >> >> >> >> >> >> > > ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-07-06 17:46 ` John Hendy @ 2012-07-06 18:41 ` Eric Schulte 2012-07-06 22:05 ` John Hendy 2012-07-06 18:45 ` Nick Dokos 1 sibling, 1 reply; 27+ messages in thread From: Eric Schulte @ 2012-07-06 18:41 UTC (permalink / raw) To: John Hendy; +Cc: Achim Gratz, nicholas.dokos, emacs-orgmode > > Update: I'm on 64bit and just now realized there's another set of R > cmds in ../R-2.15.0/bin/x64/. This is what I needed. > > Now my problem is that using R along doesn't produce any output. With > the above modification, I get: > > ,--- > | Fatal error: you must specify '--save', '--no-save' or '--vanilla' > `--- > > I'm quite close! If I add --no-save, I get exported results but they > include all of the R preamble text from when it starts. Here's my > block for reference: > > #+begin_src R :results output org :exports results > > x <- c(1:10) > summary(x) > > #+end_src > The default value for org-babel-R-command is "R --slave --no-save", so maybe adding the "--slave" option to your command will remove the R preamble text. As for your path problems, the "~" looks like a likely culprit. The command is passed to an equivalent of the `shell-command-on-region' function, which then uses a shell to run the command. Maybe the shell it uses can't handle the tilde? Best, p.s., I'm jumping into this thread part way through and didn't read all of the back-log, so I apologize if I'm repeating previous advice. -- Eric Schulte http://cs.unm.edu/~eschulte ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-07-06 18:41 ` Eric Schulte @ 2012-07-06 22:05 ` John Hendy 0 siblings, 0 replies; 27+ messages in thread From: John Hendy @ 2012-07-06 22:05 UTC (permalink / raw) To: Eric Schulte; +Cc: Achim Gratz, nicholas.dokos, emacs-orgmode On Fri, Jul 6, 2012 at 1:41 PM, Eric Schulte <eric.schulte@gmx.com> wrote: >> >> Update: I'm on 64bit and just now realized there's another set of R >> cmds in ../R-2.15.0/bin/x64/. This is what I needed. >> >> Now my problem is that using R along doesn't produce any output. With >> the above modification, I get: >> >> ,--- >> | Fatal error: you must specify '--save', '--no-save' or '--vanilla' >> `--- >> >> I'm quite close! If I add --no-save, I get exported results but they >> include all of the R preamble text from when it starts. Here's my >> block for reference: >> >> #+begin_src R :results output org :exports results >> >> x <- c(1:10) >> summary(x) >> >> #+end_src >> > > The default value for org-babel-R-command is "R --slave --no-save", so > maybe adding the "--slave" option to your command will remove the R > preamble text. Yes! It's now working. I checked out the output of just runing "R" from the command line in Windows, but did not see the --slave option. Adding these to my .emacs setup of =org-babel-R-command= has worked and it is now exporting results as expected. Thanks so much -- for the times I need to use Windows at work, it's going to be a lot easier to work with exportable/executable code blocks in org-mode. Thanks again for the persistence, John > > As for your path problems, the "~" looks like a likely culprit. The > command is passed to an equivalent of the `shell-command-on-region' > function, which then uses a shell to run the command. Maybe the shell > it uses can't handle the tilde? > > Best, > > p.s., I'm jumping into this thread part way through and didn't read all > of the back-log, so I apologize if I'm repeating previous advice. > > -- > Eric Schulte > http://cs.unm.edu/~eschulte ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-07-06 17:46 ` John Hendy 2012-07-06 18:41 ` Eric Schulte @ 2012-07-06 18:45 ` Nick Dokos 2012-07-06 22:08 ` John Hendy 1 sibling, 1 reply; 27+ messages in thread From: Nick Dokos @ 2012-07-06 18:45 UTC (permalink / raw) To: John Hendy; +Cc: Achim Gratz, emacs-orgmode John Hendy <jw.hendy@gmail.com> wrote: > On Fri, Jul 6, 2012 at 12:12 PM, Nick Dokos <nicholas.dokos@hp.com> wrote: > > John Hendy <jw.hendy@gmail.com> wrote: > > > >> Any updates on this? Could someone provide a minimal example I could > >> try? Or verify that my steps above are correct. I'm not sure why it's > >> not triggering the step by step function execution described. > >> > > > > I had sent out a note about C-u C-M-x and what you should see in the > > echo area after that, but I don't think I've seen a reply: did you try > > that and did it work as expected? > > > > Either gmane is or I am being stupid right now and cannot find the message > > (maybe it never made it, but gmane cannot seem to find the thread at all > > right now), so I append a copy of that message. > > Yes. I guess I didn't explicitly say, but I mentioned that I had > triggered something goofy by accident in my earlier hunt for edebug. > I'll walkthrough right now: > - Got to ob-R.el in emacs > - C-s to find org-babel-R-evaluate-external-process > - C-u C-M-x > - Minibuffer: "Edebug: org-babel-R-evaluate-external-process" > - Visit file test.org > - C-c C-c on the src block > - Well... of course it works now. Not sure what I was doing wrong before. > The reason that I sent out that note was that you mentioned pressing M-x C-M-x (rather than C-u C-M-x) and getting the name of the function echoed (without the "Edebug: " part), so I wanted to make sure that you were DTRT here. Could that be what you were doing wrong? or was that a typo on your part? > I pressed space continually until failure, then again to verify the > failing line. It's this one (line 313): > > ,--- > | (output (org-babel-eval org-babel-R-command body)))) > `--- > Just fyi and to clarify some basic lisp: the form (org-babel-eval org-babel-R-command body) says: evaluate the org-babel-eval function with arguments org-babel-R-command and body (actually, those variables are evaluated first and then the *values* are passed to the function). The evaluation returns a result (a string in this case) which is assigned to the local variable output for further processing (local, because this whole thing is part of a let-form which is not shown in your snippet). I.e. a function call in lisp always looks like this: (<func> <arg1> <arg2> ....) > When I run this line: > > ,--- > | (org-babel-eval org-babel-R-command > `--- > > I get this in the minibuffer: > > ,--- > | Result: "C:/Progra~1/R/R-2.15.0/bin/R" > `--- > I presume you just typed "e" when the cursor was after the variable: that just evaluates the variable. If you press SPACE then the cursor would advance to after the ``body'' variable (on the closing paren) and an "e" would evaluate *that* variable. After another SPACE, the cursor would be *after* the closing paren and an "e" would evaluate the function call and you would see the result, i.e. what would be assigned to ``output''. > Should I be able to run this from the Windows cmd prompt successfully? > I think this is my problem. Even using tab completion to ensure the > path is correct, I get the same error message "The system cannot find > the path specified" when I run this from cmd! > > I guess I honed in on my problem. I can run R from my Start Menu shortcut fine. > > Update: I'm on 64bit and just now realized there's another set of R > cmds in ../R-2.15.0/bin/x64/. This is what I needed. > > Now my problem is that using R along doesn't produce any output. With > the above modification, I get: > > ,--- > | Fatal error: you must specify '--save', '--no-save' or '--vanilla' > `--- > > I'm quite close! If I add --no-save, I get exported results but they > include all of the R preamble text from when it starts. Here's my > block for reference: > > #+begin_src R :results output org :exports results > > x <- c(1:10) > summary(x) > > #+end_src > OK, at this point I will "exit, stage left, chased by a bear", since both Windoze and R are within my areas of almost complete ignorance :-) Nick > > > Thanks, > John > > > > > > Nick > > > > > > John Hendy <jw.hendy@gmail.com> wrote: > > ... > >> > > >> > Oh, sorry: edebug is described in > >> > > >> > (info "(elisp) Edebug") > >> > > >> > The basics: visit ob-R.el, go to the org-babel-R-evaluate-external-process > >> > definition and press C-u C-M-x. Then do whatever you were doing to get the > >> > problem. It should stop at the function and you can single-step by pressing > >> > SPACE. At strategic points, you can evaluate things with "e". > >> > >> Eeks. Is the fact that I learned emacs only for org-mode showing. I > >> don't even know how to =(info "(elisp) Edebug")= -- do I put an =M-x= > >> in front of that? =M-x info= seems to bring me to a help page for > >> info! > >> > > > > You have to evaluate it somehow. If you are reading your mail in emacs, > > just place the cursor after the closing paren and press C-x C-e. If not, > > just go to emacs and "C-h i elisp RET i edebug RET" or equivalently, > > type ESC ESC : (info "(elisp) Edebug") RET. Underlying assumption: you > > have the Emacs Lisp info files installed. > > > >> Anyway... I just googled edebug and it says about the same as you did > >> (except for appending "eval-defun with a prefix argument" onto =C-u > >> C-M-x=. > >> - http://www.gnu.org/software/emacs/manual/html_node/elisp/Using-Edebug.html > >> > >> Anyway: > >> - Visited ob-R.el in emacs > >> - Found org-babel-R-evaluate-external-process > >> - Put the cursor on the line =(defun org-babel-R-evaluate-external-process= > >> - Did =M-x C-M-x= and the minibuffer echoed the name of the function > > > > C-u C-M-x please: and the echo area should say "Edebug: > > org-babel-R-evaluate-external-process" afterwards. > > > > Nick > > > >> - Visited my file, test.org and did =C-c C-c= on the R babel block > >> - Nothing different occurred; I just got "The system cannot find the > >> path specified" > >> > >> I tried the above again with regular 'ol org-babel-R-evaluate just in > >> case and had the same results. > >> > >> I'm clearly goofing something but have no idea what it is. > >> > >> > >> John > >> > >> > >> > > >> > If you mess it up (and you probably will a few times), no problem: just try > >> > again. And be patient! > >> > > >> > Good luck, > >> > Nick > >> > > >> > > >> > > >> >> > >> >> John > >> >> > >> >> > >> >> > > >> >> > Nick > >> >> > > >> >> >> Using =M-x R= works find. ESS is finding R. I successfully loaded a > >> >> >> .csv, ggplot2 and plotted. > >> >> >> > >> >> >> > >> >> >> John > >> >> >> > >> >> >> John > >> >> >> > >> >> >> > > >> >> >> > Nick > >> >> >> > > >> >> >> > >> >> > >> > > > > > ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-07-06 18:45 ` Nick Dokos @ 2012-07-06 22:08 ` John Hendy 2012-07-06 22:14 ` John Hendy 0 siblings, 1 reply; 27+ messages in thread From: John Hendy @ 2012-07-06 22:08 UTC (permalink / raw) To: nicholas.dokos; +Cc: Achim Gratz, emacs-orgmode On Fri, Jul 6, 2012 at 1:45 PM, Nick Dokos <nicholas.dokos@hp.com> wrote: > John Hendy <jw.hendy@gmail.com> wrote: > >> On Fri, Jul 6, 2012 at 12:12 PM, Nick Dokos <nicholas.dokos@hp.com> wrote: >> > John Hendy <jw.hendy@gmail.com> wrote: >> > >> >> Any updates on this? Could someone provide a minimal example I could >> >> try? Or verify that my steps above are correct. I'm not sure why it's >> >> not triggering the step by step function execution described. >> >> >> > >> > I had sent out a note about C-u C-M-x and what you should see in the >> > echo area after that, but I don't think I've seen a reply: did you try >> > that and did it work as expected? >> > >> > Either gmane is or I am being stupid right now and cannot find the message >> > (maybe it never made it, but gmane cannot seem to find the thread at all >> > right now), so I append a copy of that message. >> >> Yes. I guess I didn't explicitly say, but I mentioned that I had >> triggered something goofy by accident in my earlier hunt for edebug. >> I'll walkthrough right now: >> - Got to ob-R.el in emacs >> - C-s to find org-babel-R-evaluate-external-process >> - C-u C-M-x >> - Minibuffer: "Edebug: org-babel-R-evaluate-external-process" >> - Visit file test.org >> - C-c C-c on the src block >> - Well... of course it works now. Not sure what I was doing wrong before. >> > > The reason that I sent out that note was that you mentioned pressing M-x > C-M-x (rather than C-u C-M-x) and getting the name of the function > echoed (without the "Edebug: " part), so I wanted to make sure that you > were DTRT here. Could that be what you were doing wrong? or was that a > typo on your part? Whoops -- yes, this was me probably making a typo. Or maybe the first time around I was messing it up which is why it wasn't working. It ended up working in the end. > >> I pressed space continually until failure, then again to verify the >> failing line. It's this one (line 313): >> >> ,--- >> | (output (org-babel-eval org-babel-R-command body)))) >> `--- >> > > Just fyi and to clarify some basic lisp: the form > > (org-babel-eval org-babel-R-command body) > > says: evaluate the org-babel-eval function with arguments > org-babel-R-command and body (actually, those variables are evaluated > first and then the *values* are passed to the function). The evaluation > returns a result (a string in this case) which is assigned to the local > variable output for further processing (local, because this whole thing > is part of a let-form which is not shown in your snippet). > > I.e. a function call in lisp always looks like this: > > (<func> <arg1> <arg2> ....) > >> When I run this line: >> >> ,--- >> | (org-babel-eval org-babel-R-command >> `--- >> >> I get this in the minibuffer: >> >> ,--- >> | Result: "C:/Progra~1/R/R-2.15.0/bin/R" >> `--- >> > > I presume you just typed "e" when the cursor was after the variable: > that just evaluates the variable. If you press SPACE then the cursor > would advance to after the ``body'' variable (on the closing paren) and > an "e" would evaluate *that* variable. After another SPACE, the cursor > would be *after* the closing paren and an "e" would evaluate the function > call and you would see the result, i.e. what would be assigned to > ``output''. > Maybe I didn't get edebug right. I just kept pressing space with no 'e'... >> Should I be able to run this from the Windows cmd prompt successfully? >> I think this is my problem. Even using tab completion to ensure the >> path is correct, I get the same error message "The system cannot find >> the path specified" when I run this from cmd! >> >> I guess I honed in on my problem. I can run R from my Start Menu shortcut fine. >> >> Update: I'm on 64bit and just now realized there's another set of R >> cmds in ../R-2.15.0/bin/x64/. This is what I needed. >> >> Now my problem is that using R along doesn't produce any output. With >> the above modification, I get: >> >> ,--- >> | Fatal error: you must specify '--save', '--no-save' or '--vanilla' >> `--- >> >> I'm quite close! If I add --no-save, I get exported results but they >> include all of the R preamble text from when it starts. Here's my >> block for reference: >> >> #+begin_src R :results output org :exports results >> >> x <- c(1:10) >> summary(x) >> >> #+end_src >> > > OK, at this point I will "exit, stage left, chased by a bear", since > both Windoze and R are within my areas of almost complete ignorance :-) > No worries and serious thanks for bearing with me. Eric got it with the options to pass via the org-babel-R-command variable. Since the default includes --slave and --no-save and I changed it, I needed to add that to my custom setting of the variable. Thanks again! John > Nick > >> >> >> Thanks, >> John >> >> >> > >> > Nick >> > >> > >> > John Hendy <jw.hendy@gmail.com> wrote: >> > ... >> >> > >> >> > Oh, sorry: edebug is described in >> >> > >> >> > (info "(elisp) Edebug") >> >> > >> >> > The basics: visit ob-R.el, go to the org-babel-R-evaluate-external-process >> >> > definition and press C-u C-M-x. Then do whatever you were doing to get the >> >> > problem. It should stop at the function and you can single-step by pressing >> >> > SPACE. At strategic points, you can evaluate things with "e". >> >> >> >> Eeks. Is the fact that I learned emacs only for org-mode showing. I >> >> don't even know how to =(info "(elisp) Edebug")= -- do I put an =M-x= >> >> in front of that? =M-x info= seems to bring me to a help page for >> >> info! >> >> >> > >> > You have to evaluate it somehow. If you are reading your mail in emacs, >> > just place the cursor after the closing paren and press C-x C-e. If not, >> > just go to emacs and "C-h i elisp RET i edebug RET" or equivalently, >> > type ESC ESC : (info "(elisp) Edebug") RET. Underlying assumption: you >> > have the Emacs Lisp info files installed. >> > >> >> Anyway... I just googled edebug and it says about the same as you did >> >> (except for appending "eval-defun with a prefix argument" onto =C-u >> >> C-M-x=. >> >> - http://www.gnu.org/software/emacs/manual/html_node/elisp/Using-Edebug.html >> >> >> >> Anyway: >> >> - Visited ob-R.el in emacs >> >> - Found org-babel-R-evaluate-external-process >> >> - Put the cursor on the line =(defun org-babel-R-evaluate-external-process= >> >> - Did =M-x C-M-x= and the minibuffer echoed the name of the function >> > >> > C-u C-M-x please: and the echo area should say "Edebug: >> > org-babel-R-evaluate-external-process" afterwards. >> > >> > Nick >> > >> >> - Visited my file, test.org and did =C-c C-c= on the R babel block >> >> - Nothing different occurred; I just got "The system cannot find the >> >> path specified" >> >> >> >> I tried the above again with regular 'ol org-babel-R-evaluate just in >> >> case and had the same results. >> >> >> >> I'm clearly goofing something but have no idea what it is. >> >> >> >> >> >> John >> >> >> >> >> >> > >> >> > If you mess it up (and you probably will a few times), no problem: just try >> >> > again. And be patient! >> >> > >> >> > Good luck, >> >> > Nick >> >> > >> >> > >> >> > >> >> >> >> >> >> John >> >> >> >> >> >> >> >> >> > >> >> >> > Nick >> >> >> > >> >> >> >> Using =M-x R= works find. ESS is finding R. I successfully loaded a >> >> >> >> .csv, ggplot2 and plotted. >> >> >> >> >> >> >> >> >> >> >> >> John >> >> >> >> >> >> >> >> John >> >> >> >> >> >> >> >> > >> >> >> >> > Nick >> >> >> >> > >> >> >> >> >> >> >> >> >> >> > >> > >> ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-07-06 22:08 ` John Hendy @ 2012-07-06 22:14 ` John Hendy 2012-07-07 1:02 ` Eric Schulte 2012-07-07 1:48 ` Nick Dokos 0 siblings, 2 replies; 27+ messages in thread From: John Hendy @ 2012-07-06 22:14 UTC (permalink / raw) To: nicholas.dokos; +Cc: Achim Gratz, emacs-orgmode Jeepers. If I had just followed through with the outcome of the thread we were *both* already on! - http://lists.gnu.org/archive/html/emacs-orgmode/2012-02/msg00131.html Of course I find it only after having this drawn out troubleshooting exercise. I looked as I thought I could find a Worg page this might fit on... If it sounds good, I'll add a note for Windows users on ob-doc-R: - http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.html Sound good? I can point to both mailing list entries and note my need for a custom path due to 64bit setup and making sure to include the right arguments to the R command. John ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-07-06 22:14 ` John Hendy @ 2012-07-07 1:02 ` Eric Schulte 2012-07-07 1:48 ` Nick Dokos 1 sibling, 0 replies; 27+ messages in thread From: Eric Schulte @ 2012-07-07 1:02 UTC (permalink / raw) To: John Hendy; +Cc: Achim Gratz, nicholas.dokos, emacs-orgmode John Hendy <jw.hendy@gmail.com> writes: > Jeepers. If I had just followed through with the outcome of the thread > we were *both* already on! > - http://lists.gnu.org/archive/html/emacs-orgmode/2012-02/msg00131.html > > Of course I find it only after having this drawn out troubleshooting exercise. > > I looked as I thought I could find a Worg page this might fit on... If > it sounds good, I'll add a note for Windows users on ob-doc-R: > - http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.html > > Sound good? I can point to both mailing list entries and note my need > for a custom path due to 64bit setup and making sure to include the > right arguments to the R command. > Yes, please do add this to worg. If it will help others who run into this same issue it will definitely be worthwhile. Thanks, > > > John > -- Eric Schulte http://cs.unm.edu/~eschulte ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-07-06 22:14 ` John Hendy 2012-07-07 1:02 ` Eric Schulte @ 2012-07-07 1:48 ` Nick Dokos 2012-07-16 0:42 ` John Hendy 1 sibling, 1 reply; 27+ messages in thread From: Nick Dokos @ 2012-07-07 1:48 UTC (permalink / raw) To: John Hendy; +Cc: emacs-orgmode John Hendy <jw.hendy@gmail.com> wrote: > Jeepers. If I had just followed through with the outcome of the thread > we were *both* already on! > - http://lists.gnu.org/archive/html/emacs-orgmode/2012-02/msg00131.html > > Of course I find it only after having this drawn out troubleshooting exercise. > But you would have missed all the fun :-) I didn't even remember this thread: my involvement was a complete surprise - not sure whether that's a :-) or a :-( ... > I looked as I thought I could find a Worg page this might fit on... If > it sounds good, I'll add a note for Windows users on ob-doc-R: > - http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.html > > Sound good? I can point to both mailing list entries and note my need > for a custom path due to 64bit setup and making sure to include the > right arguments to the R command. > What Eric said: anything that would make it easier in the future is worth it. Nick ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-07-07 1:48 ` Nick Dokos @ 2012-07-16 0:42 ` John Hendy 0 siblings, 0 replies; 27+ messages in thread From: John Hendy @ 2012-07-16 0:42 UTC (permalink / raw) To: nicholas.dokos; +Cc: emacs-orgmode As promised, I updated Worg. It should cover the main things that came up here: - Setting the custom path via org-babel-R-command - Passing =--slave --no-save= when setting the command - The /path/to/R/bin/x64/R nuance for 64bit Windows http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.html#sec-2-1 Thanks again for all the help! John ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-06-29 19:31 ` John Hendy 2012-06-29 19:37 ` Nick Dokos @ 2012-06-30 5:13 ` Achim Gratz 2012-06-30 13:15 ` Eric Schulte 1 sibling, 1 reply; 27+ messages in thread From: Achim Gratz @ 2012-06-30 5:13 UTC (permalink / raw) To: emacs-orgmode John Hendy writes: >> (setq org-babel-R-command "C:/Progra~1/R/R-2.15.0/bin/R") > > Same error. Also, curiously, =M-x customize-variable RET org-babel-R > TAB= yields no results... is this the right variable? That variable doesn't seem to have acustomize interface. Might be worth a bug report. If the error persists, then it doesn't seem to be the R command that is not found. I don't know what is involved in setting up an R session, much less on Windows. You might have more luck to just install Cygwin and use Emacs/R from there if you already know your way around Linux. Regards, Achim. -- +<[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]>+ Wavetables for the Waldorf Blofeld: http://Synth.Stromeko.net/Downloads.html#BlofeldUserWavetables ^ permalink raw reply [flat|nested] 27+ messages in thread
* Re: R and babel on Windows problem 2012-06-30 5:13 ` Achim Gratz @ 2012-06-30 13:15 ` Eric Schulte 0 siblings, 0 replies; 27+ messages in thread From: Eric Schulte @ 2012-06-30 13:15 UTC (permalink / raw) To: Achim Gratz; +Cc: emacs-orgmode Achim Gratz <Stromeko@nexgo.de> writes: > John Hendy writes: >>> (setq org-babel-R-command "C:/Progra~1/R/R-2.15.0/bin/R") >> >> Same error. Also, curiously, =M-x customize-variable RET org-babel-R >> TAB= yields no results... is this the right variable? > > That variable doesn't seem to have acustomize interface. Might be worth > a bug report. > I just pushed up a change which defines the `org-babel-R-command' variable using a defcustom, so it should now be customizable. -- Eric Schulte http://cs.unm.edu/~eschulte ^ permalink raw reply [flat|nested] 27+ messages in thread
end of thread, other threads:[~2012-07-16 0:42 UTC | newest] Thread overview: 27+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- 2012-06-28 17:46 R and babel on Windows problem John Hendy 2012-06-29 14:59 ` Alexander Vorobiev 2012-06-29 15:24 ` John Hendy 2012-06-29 17:12 ` Alexander Vorobiev 2012-06-29 18:26 ` Achim Gratz 2012-06-29 19:31 ` John Hendy 2012-06-29 19:37 ` Nick Dokos 2012-06-29 20:00 ` John Hendy 2012-06-29 20:16 ` Nick Dokos 2012-07-02 20:15 ` John Hendy 2012-07-02 21:26 ` Nick Dokos 2012-07-02 21:47 ` John Hendy 2012-07-02 22:15 ` Nick Dokos 2012-07-02 22:16 ` John Hendy 2012-07-06 16:58 ` John Hendy 2012-07-06 17:12 ` Nick Dokos 2012-07-06 17:46 ` John Hendy 2012-07-06 18:41 ` Eric Schulte 2012-07-06 22:05 ` John Hendy 2012-07-06 18:45 ` Nick Dokos 2012-07-06 22:08 ` John Hendy 2012-07-06 22:14 ` John Hendy 2012-07-07 1:02 ` Eric Schulte 2012-07-07 1:48 ` Nick Dokos 2012-07-16 0:42 ` John Hendy 2012-06-30 5:13 ` Achim Gratz 2012-06-30 13:15 ` Eric Schulte
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