Re: [O] R and babel on Windows problem
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
Re: [O] R and babel on Windows problem
On Mon, Jul 2, 2012 at 5:16 PM, John Hendy jw.he...@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
Re: [O] R and babel on Windows problem
John Hendy jw.he...@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.he...@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
Re: [O] R and babel on Windows problem
On Fri, Jul 6, 2012 at 12:12 PM, Nick Dokos nicholas.do...@hp.com wrote: John Hendy jw.he...@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.he...@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
Re: [O] R and babel on Windows problem
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
Re: [O] R and babel on Windows problem
John Hendy jw.he...@gmail.com wrote: On Fri, Jul 6, 2012 at 12:12 PM, Nick Dokos nicholas.do...@hp.com wrote: John Hendy jw.he...@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.he...@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
Re: [O] R and babel on Windows problem
On Fri, Jul 6, 2012 at 1:41 PM, Eric Schulte eric.schu...@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
Re: [O] R and babel on Windows problem
On Fri, Jul 6, 2012 at 1:45 PM, Nick Dokos nicholas.do...@hp.com wrote: John Hendy jw.he...@gmail.com wrote: On Fri, Jul 6, 2012 at 12:12 PM, Nick Dokos nicholas.do...@hp.com wrote: John Hendy jw.he...@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.he...@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
Re: [O] R and babel on Windows problem
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
Re: [O] R and babel on Windows problem
John Hendy jw.he...@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
Re: [O] R and babel on Windows problem
John Hendy jw.he...@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
Re: [O] R and babel on Windows problem
On Fri, Jun 29, 2012 at 3:16 PM, Nick Dokos nicholas.do...@hp.com wrote: John Hendy jw.he...@gmail.com wrote: On Fri, Jun 29, 2012 at 2:37 PM, Nick Dokos nicholas.do...@hp.com wrote: John Hendy jw.he...@gmail.com wrote: On Fri, Jun 29, 2012 at 1:26 PM, Achim Gratz strom...@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
Re: [O] R and babel on Windows problem
John Hendy jw.he...@gmail.com wrote: On Fri, Jun 29, 2012 at 3:16 PM, Nick Dokos nicholas.do...@hp.com wrote: John Hendy jw.he...@gmail.com wrote: On Fri, Jun 29, 2012 at 2:37 PM, Nick Dokos nicholas.do...@hp.com wrote: John Hendy jw.he...@gmail.com wrote: On Fri, Jun 29, 2012 at 1:26 PM, Achim Gratz strom...@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
Re: [O] R and babel on Windows problem
On Mon, Jul 2, 2012 at 4:26 PM, Nick Dokos nicholas.do...@hp.com wrote: John Hendy jw.he...@gmail.com wrote: On Fri, Jun 29, 2012 at 3:16 PM, Nick Dokos nicholas.do...@hp.com wrote: John Hendy jw.he...@gmail.com wrote: On Fri, Jun 29, 2012 at 2:37 PM, Nick Dokos nicholas.do...@hp.com wrote: John Hendy jw.he...@gmail.com wrote: On Fri, Jun 29, 2012 at 1:26 PM, Achim Gratz strom...@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
Re: [O] R and babel on Windows problem
John Hendy jw.he...@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
Re: [O] R and babel on Windows problem
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
Re: [O] R and babel on Windows problem
Achim Gratz strom...@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
Re: [O] R and babel on Windows problem
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.he...@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
Re: [O] R and babel on Windows problem
On Fri, Jun 29, 2012 at 9:59 AM, Alexander Vorobiev alexander.vorob...@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.he...@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
Re: [O] R and babel on Windows problem
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.he...@gmail.com wrote: On Fri, Jun 29, 2012 at 9:59 AM, Alexander Vorobiev alexander.vorob...@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.he...@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
Re: [O] R and babel on Windows problem
[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
Re: [O] R and babel on Windows problem
On Fri, Jun 29, 2012 at 1:26 PM, Achim Gratz strom...@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
Re: [O] R and babel on Windows problem
John Hendy jw.he...@gmail.com wrote: On Fri, Jun 29, 2012 at 1:26 PM, Achim Gratz strom...@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
Re: [O] R and babel on Windows problem
On Fri, Jun 29, 2012 at 2:37 PM, Nick Dokos nicholas.do...@hp.com wrote: John Hendy jw.he...@gmail.com wrote: On Fri, Jun 29, 2012 at 1:26 PM, Achim Gratz strom...@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
Re: [O] R and babel on Windows problem
John Hendy jw.he...@gmail.com wrote: On Fri, Jun 29, 2012 at 2:37 PM, Nick Dokos nicholas.do...@hp.com wrote: John Hendy jw.he...@gmail.com wrote: On Fri, Jun 29, 2012 at 1:26 PM, Achim Gratz strom...@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
Re: [O] R and babel on Windows problem
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
[O] R and babel on Windows problem
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
