Re: [O] org mode R remote code evaluation
Michael Albinus writes: > Eric Schulte writes: > >> I'd rather not hard-code the value of "/tmp/". Perhaps you could rework >> the patch so that it introduces a new customizable variable (including a >> documentation string) so that users can set the value for their system. >> >> Also, please package the patch with git format-patch. > > Patch is appended. > Applied, Thanks for the patch! I've also added you to the list of contributors on worg, so I shouldn't ask you to complete the FSF paperwork again :). Cheers, > >> Thanks, > > Best regards, Michael. > > -- Eric Schulte https://cs.unm.edu/~eschulte PGP: 0x614CA05D
Re: [O] org mode R remote code evaluation
Eric Schulte writes: > I'd rather not hard-code the value of "/tmp/". Perhaps you could rework > the patch so that it introduces a new customizable variable (including a > documentation string) so that users can set the value for their system. > > Also, please package the patch with git format-patch. Patch is appended. > Thanks, Best regards, Michael. >From 2b8db5486de75ec35c2c0d3e6063847cf582ace7 Mon Sep 17 00:00:00 2001 From: Michael Albinus Date: Fri, 27 Sep 2013 13:34:03 +0200 Subject: [PATCH] * ob-core.el (org-babel-local-file-name): Simplify. (org-babel-process-file-name): Apply `expand-file-name' first. (org-babel-remote-temporary-directory): New defcustom. (org-babel-temp-file): Use it. --- lisp/ob-core.el | 19 --- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/lisp/ob-core.el b/lisp/ob-core.el index 5a032a1..a7c227b 100644 --- a/lisp/ob-core.el +++ b/lisp/ob-core.el @@ -2680,11 +2680,7 @@ Fixes a bug in `tramp-handle-call-process-region'." (defun org-babel-local-file-name (file) "Return the local name component of FILE." - (if (file-remote-p file) - (let (localname) - (with-parsed-tramp-file-name file nil - localname)) -file)) + (or (file-remote-p file 'localname) file)) (defun org-babel-process-file-name (name &optional no-quote-p) "Prepare NAME to be used in an external process. @@ -2694,7 +2690,10 @@ remotely. The file name is then processed by `expand-file-name'. Unless second argument NO-QUOTE-P is non-nil, the file name is additionally processed by `shell-quote-argument'" ((lambda (f) (if no-quote-p f (shell-quote-argument f))) - (expand-file-name (org-babel-local-file-name name + ;; We must apply `expand-file-name' on the whole filename. If we + ;; would apply it on the local filename only, undesired effects + ;; like prepending a drive letter on MS Windows could happen. + (org-babel-local-file-name (expand-file-name name (defvar org-babel-temporary-directory) (unless (or noninteractive (boundp 'org-babel-temporary-directory)) @@ -2707,6 +2706,11 @@ additionally processed by `shell-quote-argument'" Used by `org-babel-temp-file'. This directory will be removed on Emacs shutdown.")) +(defcustom org-babel-remote-temporary-directory "/tmp/" + "Directory to hold temporary files on remote hosts." + :group 'org-babel + :type 'string) + (defmacro org-babel-result-cond (result-params scalar-form &rest table-forms) "Call the code to parse raw string results according to RESULT-PARAMS." (declare (indent 1) @@ -2736,7 +2740,8 @@ of `org-babel-temporary-directory'." (if (file-remote-p default-directory) (let ((prefix (concat (file-remote-p default-directory) - (expand-file-name prefix temporary-file-directory + (expand-file-name + prefix org-babel-remote-temporary-directory (make-temp-file prefix nil suffix)) (let ((temporary-file-directory (or (and (boundp 'org-babel-temporary-directory) -- 1.8.1.2
Re: [O] org mode R remote code evaluation
Alexander Vorobiev writes: > #+BEGIN_SRC sql :engine postgresql :dir /grid: :results output : > colnames yes > select 2+2 as four, 1+1 as one; > #+END_SRC > > #+RESULTS: > | 4\t2 | > > It works! As you see there are still some problems with ob-sql (no > column names and \t is not parsed correctly) but the remote execution > seems to be fixed. Great! I will prepare the patch tomorrow, as instructed by Eric. > Thanks, > Alex Best regards, Michael.
Re: [O] org mode R remote code evaluation
#+BEGIN_SRC sql :engine postgresql :dir /grid: :results output :colnames yes select 2+2 as four, 1+1 as one; #+END_SRC #+RESULTS: | 4\t2 | It works! As you see there are still some problems with ob-sql (no column names and \t is not parsed correctly) but the remote execution seems to be fixed. Thanks, Alex On Thu, Sep 26, 2013 at 11:53 AM, Michael Albinus wrote: > Alexander Vorobiev writes: > > > Hi Michael, > > Hi Alex, > > > I can't apply the patch for some reason. > > Strange. > > > Could you send it and/or new ob-core.el as a attachment? > > It's appended. > > > Thanks, > > Alex > > Best regards, Michael. > >
Re: [O] org mode R remote code evaluation
Alexander Vorobiev writes: > Michael, Hi Alex, > * this doesn't work > #+BEGIN_SRC sql :engine postgresql :dir /grid: :results output > select 1+2 as three; > #+END_SRC > > /plinkx:grid:/tmp/sql-in-7928arv...done > psql -A -F " " -f "c:/tmp/sql-in-7928arv" -o "c:/tmp/sql-out-7928Z_E" > -f c:/tmp/sql-in-7928arv -o c:/tmp/sql-out-7928Z_E > No such file or directory 'c:/tmp/sql-in-7928arv' Try this extended patch: --8<---cut here---start->8--- diff --git a/lisp/ob-core.el b/lisp/ob-core.el index 5a032a1..2789f47 100644 --- a/lisp/ob-core.el +++ b/lisp/ob-core.el @@ -2680,11 +2680,7 @@ Fixes a bug in `tramp-handle-call-process-region'." (defun org-babel-local-file-name (file) "Return the local name component of FILE." - (if (file-remote-p file) - (let (localname) - (with-parsed-tramp-file-name file nil -localname)) -file)) + (or (file-remote-p file 'localname) file)) (defun org-babel-process-file-name (name &optional no-quote-p) "Prepare NAME to be used in an external process. @@ -2694,7 +2690,10 @@ remotely. The file name is then processed by `expand-file-name'. Unless second argument NO-QUOTE-P is non-nil, the file name is additionally processed by `shell-quote-argument'" ((lambda (f) (if no-quote-p f (shell-quote-argument f))) - (expand-file-name (org-babel-local-file-name name + ;; We must apply `expand-file-name' on the whole filename. If we + ;; would apply it on the local filename only, undesired effects + ;; like prepending a drive letter on MS Windows could happen. + (org-babel-local-file-name (expand-file-name name (defvar org-babel-temporary-directory) (unless (or noninteractive (boundp 'org-babel-temporary-directory)) @@ -2736,7 +2735,7 @@ of `org-babel-temporary-directory'." (if (file-remote-p default-directory) (let ((prefix (concat (file-remote-p default-directory) - (expand-file-name prefix temporary-file-directory + (expand-file-name prefix "/tmp/" (make-temp-file prefix nil suffix)) (let ((temporary-file-directory (or (and (boundp 'org-babel-temporary-directory) --8<---cut here---end--->8--- > Thanks > Alex Best regards, Michael. PS: the analysis of your cygwin problem is delayed. I don't run MS Windows on my machines, I need to hijack a machine from my wife or somebody else for analysis.
Re: [O] org mode R remote code evaluation
Michael,
I found that the patch doesn't work for sql code blocks. Here is an example
* this works
#+BEGIN_SRC sh :results output :dir /grid:
ls
#+END_SRC
* this doesn't work
#+BEGIN_SRC sql :engine postgresql :dir /grid: :results output
select 1+2 as three;
#+END_SRC
and here is what appears in *Messages*:
executing Sh code block...
Tramp: Encoding region using function `base64-encode-region'...done
Tramp: Decoding region into remote file
/plinkx:grid:/tmp/ob-input-7928Z4Q...done
Tramp: Encoding region using function `base64-encode-region'...done
Tramp: Decoding region into remote file
/plinkx:grid:/tmp/ob-error-7928zMd...done
Tramp: Encoding region using function `base64-encode-region'...done
Tramp: Decoding region into remote file
/plinkx:grid:/tmp/ob-input-7928Z4Q...done
Wrote /plinkx:grid:/tmp/ob-input-7928Z4Q
Code block evaluation complete.
executing Sql code block...
Tramp: Encoding region using function `base64-encode-region'...done
Tramp: Decoding region into remote file
/plinkx:grid:/tmp/sql-in-7928arv...done
Tramp: Encoding region using function `base64-encode-region'...done
Tramp: Decoding region into remote file
/plinkx:grid:/tmp/sql-out-7928Z_E...done
Tramp: Encoding region using function `base64-encode-region'...done
Tramp: Decoding region into remote file
/plinkx:grid:/tmp/sql-in-7928arv...done
psql -A -F " " -f "c:/tmp/sql-in-7928arv" -o "c:/tmp/sql-out-7928Z_E"
-f c:/tmp/sql-in-7928arv -o c:/tmp/sql-out-7928Z_E
No such file or directory 'c:/tmp/sql-in-7928arv'
Tramp: Inserting `/plinkx:grid:/tmp/sql-out-7928Z_E'...
Tramp: Encoding remote file /plinkx:grid:/tmp/sql-out-7928Z_E...done
Tramp: Decoding remote file /plinkx:grid:/tmp/sql-out-7928Z_E with function
base64-decode-region...
Wrote c:/Users/avorobi/AppData/Local/Temp/tramp.7928AeX
Tramp: Decoding remote file /plinkx:grid:/tmp/sql-out-7928Z_E with function
base64-decode-region...done
Tramp: Inserting `/plinkx:grid:/tmp/sql-out-7928Z_E'...done
So shell commands work but the arguments passed to psql have "c:" at the
beginning.
Thanks
Alex
On Wed, Sep 25, 2013 at 2:03 PM, Michael Albinus wrote:
> Eric Schulte writes:
>
> > I'd rather not hard-code the value of "/tmp/". Perhaps you could rework
> > the patch so that it introduces a new customizable variable (including a
> > documentation string) so that users can set the value for their system.
>
> Will do, tomorrow. I would even prefer a more general solution, a new
> function which returns a ("the") temp directory on a remote host. This
> would be useful also outside org-mode. But this would require changes in
> Emacs/Tramp, which won't be applicable for org immediately (backwards
> compatibility, and alike).
>
> > If you can keep the patch under 15LOC we can include it w/o requiring
> > FSF copyright assignment, otherwise see [1] for contribution details.
>
> No problem. As Tramp maintainer, I have signed the FSF papers for Emacs
> 10+ years ago. This shall be valid also for org patches.
>
> > Thanks,
>
> Best regards, Michael.
>
Re: [O] org mode R remote code evaluation
Eric Schulte writes:
> I'd rather not hard-code the value of "/tmp/". Perhaps you could rework
> the patch so that it introduces a new customizable variable (including a
> documentation string) so that users can set the value for their system.
Will do, tomorrow. I would even prefer a more general solution, a new
function which returns a ("the") temp directory on a remote host. This
would be useful also outside org-mode. But this would require changes in
Emacs/Tramp, which won't be applicable for org immediately (backwards
compatibility, and alike).
> If you can keep the patch under 15LOC we can include it w/o requiring
> FSF copyright assignment, otherwise see [1] for contribution details.
No problem. As Tramp maintainer, I have signed the FSF papers for Emacs
10+ years ago. This shall be valid also for org patches.
> Thanks,
Best regards, Michael.
Re: [O] org mode R remote code evaluation
Michael Albinus writes: > Alexander Vorobiev writes: > >> Hi Michael, > > Hi Alex, > >> The patch seems to be working, the only thing I noticed is having >> http://www.emacswiki.org/emacs/setup-cygwin.el loaded together with >> the patched ob-core.el makes tramp prepend "/cygwin" to /tmp/. When I >> disabled (require 'setup-cygwin) the patch works as expected. Outside >> of org/babel setup-cygwin has no effect on Tramp. > > This problem does not seem to be related to org-mode code. Could > somebody, please, commit my patch to org's repository? Thanks. > I'd rather not hard-code the value of "/tmp/". Perhaps you could rework the patch so that it introduces a new customizable variable (including a documentation string) so that users can set the value for their system. If you can keep the patch under 15LOC we can include it w/o requiring FSF copyright assignment, otherwise see [1] for contribution details. Also, please package the patch with git format-patch. Thanks, > > I will try to find out what's up with Tramp and Cygwin. Sadly, it has > been a misalliance very often :-( > >> Thanks, >> Alex > > Best regards, Michael. > Footnotes: [1] http://orgmode.org/worg/org-contribute.html -- Eric Schulte https://cs.unm.edu/~eschulte PGP: 0x614CA05D
Re: [O] org mode R remote code evaluation
Alexander Vorobiev writes: > Hi Michael, Hi Alex, > The patch seems to be working, the only thing I noticed is having > http://www.emacswiki.org/emacs/setup-cygwin.el loaded together with > the patched ob-core.el makes tramp prepend "/cygwin" to /tmp/. When I > disabled (require 'setup-cygwin) the patch works as expected. Outside > of org/babel setup-cygwin has no effect on Tramp. This problem does not seem to be related to org-mode code. Could somebody, please, commit my patch to org's repository? Thanks. I will try to find out what's up with Tramp and Cygwin. Sadly, it has been a misalliance very often :-( > Thanks, > Alex Best regards, Michael.
Re: [O] org mode R remote code evaluation
Hi Michael, The patch seems to be working, the only thing I noticed is having http://www.emacswiki.org/emacs/setup-cygwin.el loaded together with the patched ob-core.el makes tramp prepend "/cygwin" to /tmp/. When I disabled (require 'setup-cygwin) the patch works as expected. Outside of org/babel setup-cygwin has no effect on Tramp. Thanks, Alex On Tue, Sep 24, 2013 at 1:40 PM, Michael Albinus wrote: > Alexander Vorobiev writes: > > > Hi Michael, > > Hi Alex, > > > Here it is. > > Thanks. I believe, the following patch shall cure it: > > --8<---cut here---start->8--- > --- a/lisp/ob-core.el > +++ b/lisp/ob-core.el > @@ -2735,8 +2735,12 @@ > value of `temporary-file-directory' temporarily set to the value > of `org-babel-temporary-directory'." >(if (file-remote-p default-directory) >(let ((prefix > +;; We cannot use `temporary-file-directory' as local part > +;; on the remote host, because it might be another OS > +;; there. So we assume "/tmp", which ought to exist on > +;; relevant architectures. > (concat (file-remote-p default-directory) > - (expand-file-name prefix temporary-file-directory > + (expand-file-name prefix "/tmp/" > (make-temp-file prefix nil suffix)) > (let ((temporary-file-directory >(or (and (boundp 'org-babel-temporary-directory) > --8<---cut here---end--->8--- > > Could you, please, test? > > > Thanks, > > Alex > > Best regards, Michael. >
Re: [O] org mode R remote code evaluation
Alexander Vorobiev writes: > Hi Michael, Hi Alex, > Here it is. Thanks. I believe, the following patch shall cure it: --8<---cut here---start->8--- --- a/lisp/ob-core.el +++ b/lisp/ob-core.el @@ -2735,8 +2735,12 @@ value of `temporary-file-directory' temporarily set to the value of `org-babel-temporary-directory'." (if (file-remote-p default-directory) (let ((prefix +;; We cannot use `temporary-file-directory' as local part +;; on the remote host, because it might be another OS +;; there. So we assume "/tmp", which ought to exist on +;; relevant architectures. (concat (file-remote-p default-directory) - (expand-file-name prefix temporary-file-directory + (expand-file-name prefix "/tmp/" (make-temp-file prefix nil suffix)) (let ((temporary-file-directory (or (and (boundp 'org-babel-temporary-directory) --8<---cut here---end--->8--- Could you, please, test? > Thanks, > Alex Best regards, Michael.
Re: [O] org mode R remote code evaluation
Alexander Vorobiev writes: > Here is what I have: > > ELISP> emacs-version > "24.3.1" > ELISP> tramp-version > "2.2.7" > ELISP> org-version > "8.2" Well, that sounds recent. Could you, please, perform (setq tramp-verbose 6) prior your test? There will be a Tramp debug buffer, which I would like to analyze. > Thanks, > Alex Best regards, Michael.
Re: [O] org mode R remote code evaluation
Here is what I have: ELISP> emacs-version "24.3.1" ELISP> tramp-version "2.2.7" ELISP> org-version "8.2" Thanks, Alex On Tue, Sep 24, 2013 at 7:57 AM, Michael Albinus wrote: > Alexander Vorobiev writes: > > > The ":results output" doesn't help in my setup (I'm on Windows, the > > remote system is linux, access is via putty/plink) > > I do not run Windows, so I cannot reproduce exactly. However, ... > > > #+BEGIN_SRC sh :results output :dir /grid: > > ls > > #+END_SRC > > > > executing Sh code block... > > Tramp: Encoding region using function `base64-encode-region'...done > > Tramp: Decoding region into remote file > > /plinkx:grid:/Users/avorobi/AppData/Local/Temp/ob-input-6116fuY...done > > byte-code: Couldn't write region to > > `/plinkx:grid:/Users/avorobi/AppData/Local/Temp/ob-input-6116fuY', > > decode using `tramp_perl_decode_with_module >%s' failed > > > > The /Users directory obviously does not exist on linux. > > ... this looks like an old problem. Which Emacs/Tramp version are you > using? > Check variables `emacs-version' and `tramp-version'. > > > Thanks, > > Alex > > Best regards, Michael. >
Re: [O] org mode R remote code evaluation
Alexander Vorobiev writes: > The ":results output" doesn't help in my setup (I'm on Windows, the > remote system is linux, access is via putty/plink) I do not run Windows, so I cannot reproduce exactly. However, ... > #+BEGIN_SRC sh :results output :dir /grid: > ls > #+END_SRC > > executing Sh code block... > Tramp: Encoding region using function `base64-encode-region'...done > Tramp: Decoding region into remote file > /plinkx:grid:/Users/avorobi/AppData/Local/Temp/ob-input-6116fuY...done > byte-code: Couldn't write region to > `/plinkx:grid:/Users/avorobi/AppData/Local/Temp/ob-input-6116fuY', > decode using `tramp_perl_decode_with_module >%s' failed > > The /Users directory obviously does not exist on linux. ... this looks like an old problem. Which Emacs/Tramp version are you using? Check variables `emacs-version' and `tramp-version'. > Thanks, > Alex Best regards, Michael.
Re: [O] org mode R remote code evaluation
The ":results output" doesn't help in my setup (I'm on Windows, the remote
system is linux, access is via putty/plink)
#+BEGIN_SRC sh :results output :dir /grid:
ls
#+END_SRC
executing Sh code block...
Tramp: Encoding region using function `base64-encode-region'...done
Tramp: Decoding region into remote file
/plinkx:grid:/Users/avorobi/AppData/Local/Temp/ob-input-6116fuY...done
byte-code: Couldn't write region to
`/plinkx:grid:/Users/avorobi/AppData/Local/Temp/ob-input-6116fuY', decode
using `tramp_perl_decode_with_module >%s' failed
The /Users directory obviously does not exist on linux.
Tramp itself works in my configuration, I can open files, etc. I have the
latest org-mode from elpa.
Thanks,
Alex
On Thu, Aug 29, 2013 at 5:42 AM, Johannes Rainer <
johannes.rai...@i-med.ac.at> wrote:
> thanks! so the ":results output" does the trick.
>
>
>
>
> On Thu, Aug 29, 2013 at 10:25 AM, Loris Bennett <
> loris.benn...@fu-berlin.de> wrote:
>
>> Johannes Rainer writes:
>>
>> > dear all,
>> >
>> > I have some computation intense R-code that I want to run remotely on
>> my server,
>> > and, according to the org manual that should be possible with the ":dir"
>> > parameter. so I went on and tried the following (user/server masked):
>> >
>> > #+BEGIN_SRC R :dir /xx@xxx:
>> > system("hostname")
>> > #+END_SRC
>> >
>> > when I execute it I get the error:
>> >
>> > Tramp: Encoding region using function `base64-encode-region'...done
>> > Tramp: Decoding region into remote file
>> > /ssh:xx@xxx
>> :/var/folders/ny/6kbb36310wz2kww8y8ctry60gn/T/R-46345BQs...done
>> > byte-code: Couldn't write region to
>> > `/ssh:xx@xxx
>> :/var/folders/ny/6kbb36310wz2kww8y8ctry60gn/T/R-46345BQs',
>> > decode using `base64 -d -i >%s' failed
>> >
>> > apparently, this temp folder does not exist on the linux server, it is
>> actually
>> > the temp folder from my local machine.
>> >
>> > I get the same error when I try to execute remote shell code, so it's
>> not R
>> > related.
>> >
>> > I also tried to start a ssh session using "M-x ssh" and used the source
>> block
>> >
>> > #+BEGIN_SRC R :exports both :session *ssh xxx*
>> > system("hostname")
>> > #+END_SRC
>> >
>> > on the server it executes the command but it can not write the results:
>> >
>> >> xxx
>> >> Warning message:
>> > In file.rename(tfile, transfer.file) :
>> > cannot rename file '/tmp/RtmpsirjGl/file51c8f6ce4ec' to
>> >
>> '/var/folders/ny/6kbb36310wz2kww8y8ctry60gn/T/babel-46345zSH/R-46345a4N',
>> > reason 'No such file or directory'
>> >>
>> >
>> > I am using emacs 24.3 and Org-mode version 8.0.7
>> (release_8.0.7-384-g6fdc23)
>> >
>> > I would be helpful for any suggestions how I could solve this problem.
>> >
>> > thanks in advance
>>
>> The following works for me:
>>
>> #+BEGIN_SRC R :results output :dir /xxx@x:
>> system("hostname")
>> #+END_SRC
>>
>> with Emacs 24.2.1 and 8.0.7 (8.0.7-6-g13cb28-elpaplus)
>>
>> Cheers,
>>
>> Loris
>>
>> --
>> This signature is currently under construction.
>>
>>
>>
>
>
> --
> Johannes Rainer, PhD
> Applied Bioinformatics Group,
> Division Molecular Pathophysiology,
> Biocenter, Medical University Innsbruck,
> Innrain 80/82 II, 6020 Innsbruck, Austria
> and
> Tyrolean Cancer Research Institute
> Innrain 66, 6020 Innsbruck, Austria
>
> Tel.: +43 (0)512 9003 70961
> Email: johannes.rai...@i-med.ac.at
> johannes.rai...@tcri.at
> URL: http://bioinfo.i-med.ac.at
>
>
>
Re: [O] org mode R remote code evaluation
thanks! so the ":results output" does the trick.
On Thu, Aug 29, 2013 at 10:25 AM, Loris Bennett
wrote:
> Johannes Rainer writes:
>
> > dear all,
> >
> > I have some computation intense R-code that I want to run remotely on my
> server,
> > and, according to the org manual that should be possible with the ":dir"
> > parameter. so I went on and tried the following (user/server masked):
> >
> > #+BEGIN_SRC R :dir /xx@xxx:
> > system("hostname")
> > #+END_SRC
> >
> > when I execute it I get the error:
> >
> > Tramp: Encoding region using function `base64-encode-region'...done
> > Tramp: Decoding region into remote file
> > /ssh:xx@xxx
> :/var/folders/ny/6kbb36310wz2kww8y8ctry60gn/T/R-46345BQs...done
> > byte-code: Couldn't write region to
> > `/ssh:xx@xxx
> :/var/folders/ny/6kbb36310wz2kww8y8ctry60gn/T/R-46345BQs',
> > decode using `base64 -d -i >%s' failed
> >
> > apparently, this temp folder does not exist on the linux server, it is
> actually
> > the temp folder from my local machine.
> >
> > I get the same error when I try to execute remote shell code, so it's
> not R
> > related.
> >
> > I also tried to start a ssh session using "M-x ssh" and used the source
> block
> >
> > #+BEGIN_SRC R :exports both :session *ssh xxx*
> > system("hostname")
> > #+END_SRC
> >
> > on the server it executes the command but it can not write the results:
> >
> >> xxx
> >> Warning message:
> > In file.rename(tfile, transfer.file) :
> > cannot rename file '/tmp/RtmpsirjGl/file51c8f6ce4ec' to
> >
> '/var/folders/ny/6kbb36310wz2kww8y8ctry60gn/T/babel-46345zSH/R-46345a4N',
> > reason 'No such file or directory'
> >>
> >
> > I am using emacs 24.3 and Org-mode version 8.0.7
> (release_8.0.7-384-g6fdc23)
> >
> > I would be helpful for any suggestions how I could solve this problem.
> >
> > thanks in advance
>
> The following works for me:
>
> #+BEGIN_SRC R :results output :dir /xxx@x:
> system("hostname")
> #+END_SRC
>
> with Emacs 24.2.1 and 8.0.7 (8.0.7-6-g13cb28-elpaplus)
>
> Cheers,
>
> Loris
>
> --
> This signature is currently under construction.
>
>
>
--
Johannes Rainer, PhD
Applied Bioinformatics Group,
Division Molecular Pathophysiology,
Biocenter, Medical University Innsbruck,
Innrain 80/82 II, 6020 Innsbruck, Austria
and
Tyrolean Cancer Research Institute
Innrain 66, 6020 Innsbruck, Austria
Tel.: +43 (0)512 9003 70961
Email: johannes.rai...@i-med.ac.at
johannes.rai...@tcri.at
URL: http://bioinfo.i-med.ac.at
Re: [O] org mode R remote code evaluation
Johannes Rainer writes:
> dear all,
>
> I have some computation intense R-code that I want to run remotely on my
> server,
> and, according to the org manual that should be possible with the ":dir"
> parameter. so I went on and tried the following (user/server masked):
>
> #+BEGIN_SRC R :dir /xx@xxx:
> system("hostname")
> #+END_SRC
>
> when I execute it I get the error:
>
> Tramp: Encoding region using function `base64-encode-region'...done
> Tramp: Decoding region into remote file
> /ssh:xx@xxx:/var/folders/ny/6kbb36310wz2kww8y8ctry60gn/T/R-46345BQs...done
> byte-code: Couldn't write region to
> `/ssh:xx@xxx:/var/folders/ny/6kbb36310wz2kww8y8ctry60gn/T/R-46345BQs',
> decode using `base64 -d -i >%s' failed
>
> apparently, this temp folder does not exist on the linux server, it is
> actually
> the temp folder from my local machine.
>
> I get the same error when I try to execute remote shell code, so it's not R
> related.
>
> I also tried to start a ssh session using "M-x ssh" and used the source block
>
> #+BEGIN_SRC R :exports both :session *ssh xxx*
> system("hostname")
> #+END_SRC
>
> on the server it executes the command but it can not write the results:
>
>> xxx
>> Warning message:
> In file.rename(tfile, transfer.file) :
> cannot rename file '/tmp/RtmpsirjGl/file51c8f6ce4ec' to
> '/var/folders/ny/6kbb36310wz2kww8y8ctry60gn/T/babel-46345zSH/R-46345a4N',
> reason 'No such file or directory'
>>
>
> I am using emacs 24.3 and Org-mode version 8.0.7 (release_8.0.7-384-g6fdc23)
>
> I would be helpful for any suggestions how I could solve this problem.
>
> thanks in advance
The following works for me:
#+BEGIN_SRC R :results output :dir /xxx@x:
system("hostname")
#+END_SRC
with Emacs 24.2.1 and 8.0.7 (8.0.7-6-g13cb28-elpaplus)
Cheers,
Loris
--
This signature is currently under construction.
[O] org mode R remote code evaluation
dear all,
I have some computation intense R-code that I want to run remotely on my
server, and, according to the org manual that should be possible with the
":dir" parameter. so I went on and tried the following (user/server masked):
#+BEGIN_SRC R :dir /xx@xxx:
system("hostname")
#+END_SRC
when I execute it I get the error:
Tramp: Encoding region using function `base64-encode-region'...done
Tramp: Decoding region into remote file /ssh:xx@xxx
:/var/folders/ny/6kbb36310wz2kww8y8ctry60gn/T/R-46345BQs...done
byte-code: Couldn't write region to
`/ssh:xx@xxx:/var/folders/ny/6kbb36310wz2kww8y8ctry60gn/T/R-46345BQs',
decode using `base64 -d -i >%s' failed
apparently, this temp folder does not exist on the linux server, it is
actually the temp folder from my local machine.
I get the same error when I try to execute remote shell code, so it's not R
related.
I also tried to start a ssh session using "M-x ssh" and used the source
block
#+BEGIN_SRC R :exports both :session *ssh xxx*
system("hostname")
#+END_SRC
on the server it executes the command but it can not write the results:
> xxx
> Warning message:
In file.rename(tfile, transfer.file) :
cannot rename file '/tmp/RtmpsirjGl/file51c8f6ce4ec' to
'/var/folders/ny/6kbb36310wz2kww8y8ctry60gn/T/babel-46345zSH/R-46345a4N',
reason 'No such file or directory'
>
I am using emacs 24.3 and Org-mode version 8.0.7 (release_8.0.7-384-g6fdc23)
I would be helpful for any suggestions how I could solve this problem.
thanks in advance
