* Using tramp to run R source code blocks on remote server
@ 2016-04-21 10:53 Vikas Rawal
2016-04-21 16:48 ` Charles C. Berry
` (3 more replies)
0 siblings, 4 replies; 12+ messages in thread
From: Vikas Rawal @ 2016-04-21 10:53 UTC (permalink / raw)
To: org-mode mailing list
I am trying to run R source code blocks on a remote server (defined in my ~/.ssh/config as cesp).
I am facing several problems.
1. The following sample block, when used with ":results value" does not give any results.
#+NAME: level1
#+begin_src R :results value :exports results :colnames yes :hline yes :session cesp :dir /cesp:/home/vikas/
c(1:5)
#+end_src
I get the following message:
tramp-flush-directory-property: Wrong type argument: arrayp, nil
I get the expected output if I use ":results output”, but I don’t want that.
2. Is there a way to be able to use screen/byobu with remote processing? I have tried various options of using shell, term, or ansi-term. Each of them gives some problem or the other. Does anyone have experience with using any of these?
Would appreciate help
Vikas
^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: Using tramp to run R source code blocks on remote server
2016-04-21 10:53 Using tramp to run R source code blocks on remote server Vikas Rawal
@ 2016-04-21 16:48 ` Charles C. Berry
2016-04-21 21:29 ` Charles C. Berry
2016-04-22 3:26 ` Vikas Rawal
2016-04-21 23:33 ` Tim Howes
` (2 subsequent siblings)
3 siblings, 2 replies; 12+ messages in thread
From: Charles C. Berry @ 2016-04-21 16:48 UTC (permalink / raw)
To: Vikas Rawal; +Cc: org-mode mailing list
On Thu, 21 Apr 2016, Vikas Rawal wrote:
> I am trying to run R source code blocks on a remote server (defined in my ~/.ssh/config as cesp).
>
> I am facing several problems.
>
> 1. The following sample block, when used with ":results value" does not give any results.
>
> #+NAME: level1
> #+begin_src R :results value :exports results :colnames yes :hline yes :session cesp :dir /cesp:/home/vikas/
> c(1:5)
> #+end_src
>
> I get the following message:
>
> tramp-flush-directory-property: Wrong type argument: arrayp, nil
>
I think this is an issue with having different version of ESS on your
local and remote systems.
In particular, newer and older versions of `.ess.eval' have different
arguments. You can check this by running `args(.ess.eval)' in the session
of your remote server and in a session on your local system.
In any case, I'd suggest asking on ess-help@r-project.org for help in
fixing this.
HTH,
Chuck
^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: Using tramp to run R source code blocks on remote server
2016-04-21 16:48 ` Charles C. Berry
@ 2016-04-21 21:29 ` Charles C. Berry
2016-04-21 22:04 ` Charles C. Berry
2016-04-22 3:26 ` Vikas Rawal
1 sibling, 1 reply; 12+ messages in thread
From: Charles C. Berry @ 2016-04-21 21:29 UTC (permalink / raw)
To: Vikas Rawal; +Cc: org-mode mailing list
On Thu, 21 Apr 2016, Charles C. Berry wrote:
> On Thu, 21 Apr 2016, Vikas Rawal wrote:
>
>> I am trying to run R source code blocks on a remote server (defined in my
>> ~/.ssh/config as cesp).
>>
>> I am facing several problems.
>>
>> 1. The following sample block, when used with ":results value" does not
>> give any results.
>>
>> #+NAME: level1
>> #+begin_src R :results value :exports results :colnames yes :hline yes
>> :session cesp :dir /cesp:/home/vikas/
>> c(1:5)
>> #+end_src
>>
>> I get the following message:
>>
>> tramp-flush-directory-property: Wrong type argument: arrayp, nil
>>
>
> I think this is an issue with having different version of ESS on your local
> and remote systems.
>
OOPS!
The `different versions' issue affected my setup. But after
correcting it, I still get the error you cited above.
Not sure exactly where the fault lies.
Chuck
^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: Using tramp to run R source code blocks on remote server
2016-04-21 21:29 ` Charles C. Berry
@ 2016-04-21 22:04 ` Charles C. Berry
2016-04-21 22:20 ` Cook, Malcolm
0 siblings, 1 reply; 12+ messages in thread
From: Charles C. Berry @ 2016-04-21 22:04 UTC (permalink / raw)
To: Vikas Rawal; +Cc: org-mode mailing list
On Thu, 21 Apr 2016, Charles C. Berry wrote:
> On Thu, 21 Apr 2016, Charles C. Berry wrote:
>
>> On Thu, 21 Apr 2016, Vikas Rawal wrote:
>>
>>> I am trying to run R source code blocks on a remote server (defined in my
>>> ~/.ssh/config as cesp).
>>>
>>> I am facing several problems.
>>>
>>> 1. The following sample block, when used with ":results value" does not
>>> give any results.
>>>
>>> #+NAME: level1
>>> #+begin_src R :results value :exports results :colnames yes :hline yes
>>> :session cesp :dir /cesp:/home/vikas/
>>> c(1:5)
>>> #+end_src
>>>
>>> I get the following message:
>>>
>>> tramp-flush-directory-property: Wrong type argument: arrayp, nil
>>>
>>
>> I think this is an issue with having different version of ESS on your local
>> and remote systems.
>>
>
> OOPS!
>
> The `different versions' issue affected my setup. But after correcting it, I
> still get the error you cited above.
>
> Not sure exactly where the fault lies.
>
Maybe in `org-babel-comint-eval-invisibly-and-wait-for-file', but I am not
sure what/how.
I tried to instrument the function (C-u C-M-x on the function source) and
run it. And it ran without error when I stepped thru it. Then I removed
instrumentation with C-M-x and reran - again no error.
I tried removing the *.elc and restarting emacs, but that seems to make no
difference - the error is still there till I instrument the code.
Until this is sorted out, you might try the instrument/uninstrument gambit
as a workaround.
HTH,
Chuck
^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: Using tramp to run R source code blocks on remote server
2016-04-21 22:04 ` Charles C. Berry
@ 2016-04-21 22:20 ` Cook, Malcolm
0 siblings, 0 replies; 12+ messages in thread
From: Cook, Malcolm @ 2016-04-21 22:20 UTC (permalink / raw)
To: 'Charles C. Berry', 'Vikas Rawal'
Cc: 'org-mode mailing list'
I believe some of the inter-process communication magic depends upon i/o through a file that exists in /tmp on the remote host
If the remote server shares a file system with localhost (does it?), you could contrive for that temp file to live there (~/.emacs.d/ESS.IPC.HACK) instead.
I've been stung by similar in the past.
What version of ESS and org are you using? (meta-x org-version and meta-x ess-version) - this has been a bit of a moving target. I've most recently had tramp/ess/org work FINE. That is when I am editing a file on a remote host via tramp. The R process starts up on the remote host (as does a shell for "#+SRC sh" blocks). This _should_ work for you....
~Malcolm
> -----Original Message-----
> From: Emacs-orgmode [mailto:emacs-orgmode-
> bounces+mec=stowers.org@gnu.org] On Behalf Of Charles C. Berry
> Sent: Thursday, April 21, 2016 5:05 PM
> To: Vikas Rawal <vikaslists@agrarianresearch.org>
> Cc: org-mode mailing list <emacs-orgmode@gnu.org>
> Subject: Re: [O] Using tramp to run R source code blocks on remote server
>
> On Thu, 21 Apr 2016, Charles C. Berry wrote:
>
> > On Thu, 21 Apr 2016, Charles C. Berry wrote:
> >
> >> On Thu, 21 Apr 2016, Vikas Rawal wrote:
> >>
> >>> I am trying to run R source code blocks on a remote server (defined in my
> >>> ~/.ssh/config as cesp).
> >>>
> >>> I am facing several problems.
> >>>
> >>> 1. The following sample block, when used with ":results value" does not
> >>> give any results.
> >>>
> >>> #+NAME: level1
> >>> #+begin_src R :results value :exports results :colnames yes :hline yes
> >>> :session cesp :dir /cesp:/home/vikas/
> >>> c(1:5)
> >>> #+end_src
> >>>
> >>> I get the following message:
> >>>
> >>> tramp-flush-directory-property: Wrong type argument: arrayp, nil
> >>>
> >>
> >> I think this is an issue with having different version of ESS on your local
> >> and remote systems.
> >>
> >
> > OOPS!
> >
> > The `different versions' issue affected my setup. But after correcting it, I
> > still get the error you cited above.
> >
> > Not sure exactly where the fault lies.
> >
>
>
> Maybe in `org-babel-comint-eval-invisibly-and-wait-for-file', but I am not
> sure what/how.
>
> I tried to instrument the function (C-u C-M-x on the function source) and
> run it. And it ran without error when I stepped thru it. Then I removed
> instrumentation with C-M-x and reran - again no error.
>
> I tried removing the *.elc and restarting emacs, but that seems to make no
> difference - the error is still there till I instrument the code.
>
> Until this is sorted out, you might try the instrument/uninstrument gambit
> as a workaround.
>
> HTH,
>
> Chuck
>
^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: Using tramp to run R source code blocks on remote server
2016-04-21 10:53 Using tramp to run R source code blocks on remote server Vikas Rawal
2016-04-21 16:48 ` Charles C. Berry
@ 2016-04-21 23:33 ` Tim Howes
2016-04-23 4:15 ` [PATCH] ob-comint.el bug WAS: " Charles C. Berry
2016-05-10 4:04 ` Benda Xu
3 siblings, 0 replies; 12+ messages in thread
From: Tim Howes @ 2016-04-21 23:33 UTC (permalink / raw)
To: emacs-orgmode
On 4/21/16 3:53 AM, Vikas Rawal wrote:
>
> 2. Is there a way to be able to use screen/byobu with remote processing?
This thread suggests using dtach:
http://grokbase.com/t/r/ess-help/1536b42tjy/ess-remote-r
^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: Using tramp to run R source code blocks on remote server
2016-04-21 16:48 ` Charles C. Berry
2016-04-21 21:29 ` Charles C. Berry
@ 2016-04-22 3:26 ` Vikas Rawal
2016-04-22 15:22 ` Nick Dokos
1 sibling, 1 reply; 12+ messages in thread
From: Vikas Rawal @ 2016-04-22 3:26 UTC (permalink / raw)
To: Charles C. Berry; +Cc: org-mode mailing list
[-- Attachment #1: Type: text/plain, Size: 1337 bytes --]
>
>> I am trying to run R source code blocks on a remote server (defined in my ~/.ssh/config as cesp).
>>
>> I am facing several problems.
>>
>> 1. The following sample block, when used with ":results value" does not give any results.
>>
>> #+NAME: level1
>> #+begin_src R :results value :exports results :colnames yes :hline yes :session cesp :dir /cesp:/home/vikas/
>> c(1:5)
>> #+end_src
>>
>> I get the following message:
>>
>> tramp-flush-directory-property: Wrong type argument: arrayp, nil
>>
>
> I think this is an issue with having different version of ESS on your local and remote systems.
>
> In particular, newer and older versions of `.ess.eval' have different arguments. You can check this by running `args(.ess.eval)' in the session of your remote server and in a session on your local system.
>
> In any case, I'd suggest asking on ess-help@r-project.org <mailto:ess-help@r-project.org> for help in fixing this.
>
Thanks for this. I did not think that ess on the remote system would be needed at all. I just want emacs+ess on my system to use R on the remote system.
Having to maintain version compatibility between every machine, and across multiple users, is an impossible situation.
But let me see what folks at ess-help have to say.
Thanks very much,
Vikas
[-- Attachment #2: Type: text/html, Size: 6917 bytes --]
^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: Using tramp to run R source code blocks on remote server
2016-04-22 3:26 ` Vikas Rawal
@ 2016-04-22 15:22 ` Nick Dokos
2016-04-22 16:17 ` Charles C. Berry
0 siblings, 1 reply; 12+ messages in thread
From: Nick Dokos @ 2016-04-22 15:22 UTC (permalink / raw)
To: emacs-orgmode
Vikas Rawal <vikaslists@agrarianresearch.org> writes:
> I am trying to run R source code blocks on a remote server (defined in my ~/.ssh/config as
> cesp).
>
> I am facing several problems.
>
> 1. The following sample block, when used with ":results value" does not give any results.
>
> #+NAME: level1
> #+begin_src R :results value :exports results :colnames yes :hline yes :session cesp :dir /cesp:
> /home/vikas/
> c(1:5)
> #+end_src
>
> I get the following message:
>
> tramp-flush-directory-property: Wrong type argument: arrayp, nil
>
You might also want to ping Michael Albinus on the tramp mailing list about
this.
--
Nick
> I think this is an issue with having different version of ESS on your local and remote systems.
>
> In particular, newer and older versions of `.ess.eval' have different arguments. You can check this
> by running `args(.ess.eval)' in the session of your remote server and in a session on your local
> system.
>
> In any case, I'd suggest asking on ess-help@r-project.org for help in fixing this.
>
> Thanks for this. I did not think that ess on the remote system would be needed at all. I just want
> emacs+ess on my system to use R on the remote system.
>
> Having to maintain version compatibility between every machine, and across multiple users, is an
> impossible situation.
>
> But let me see what folks at ess-help have to say.
>
> Thanks very much,
>
> Vikas
^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: Using tramp to run R source code blocks on remote server
2016-04-22 15:22 ` Nick Dokos
@ 2016-04-22 16:17 ` Charles C. Berry
2016-04-22 18:22 ` Cook, Malcolm
0 siblings, 1 reply; 12+ messages in thread
From: Charles C. Berry @ 2016-04-22 16:17 UTC (permalink / raw)
To: Nick Dokos; +Cc: emacs-orgmode
On Fri, 22 Apr 2016, Nick Dokos wrote:
> Vikas Rawal <vikaslists@agrarianresearch.org> writes:
>
>> I am trying to run R source code blocks on a remote server (defined in my ~/.ssh/config as
>> cesp).
>>
>> I am facing several problems.
>>
>> 1. The following sample block, when used with ":results value" does not give any results.
>>
>> #+NAME: level1
>> #+begin_src R :results value :exports results :colnames yes :hline yes :session cesp :dir /cesp:
>> /home/vikas/
>> c(1:5)
>> #+end_src
>>
>> I get the following message:
>>
>> tramp-flush-directory-property: Wrong type argument: arrayp, nil
>>
>
> You might also want to ping Michael Albinus on the tramp mailing list about
> this.
>
And contrary to what I said earlier this *is* related to compilation. Not
sure if this is a tramp issue for ob-comint.el issue.
Details:
If I run org-reload uncompiled, C-u C-c C-x !, code like
#+BEGIN_SRC R :session :dir /user@remote:/userdir
c(3,2,6)
#+END_SRC
runs fine and produces the expected result.
But reloading compiled, C-c C-x !, the code produces the
: tramp-flush-directory-property: Wrong type argument: arrayp, nil
message.
HTH,
Chuck
^ permalink raw reply [flat|nested] 12+ messages in thread
* Re: Using tramp to run R source code blocks on remote server
2016-04-22 16:17 ` Charles C. Berry
@ 2016-04-22 18:22 ` Cook, Malcolm
0 siblings, 0 replies; 12+ messages in thread
From: Cook, Malcolm @ 2016-04-22 18:22 UTC (permalink / raw)
To: 'Charles C. Berry', 'Nick Dokos'
Cc: 'emacs-orgmode@gnu.org'
> On Fri, 22 Apr 2016, Nick Dokos wrote:
>
> > Vikas Rawal <vikaslists@agrarianresearch.org> writes:
> >
> >> I am trying to run R source code blocks on a remote server (defined in
> my ~/.ssh/config as
> >> cesp).
> >>
> >> I am facing several problems.
> >>
> >> 1. The following sample block, when used with ":results value" does
> not give any results.
> >>
> >> #+NAME: level1
> >> #+begin_src R :results value :exports results :colnames yes :hline yes
> :session cesp :dir /cesp:
> >> /home/vikas/
> >> c(1:5)
> >> #+end_src
> >>
> >> I get the following message:
> >>
> >> tramp-flush-directory-property: Wrong type argument: arrayp, nil
> >>
> >
> > You might also want to ping Michael Albinus on the tramp mailing list about
> > this.
> >
>
>
> And contrary to what I said earlier this *is* related to compilation. Not
> sure if this is a tramp issue for ob-comint.el issue.
I do not trust org-reload. If I want a fresh org environment, I quit and restart emacs.
Also, when I am playing with effect of (re)compiling org, I don't compile it with org already loaded. I compile it in a fresh emacs.
I don't trust results gained other ways.
YMMV
>
> Details:
>
> If I run org-reload uncompiled, C-u C-c C-x !, code like
>
> #+BEGIN_SRC R :session :dir /user@remote:/userdir
> c(3,2,6)
> #+END_SRC
>
> runs fine and produces the expected result.
>
> But reloading compiled, C-c C-x !, the code produces the
>
> : tramp-flush-directory-property: Wrong type argument: arrayp, nil
>
> message.
>
> HTH,
>
> Chuck
^ permalink raw reply [flat|nested] 12+ messages in thread
* [PATCH] ob-comint.el bug WAS: Re: Using tramp to run R source code blocks on remote server
2016-04-21 10:53 Using tramp to run R source code blocks on remote server Vikas Rawal
2016-04-21 16:48 ` Charles C. Berry
2016-04-21 23:33 ` Tim Howes
@ 2016-04-23 4:15 ` Charles C. Berry
2016-05-10 4:04 ` Benda Xu
3 siblings, 0 replies; 12+ messages in thread
From: Charles C. Berry @ 2016-04-23 4:15 UTC (permalink / raw)
To: Vikas Rawal; +Cc: Nick Dokos, org-mode mailing list
[-- Attachment #1: Type: text/plain, Size: 670 bytes --]
On Thu, 21 Apr 2016, Vikas Rawal wrote:
> I am trying to run R source code blocks on a remote server (defined in my ~/.ssh/config as cesp).
>
> I am facing several problems.
>
> 1. The following sample block, when used with ":results value" does not give any results.
>
> #+NAME: level1
> #+begin_src R :results value :exports results :colnames yes :hline yes :session cesp :dir /cesp:/home/vikas/
> c(1:5)
> #+end_src
>
> I get the following message:
>
> tramp-flush-directory-property: Wrong type argument: arrayp, nil
>
This was a near trivial byte-compiler issue.
`tramp-flush-directory-property' is in tramp-cache.el not tramp.el.
I'll push it tomorrow.
Chuck
[-- Attachment #2: patch --]
[-- Type: text/plain, Size: 1171 bytes --]
From b108391e0ba56e0a272aae1d1fb2eed4f1c4a03c Mon Sep 17 00:00:00 2001
From: Charles Berry <ccberry@ucsd.edu>
Date: Fri, 22 Apr 2016 21:04:16 -0700
Subject: [PATCH] ob-comint.el: Fix byte-compiler/declare-function bug
* ob-comint.el: (tramp-flush-directory-property declaration): The
file is now "tramp-cache".
Bug reported by
From: Vikas Rawal
Subject: Using tramp to run R source code blocks on remote server
Archived-At: <http://permalink.gmane.org/gmane.emacs.orgmode/106557>
---
lisp/ob-comint.el | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/lisp/ob-comint.el b/lisp/ob-comint.el
index a5a7888..833d492 100644
--- a/lisp/ob-comint.el
+++ b/lisp/ob-comint.el
@@ -35,7 +35,7 @@
(require 'comint)
(eval-when-compile (require 'cl))
(declare-function with-parsed-tramp-file-name "tramp" (filename var &rest body))
-(declare-function tramp-flush-directory-property "tramp" (vec directory))
+(declare-function tramp-flush-directory-property "tramp-cache" (vec directory))
(defun org-babel-comint-buffer-livep (buffer)
"Check if BUFFER is a comint buffer with a live process."
--
2.6.4 (Apple Git-63)
^ permalink raw reply related [flat|nested] 12+ messages in thread
* Re: Using tramp to run R source code blocks on remote server
2016-04-21 10:53 Using tramp to run R source code blocks on remote server Vikas Rawal
` (2 preceding siblings ...)
2016-04-23 4:15 ` [PATCH] ob-comint.el bug WAS: " Charles C. Berry
@ 2016-05-10 4:04 ` Benda Xu
3 siblings, 0 replies; 12+ messages in thread
From: Benda Xu @ 2016-05-10 4:04 UTC (permalink / raw)
To: Vikas Rawal; +Cc: org-mode
Hi Vikas,
I cannot address your problem directly. I have a workaround.
Vikas Rawal <vikaslists@agrarianresearch.org> writes:
> I am trying to run R source code blocks on a remote server (defined in
> my ~/.ssh/config as cesp).
>
> I am facing several problems.
>
> 1. The following sample block, when used with ":results value" does
> not give any results.
>
> #+NAME: level1
> #+begin_src R :results value :exports results :colnames yes :hline yes :session cesp :dir /cesp:/home/vikas/
> c(1:5)
> #+end_src
>
> I get the following message:
>
> tramp-flush-directory-property: Wrong type argument: arrayp, nil
>
> I get the expected output if I use ":results output”, but I don’t want
> that.
I have gone through similar pains as you did.
> 2. Is there a way to be able to use screen/byobu with remote
> processing? I have tried various options of using shell, term, or
> ansi-term. Each of them gives some problem or the other. Does anyone
> have experience with using any of these?
This might be possible with the future async executions.
For the moment, I have settled down with the following solution:
1. Tangle each source blocks as a script to the remote host.
2. Tangle a Makefile to manage the execution, e.g. how the scripts are
executed with which arguments.
3. Login the remote host and open a tmux session and run "make" in the
tangled directory.
With this workflow, all the programs are managed by org-mode, and they
are executed asychronously. At the same time, I lose the flexibility to
run the scripts in a org spawned session, which is a trade-off.
Cheers,
Benda
^ permalink raw reply [flat|nested] 12+ messages in thread
end of thread, other threads:[~2016-05-10 4:04 UTC | newest]
Thread overview: 12+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2016-04-21 10:53 Using tramp to run R source code blocks on remote server Vikas Rawal
2016-04-21 16:48 ` Charles C. Berry
2016-04-21 21:29 ` Charles C. Berry
2016-04-21 22:04 ` Charles C. Berry
2016-04-21 22:20 ` Cook, Malcolm
2016-04-22 3:26 ` Vikas Rawal
2016-04-22 15:22 ` Nick Dokos
2016-04-22 16:17 ` Charles C. Berry
2016-04-22 18:22 ` Cook, Malcolm
2016-04-21 23:33 ` Tim Howes
2016-04-23 4:15 ` [PATCH] ob-comint.el bug WAS: " Charles C. Berry
2016-05-10 4:04 ` Benda Xu
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