* org mode R remote code evaluation
@ 2013-08-29 6:31 Johannes Rainer
2013-08-29 8:25 ` Loris Bennett
0 siblings, 1 reply; 18+ messages in thread
From: Johannes Rainer @ 2013-08-29 6:31 UTC (permalink / raw)
To: emacs-orgmode
[-- Attachment #1: Type: text/plain, Size: 1512 bytes --]
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/6kbb36310wz2kww8y8ctry600000gn/T/R-46345BQs...done
byte-code: Couldn't write region to
`/ssh:xx@xxx:/var/folders/ny/6kbb36310wz2kww8y8ctry600000gn/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/6kbb36310wz2kww8y8ctry600000gn/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
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^ permalink raw reply [flat|nested] 18+ messages in thread* Re: org mode R remote code evaluation 2013-08-29 6:31 org mode R remote code evaluation Johannes Rainer @ 2013-08-29 8:25 ` Loris Bennett 2013-08-29 10:42 ` Johannes Rainer 0 siblings, 1 reply; 18+ messages in thread From: Loris Bennett @ 2013-08-29 8:25 UTC (permalink / raw) To: emacs-orgmode Johannes Rainer <johannes.rainer@gmail.com> 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/6kbb36310wz2kww8y8ctry600000gn/T/R-46345BQs...done > byte-code: Couldn't write region to > `/ssh:xx@xxx:/var/folders/ny/6kbb36310wz2kww8y8ctry600000gn/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/6kbb36310wz2kww8y8ctry600000gn/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@xxxxx: 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. ^ permalink raw reply [flat|nested] 18+ messages in thread
* Re: org mode R remote code evaluation 2013-08-29 8:25 ` Loris Bennett @ 2013-08-29 10:42 ` Johannes Rainer 2013-09-23 16:45 ` Alexander Vorobiev 0 siblings, 1 reply; 18+ messages in thread From: Johannes Rainer @ 2013-08-29 10:42 UTC (permalink / raw) To: Loris Bennett; +Cc: emacs-orgmode [-- Attachment #1: Type: text/plain, Size: 2540 bytes --] thanks! so the ":results output" does the trick. On Thu, Aug 29, 2013 at 10:25 AM, Loris Bennett <loris.bennett@fu-berlin.de>wrote: > Johannes Rainer <johannes.rainer@gmail.com> 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/6kbb36310wz2kww8y8ctry600000gn/T/R-46345BQs...done > > byte-code: Couldn't write region to > > `/ssh:xx@xxx > :/var/folders/ny/6kbb36310wz2kww8y8ctry600000gn/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/6kbb36310wz2kww8y8ctry600000gn/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@xxxxx: > 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.rainer@i-med.ac.at johannes.rainer@tcri.at URL: http://bioinfo.i-med.ac.at [-- Attachment #2: Type: text/html, Size: 3734 bytes --] ^ permalink raw reply [flat|nested] 18+ messages in thread
* Re: org mode R remote code evaluation 2013-08-29 10:42 ` Johannes Rainer @ 2013-09-23 16:45 ` Alexander Vorobiev 2013-09-24 12:57 ` Michael Albinus 0 siblings, 1 reply; 18+ messages in thread From: Alexander Vorobiev @ 2013-09-23 16:45 UTC (permalink / raw) To: Johannes Rainer; +Cc: Loris Bennett, emacs-orgmode [-- Attachment #1: Type: text/plain, Size: 3468 bytes --] 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.rainer@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.bennett@fu-berlin.de> wrote: > >> Johannes Rainer <johannes.rainer@gmail.com> 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/6kbb36310wz2kww8y8ctry600000gn/T/R-46345BQs...done >> > byte-code: Couldn't write region to >> > `/ssh:xx@xxx >> :/var/folders/ny/6kbb36310wz2kww8y8ctry600000gn/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/6kbb36310wz2kww8y8ctry600000gn/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@xxxxx: >> 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.rainer@i-med.ac.at > johannes.rainer@tcri.at > URL: http://bioinfo.i-med.ac.at > > > [-- Attachment #2: Type: text/html, Size: 5220 bytes --] ^ permalink raw reply [flat|nested] 18+ messages in thread
* Re: org mode R remote code evaluation 2013-09-23 16:45 ` Alexander Vorobiev @ 2013-09-24 12:57 ` Michael Albinus 2013-09-24 13:21 ` Alexander Vorobiev 0 siblings, 1 reply; 18+ messages in thread From: Michael Albinus @ 2013-09-24 12:57 UTC (permalink / raw) To: Alexander Vorobiev; +Cc: Loris Bennett, emacs-orgmode, Johannes Rainer Alexander Vorobiev <alexander.vorobiev@gmail.com> 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. ^ permalink raw reply [flat|nested] 18+ messages in thread
* Re: org mode R remote code evaluation 2013-09-24 12:57 ` Michael Albinus @ 2013-09-24 13:21 ` Alexander Vorobiev 2013-09-24 13:25 ` Michael Albinus 0 siblings, 1 reply; 18+ messages in thread From: Alexander Vorobiev @ 2013-09-24 13:21 UTC (permalink / raw) To: Michael Albinus; +Cc: Loris Bennett, emacs-orgmode, Johannes Rainer [-- Attachment #1: Type: text/plain, Size: 1183 bytes --] 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 <michael.albinus@gmx.de>wrote: > Alexander Vorobiev <alexander.vorobiev@gmail.com> 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. > [-- Attachment #2: Type: text/html, Size: 1947 bytes --] ^ permalink raw reply [flat|nested] 18+ messages in thread
* Re: org mode R remote code evaluation 2013-09-24 13:21 ` Alexander Vorobiev @ 2013-09-24 13:25 ` Michael Albinus [not found] ` <CAGOCFPUyTaQzVTSwjUOJBfwF8vUzyw=Gn43+bHs8Go8+RUU+nA@mail.gmail.com> 0 siblings, 1 reply; 18+ messages in thread From: Michael Albinus @ 2013-09-24 13:25 UTC (permalink / raw) To: Alexander Vorobiev; +Cc: Loris Bennett, emacs-orgmode, Johannes Rainer Alexander Vorobiev <alexander.vorobiev@gmail.com> 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. ^ permalink raw reply [flat|nested] 18+ messages in thread
[parent not found: <CAGOCFPUyTaQzVTSwjUOJBfwF8vUzyw=Gn43+bHs8Go8+RUU+nA@mail.gmail.com>]
* Re: org mode R remote code evaluation [not found] ` <CAGOCFPUyTaQzVTSwjUOJBfwF8vUzyw=Gn43+bHs8Go8+RUU+nA@mail.gmail.com> @ 2013-09-24 18:40 ` Michael Albinus 2013-09-25 4:24 ` Alexander Vorobiev 0 siblings, 1 reply; 18+ messages in thread From: Michael Albinus @ 2013-09-24 18:40 UTC (permalink / raw) To: Alexander Vorobiev; +Cc: Loris Bennett, emacs-orgmode, Johannes Rainer Alexander Vorobiev <alexander.vorobiev@gmail.com> 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. ^ permalink raw reply [flat|nested] 18+ messages in thread
* Re: org mode R remote code evaluation 2013-09-24 18:40 ` Michael Albinus @ 2013-09-25 4:24 ` Alexander Vorobiev 2013-09-25 10:44 ` Michael Albinus 0 siblings, 1 reply; 18+ messages in thread From: Alexander Vorobiev @ 2013-09-25 4:24 UTC (permalink / raw) To: Michael Albinus; +Cc: Loris Bennett, emacs-orgmode, Johannes Rainer [-- Attachment #1: Type: text/plain, Size: 1667 bytes --] 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 <michael.albinus@gmx.de>wrote: > Alexander Vorobiev <alexander.vorobiev@gmail.com> 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. > [-- Attachment #2: Type: text/html, Size: 2418 bytes --] ^ permalink raw reply [flat|nested] 18+ messages in thread
* Re: org mode R remote code evaluation 2013-09-25 4:24 ` Alexander Vorobiev @ 2013-09-25 10:44 ` Michael Albinus 2013-09-25 18:15 ` Eric Schulte 0 siblings, 1 reply; 18+ messages in thread From: Michael Albinus @ 2013-09-25 10:44 UTC (permalink / raw) To: Alexander Vorobiev; +Cc: Loris Bennett, emacs-orgmode, Johannes Rainer Alexander Vorobiev <alexander.vorobiev@gmail.com> 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. ^ permalink raw reply [flat|nested] 18+ messages in thread
* Re: org mode R remote code evaluation 2013-09-25 10:44 ` Michael Albinus @ 2013-09-25 18:15 ` Eric Schulte 2013-09-25 19:03 ` Michael Albinus 2013-09-27 11:39 ` Michael Albinus 0 siblings, 2 replies; 18+ messages in thread From: Eric Schulte @ 2013-09-25 18:15 UTC (permalink / raw) To: Michael Albinus Cc: Loris Bennett, emacs-orgmode, Alexander Vorobiev, Johannes Rainer Michael Albinus <michael.albinus@gmx.de> writes: > Alexander Vorobiev <alexander.vorobiev@gmail.com> 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 ^ permalink raw reply [flat|nested] 18+ messages in thread
* Re: org mode R remote code evaluation 2013-09-25 18:15 ` Eric Schulte @ 2013-09-25 19:03 ` Michael Albinus 2013-09-25 20:36 ` Alexander Vorobiev 2013-09-27 11:39 ` Michael Albinus 1 sibling, 1 reply; 18+ messages in thread From: Michael Albinus @ 2013-09-25 19:03 UTC (permalink / raw) To: Eric Schulte Cc: Loris Bennett, emacs-orgmode, Alexander Vorobiev, Johannes Rainer Eric Schulte <schulte.eric@gmail.com> 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. ^ permalink raw reply [flat|nested] 18+ messages in thread
* Re: org mode R remote code evaluation 2013-09-25 19:03 ` Michael Albinus @ 2013-09-25 20:36 ` Alexander Vorobiev 2013-09-26 8:11 ` Michael Albinus 0 siblings, 1 reply; 18+ messages in thread From: Alexander Vorobiev @ 2013-09-25 20:36 UTC (permalink / raw) To: Michael Albinus Cc: Loris Bennett, emacs-orgmode, Johannes Rainer, Eric Schulte [-- Attachment #1: Type: text/plain, Size: 3071 bytes --] 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 <michael.albinus@gmx.de>wrote: > Eric Schulte <schulte.eric@gmail.com> 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. > [-- Attachment #2: Type: text/html, Size: 4277 bytes --] ^ permalink raw reply [flat|nested] 18+ messages in thread
* Re: org mode R remote code evaluation 2013-09-25 20:36 ` Alexander Vorobiev @ 2013-09-26 8:11 ` Michael Albinus [not found] ` <CAGOCFPXj2-3FruuD=K7=H+SQ308dzkH1P=qP0b17xQuoW9MkPQ@mail.gmail.com> 0 siblings, 1 reply; 18+ messages in thread From: Michael Albinus @ 2013-09-26 8:11 UTC (permalink / raw) To: Alexander Vorobiev Cc: Loris Bennett, emacs-orgmode, Johannes Rainer, Eric Schulte Alexander Vorobiev <alexander.vorobiev@gmail.com> 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. ^ permalink raw reply related [flat|nested] 18+ messages in thread
[parent not found: <CAGOCFPXj2-3FruuD=K7=H+SQ308dzkH1P=qP0b17xQuoW9MkPQ@mail.gmail.com>]
[parent not found: <87mwmzy16d.fsf@gmx.de>]
* Re: org mode R remote code evaluation [not found] ` <87mwmzy16d.fsf@gmx.de> @ 2013-09-26 17:28 ` Alexander Vorobiev 2013-09-26 17:43 ` Michael Albinus 0 siblings, 1 reply; 18+ messages in thread From: Alexander Vorobiev @ 2013-09-26 17:28 UTC (permalink / raw) To: Michael Albinus, emacs-orgmode, Johannes Rainer, Loris Bennett [-- Attachment #1: Type: text/plain, Size: 684 bytes --] #+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 <michael.albinus@gmx.de>wrote: > Alexander Vorobiev <alexander.vorobiev@gmail.com> 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. > > [-- Attachment #2: Type: text/html, Size: 1381 bytes --] ^ permalink raw reply [flat|nested] 18+ messages in thread
* Re: org mode R remote code evaluation 2013-09-26 17:28 ` Alexander Vorobiev @ 2013-09-26 17:43 ` Michael Albinus 0 siblings, 0 replies; 18+ messages in thread From: Michael Albinus @ 2013-09-26 17:43 UTC (permalink / raw) To: Alexander Vorobiev; +Cc: Loris Bennett, emacs-orgmode, Johannes Rainer Alexander Vorobiev <alexander.vorobiev@gmail.com> 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. ^ permalink raw reply [flat|nested] 18+ messages in thread
* Re: org mode R remote code evaluation 2013-09-25 18:15 ` Eric Schulte 2013-09-25 19:03 ` Michael Albinus @ 2013-09-27 11:39 ` Michael Albinus 2013-09-28 11:41 ` Eric Schulte 1 sibling, 1 reply; 18+ messages in thread From: Michael Albinus @ 2013-09-27 11:39 UTC (permalink / raw) To: Eric Schulte Cc: Loris Bennett, emacs-orgmode, Alexander Vorobiev, Johannes Rainer [-- Attachment #1: Type: text/plain, Size: 385 bytes --] Eric Schulte <schulte.eric@gmail.com> 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. [-- Warning: decoded text below may be mangled, UTF-8 assumed --] [-- Attachment #2: 0001-ob-core.el-org-babel-local-file-name-Simplify.patch --] [-- Type: text/x-diff, Size: 2737 bytes --] From 2b8db5486de75ec35c2c0d3e6063847cf582ace7 Mon Sep 17 00:00:00 2001 From: Michael Albinus <michael.albinus@gmx.de> 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 ^ permalink raw reply related [flat|nested] 18+ messages in thread
* Re: org mode R remote code evaluation 2013-09-27 11:39 ` Michael Albinus @ 2013-09-28 11:41 ` Eric Schulte 0 siblings, 0 replies; 18+ messages in thread From: Eric Schulte @ 2013-09-28 11:41 UTC (permalink / raw) To: Michael Albinus Cc: Loris Bennett, emacs-orgmode, Alexander Vorobiev, Eric Schulte, Johannes Rainer Michael Albinus <michael.albinus@gmx.de> writes: > Eric Schulte <schulte.eric@gmail.com> 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 ^ permalink raw reply [flat|nested] 18+ messages in thread
end of thread, other threads:[~2013-09-28 12:39 UTC | newest]
Thread overview: 18+ messages (download: mbox.gz / follow: Atom feed)
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2013-08-29 6:31 org mode R remote code evaluation Johannes Rainer
2013-08-29 8:25 ` Loris Bennett
2013-08-29 10:42 ` Johannes Rainer
2013-09-23 16:45 ` Alexander Vorobiev
2013-09-24 12:57 ` Michael Albinus
2013-09-24 13:21 ` Alexander Vorobiev
2013-09-24 13:25 ` Michael Albinus
[not found] ` <CAGOCFPUyTaQzVTSwjUOJBfwF8vUzyw=Gn43+bHs8Go8+RUU+nA@mail.gmail.com>
2013-09-24 18:40 ` Michael Albinus
2013-09-25 4:24 ` Alexander Vorobiev
2013-09-25 10:44 ` Michael Albinus
2013-09-25 18:15 ` Eric Schulte
2013-09-25 19:03 ` Michael Albinus
2013-09-25 20:36 ` Alexander Vorobiev
2013-09-26 8:11 ` Michael Albinus
[not found] ` <CAGOCFPXj2-3FruuD=K7=H+SQ308dzkH1P=qP0b17xQuoW9MkPQ@mail.gmail.com>
[not found] ` <87mwmzy16d.fsf@gmx.de>
2013-09-26 17:28 ` Alexander Vorobiev
2013-09-26 17:43 ` Michael Albinus
2013-09-27 11:39 ` Michael Albinus
2013-09-28 11:41 ` Eric Schulte
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