From: "Charles C. Berry" <ccberry@ucsd.edu>
To: Aaron Ecay <aaronecay@gmail.com>
Cc: emacs-orgmode@gnu.org
Subject: Re: R code block produces only partial output
Date: Mon, 1 Sep 2014 09:08:45 -0700 [thread overview]
Message-ID: <alpine.OSX.2.00.1409010836220.366@charles-berrys-macbook.local> (raw)
In-Reply-To: <87k35orl2w.fsf@gmail.com>
[-- Attachment #1: Type: TEXT/PLAIN, Size: 3075 bytes --]
On Sun, 31 Aug 2014, Aaron Ecay wrote:
> Hi Chuck,
>
> Attached is a new version of the patch, including a few more tests. I
> have one question:
>
> 2014ko abuztuak 28an, Aaron Ecay-ek idatzi zuen:
>>> but the patch here uses on.exit(file.create(...)) to ensure that that
>>> file is created. One hiccup (not sure if it exists in master,too) is
>>> that starting a remote session and then trying to run src blocks from
>>> a buffer for a local file will hang (because a local temp file is used
>>> for sentinel). So there is still stuff to do.
>>
>> Hmm, OK.
>
> Can you give a recipe to reproduce this? Everything seems to work for
> me using the following test code, although there is an unexplained ~10s
> delay while babel sits in the ‘(while (not (file-exists-p file)) ...)’
> loop at the end of ‘org-babel-comint-eval-invisibly-and-wait-for-file’.
> ,----
> | #+name: foo
> | #+begin_src R :session *foo* :dir /ssh:aecay@foo:/home/aecay :results output
> | 1+1
> | #+end_src
> |
> | #+RESULTS: foo
> | : [1] 2
> `----
Aaron,
I installed your patch.
Two cases:
1) I open a connection to a remote server by opening a directory there.
From *Messages*:
Tramp: Opening connection for berry@<censored> using scpc...
Then start an R session, type 'library(evaluate)', then change to a local
buffer with an R src block and C-c C-c, wait a long while then C-g, then
change to the *R* buffer and quit the session. I get this in the *R*
buffer:
,----
| > > options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient',
| show.error.locations=TRUE)
| > library(evaluate)
| >
| + + + + . + + + Error in file(file, ifelse(append, "a", "w")) (from #3) :
| cannot open the connection
| In addition: Warning message:
| In file(file, ifelse(append, "a", "w")) :
| cannot open file
| '/var/folders/kb/2hchpbyj7lb6z76l0q73w_fh0000gn/T/babel-392ywI/R-392jUu':
| No such file or directory
| > q()
| Save workspace image? [y/n/c]: n
| Warning message:
| In
| file.create("/var/folders/kb/2hchpbyj7lb6z76l0q73w_fh0000gn/T/babel-392ywI/R-392jUu-sentinel")
| :
| cannot create file
| '/var/folders/kb/2hchpbyj7lb6z76l0q73w_fh0000gn/T/babel-392ywI/R-392jUu-sentinel',
| reason 'No such file or directory'
|
| Process R finished at Mon Sep 1 08:31:19 2014
`----
This worked OK with master.
2) If I modify your 'foo' block to use :dir /ssh:berry@<censored>/<censored>
and C-c C-c, I get an error message 'Invalid function: with-parsed-tramp-file-name'
In the *Messages* buffer, I see:
,----
| Tramp: Decoding region into remote file /ssh:berry@microb215.med.upenn.edu:/tmp/R-39288P...done
| org-babel-comint-eval-invisibly-and-wait-for-file: Invalid function: with-parsed-tramp-file-name
`----
FWIW, the emacs on that remote system is 22.1.
I thought maybe tramp does some magic that I do not grok, tries to
use the remote emacs and fails. If so, note:
On the remote system
C-h f with-parsed TAB RET shows
,----
| with-parsed-tramp-file-name is a Lisp macro in `tramp.el'.
| ...
`----
so it *does* have that function.
???
HTH,
Chuck
next prev parent reply other threads:[~2014-09-01 16:09 UTC|newest]
Thread overview: 41+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-08-04 11:18 R code block produces only partial output Andreas Kiermeier
2014-08-04 11:53 ` Eric Schulte
2014-08-04 12:23 ` Andreas Kiermeier
2014-08-04 13:10 ` Eric Schulte
2014-08-05 0:46 ` Andreas Kiermeier
2014-08-05 4:00 ` John Hendy
2014-08-05 4:31 ` Andreas Kiermeier
2014-08-05 18:05 ` Charles Berry
2014-08-05 19:02 ` Eric Schulte
2014-08-05 19:11 ` John Hendy
2014-08-05 19:57 ` Nick Dokos
2014-08-05 20:10 ` Nick Dokos
2014-08-05 22:21 ` Charles C. Berry
2014-08-06 3:32 ` Aaron Ecay
2014-08-06 11:30 ` Eric Schulte
2014-08-07 6:00 ` Aaron Ecay
2014-08-07 17:42 ` Charles C. Berry
2014-08-07 18:06 ` Aaron Ecay
2014-08-07 18:42 ` Charles C. Berry
2014-08-07 19:06 ` Thomas S. Dye
2014-08-09 8:54 ` Rainer M Krug
2014-08-16 5:05 ` Aaron Ecay
2014-08-16 18:50 ` Charles C. Berry
2014-08-16 20:58 ` Aaron Ecay
2014-08-17 6:03 ` Achim Gratz
2014-08-19 0:13 ` Aaron Ecay
2014-08-19 5:36 ` Achim Gratz
2014-08-23 8:32 ` Aaron Ecay
2014-08-23 9:24 ` Andreas Kiermeier
2014-08-23 17:10 ` Aaron Ecay
2014-08-23 18:35 ` Thomas S. Dye
2014-08-23 19:37 ` Ista Zahn
2014-08-24 0:10 ` Charles C. Berry
2014-08-28 5:24 ` Aaron Ecay
2014-09-01 5:00 ` Aaron Ecay
2014-09-01 16:08 ` Charles C. Berry [this message]
2014-08-09 8:48 ` Rainer M Krug
2014-08-06 1:11 ` Andreas Kiermeier
2014-08-06 2:21 ` Charles C. Berry
2014-08-06 3:24 ` Aaron Ecay
2014-08-06 15:59 ` Charles C. Berry
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
List information: https://www.orgmode.org/
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=alpine.OSX.2.00.1409010836220.366@charles-berrys-macbook.local \
--to=ccberry@ucsd.edu \
--cc=aaronecay@gmail.com \
--cc=emacs-orgmode@gnu.org \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
Code repositories for project(s) associated with this public inbox
https://git.savannah.gnu.org/cgit/emacs/org-mode.git
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).