Re: [O] R code block produces only partial output

[Charles C. Berry]

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:address@hidden:/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:address@hidden:/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