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From: Eric Schulte <schulte.eric@gmail.com>
To: Thomas Alexander Gerds <tag@biostat.ku.dk>
Cc: Bastien <bzg@gnu.org>, emacs-orgmode@gnu.org
Subject: Re: minor bug in babel with silent output and remote R session
Date: Sun, 14 Apr 2013 09:23:07 -0600	[thread overview]
Message-ID: <871uadf39l.fsf@gmail.com> (raw)
In-Reply-To: 86txn95tls.fsf@biostat.ku.dk

It is a shame that this can't be handled gracefully either through ESS
or R code.

I agree it would be nice to raise a warning rather than hang waiting for
a file which won't ever exist.  So, how can we tell from the Babel
source if the R session is remote?


Thomas Alexander Gerds <tag@biostat.ku.dk> writes:

> yes, I am using ESS. ess-remote allows me to evaluate R-code from the local
> emacs-session on a remote machine connected to via ssh.
> there are two problems:
> 1) the remote machine cannot write to org-babel-temp-file because the
>    tmp-directory exists on the local machine. here we could add
>    if(!file.exists(dirname(transfer.file))){dir.create(dirname(transfer.file))}
> in the middle of the variable org-babel-R-write-object-command
> this would achieve that the file is at least  generated on the remote host.
> 2) however, still the transfer file does not exist on the local
> machine. there are several possiblities:
> a) tell org-babel-comint-eval-invisibly-and-wait-for-file
>  that the file is remote and then test if
>  (concat "/" username "@" host ":" file) exists instead of file.
> b) use tramp to transfer the file from the remote to the local
> machine. the function ssh does define ssh-host and ssh-username,
> however, calling ess-remote removes these variables again.
> c) tell org-babel-comint-eval-invisibly-and-wait-for-file not to wait
>  for file if it is remote
> my conclusion: it would be nice to have this functionality, but perhaps
> it is not worth the efforts and it would be sufficient to avoid the
> endless loop when waiting for a file which never will generated.
> cheers thomas
> Eric Schulte <schulte.eric@gmail.com> writes:
>> Bastien <bzg@gnu.org> writes:
>>> Hi Thomas,
>>> thanks for the follow-up.
>>> Thomas Alexander Gerds <tag@biostat.ku.dk> writes:
>>>> I think that I can describe the problem a bit better now. It is not
>>>> related to the silent option but occurs whenever ":results value".
>>>> Emacs freezes due to the following line in
>>>> org-babel-comint-eval-invisibly-and-wait-for-file
>>>> (while (not (file-exists-p file)) (sit-for (or period 0.25)))
>>>> it seems that R cannot transfer the file and hence this is an
>>>> endless loop.
>>> I'm not knowledgeable enough in this area to provide a fix, maybe
>>> someone else will.
>> Could this be a problem with whatever tool (I'm assuming ESS) you are
>> using to maintain the R session and generate the R file?
>> Perhaps babel needs to modify the R code used to create the file (held
>> in the `org-babel-R-write-object-command' variable).  Could you take a
>> shot at providing another version of this variable?  I don't really
>> use R myself.
>> Thanks,
> --
> Thomas A. Gerds -- Assoc. Prof. Department of Biostatistics
> University of Copenhagen, Øster Farimagsgade 5, 1014 Copenhagen, Denmark
> Office: CSS-15.2.07 (Gamle Kommunehospital)
> tel: 35327914 (sec: 35327901) 

Eric Schulte

  reply	other threads:[~2013-04-14 17:09 UTC|newest]

Thread overview: 12+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2013-03-13  7:49 minor bug in babel with silent output and remote R session Thomas Alexander Gerds
2013-03-13 15:11 ` Eric Schulte
2013-03-13 16:29   ` Thomas Alexander Gerds
2013-04-07  7:45 ` Bastien
2013-04-07  8:42   ` Achim Gratz
2013-04-09  8:13   ` Thomas Alexander Gerds
2013-04-10 12:44     ` Bastien
2013-04-12 21:57       ` Eric Schulte
2013-04-14  9:50         ` Thomas Alexander Gerds
2013-04-14 15:23           ` Eric Schulte [this message]
2013-04-15 12:56             ` Thomas Alexander Gerds
2013-04-15 12:34     ` Andreas Leha

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