Re: minor bug in babel with silent output and remote R session

[Thomas Alexander Gerds <tag@biostat.ku.dk>]

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)