From mboxrd@z Thu Jan 1 00:00:00 1970 From: Thomas Alexander Gerds Subject: Re: minor bug in babel with silent output and remote R session Date: Wed, 13 Mar 2013 17:29:10 +0100 Message-ID: References: <87obencp2t.fsf@gmail.com> Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([208.118.235.92]:36539) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1UFoYL-0002oe-PG for emacs-orgmode@gnu.org; Wed, 13 Mar 2013 12:29:31 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1UFoYD-0001H8-Lv for emacs-orgmode@gnu.org; Wed, 13 Mar 2013 12:29:21 -0400 Received: from mail-ee0-f45.google.com ([74.125.83.45]:57464) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1UFoYD-0001Gv-Gb for emacs-orgmode@gnu.org; Wed, 13 Mar 2013 12:29:13 -0400 Received: by mail-ee0-f45.google.com with SMTP id b57so586499eek.32 for ; Wed, 13 Mar 2013 09:29:12 -0700 (PDT) In-Reply-To: <87obencp2t.fsf@gmail.com> (Eric Schulte's message of "Wed, 13 Mar 2013 09:11:06 -0600") List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: Eric Schulte Cc: emacs-orgmode@gnu.org yes, I am quite sure. here is the org code ,---- | | #+BEGIN_SRC R :results silent :exports results :session *ssh gauss* :cache yes | a=1 | 1 | #+END_SRC | | #+BEGIN_SRC R :results output :exports results :session *ssh gauss* :cache yes | a=1 | 1 | #+END_SRC | | #+RESULTS[<2013-03-13 17:26:16> 4d5d8eeab67e30060345cd66f44466bd168af55a]: | : [1] 1 `---- and here the contents of the *ssh gauss* buffer ,---- | | Last login: Wed Mar 13 08:41:53 2013 from 10.128.132.66 | IFSV default server Policy. | NFS monteret home under /home/ifsv | $ R | WARNING: ignoring environment value of R_HOME | | R version 2.15.2 (2012-10-26) -- "Trick or Treat" | Copyright (C) 2012 The R Foundation for Statistical Computing | ISBN 3-900051-07-0 | Platform: x86_64-unknown-linux-gnu (64-bit) | | R is free software and comes with ABSOLUTELY NO WARRANTY. | You are welcome to redistribute it under certain conditions. | Type 'license()' or 'licence()' for distribution details. | | Natural language support but running in an English locale | | R is a collaborative project with many contributors. | Type 'contributors()' for more information and | 'citation()' on how to cite R or R packages in publications. | | Type 'demo()' for some demos, 'help()' for on-line help, or | 'help.start()' for an HTML browser interface to help. | Type 'q()' to quit R. | | options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient', show.error.locations=TRUE) | [Previously saved workspace restored] | | > > > [1] 1 | > Warning message: | In file.rename(tfile, transfer.file) : | cannot rename file '/tmp/RtmpLkxWKf/file8bd75fb3ce' to '/tmp/babel-8270IwX/R-8270vVe', reason 'No such file or directory' | > a=1 | 1 | 'org_babel_R_eoe' | a=1 | > 1 | [1] 1 | > 'org_babel_R_eoe' | [1] "org_babel_R_eoe" | > `---- cheers Thomas Eric Schulte writes: > Thomas Alexander Gerds writes: > >> Using the silent option together with a remote R session block >> (started via ssh.el and ess-remote), like this: >> #+BEGIN_SRC R :results silent :exports results :session *ssh gauss* >> :cache yes a=1 1 #+END_SRC >> produces: >> ,---- >> | > > > [1] 1 Warning message: >> | In file.rename(tfile, transfer.file) : cannot rename file >> | /tmp/RtmpQwlyCf/file7c9b78867f6c' to >> | /tmp/babel-4977UIT/R-4977ucf', reason 'No such file or directory' >> | > >> `---- >> and emacs freezes. No big deal because C-g gets me out of it, but >> slightly annoying. >> with `:results output' instead of `:results: silent' everything >> works fine. >> > > Are you sure this problem is related to the ":results silent" header > argument? I would expect this problem to arise *any* time results are > requested from a remove R session. This is because R and Emacs use > the file system to hand results back and forth, and when the R session > refers to a remote file system, this communication fails. > > One possible solution would be to use the :dir header argument to > specify to the code block the machine on which the execution is taking > place. > > Best, > >> >> best, Thomas >>