From mboxrd@z Thu Jan 1 00:00:00 1970 From: "Cook, Malcolm" Subject: Re: [PATCH] WAS Re: Bug: problem w/ R code blocks [8.3beta (release_8.3beta-362-ga92789 /usr/local/share/emacs/site-lisp/org/)] Date: Thu, 18 Sep 2014 21:13:18 +0000 Message-ID: References: <87bnqgzljd.fsf@kademan.org> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:45478) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1XUj18-0007qr-SR for emacs-orgmode@gnu.org; Thu, 18 Sep 2014 17:13:35 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1XUj14-00015K-IC for emacs-orgmode@gnu.org; Thu, 18 Sep 2014 17:13:30 -0400 Received: from smtp01.stowers.org ([40.141.174.61]:44325) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1XUj14-00013G-CQ for emacs-orgmode@gnu.org; Thu, 18 Sep 2014 17:13:26 -0400 In-Reply-To: Content-Language: en-US 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: 'Rainer M Krug' , 'Charles Berry' Cc: "'emacs-orgmode@gnu.org'" Hi, Hmm, I spoke too soon.... the problem is only partially fixed by this patch= ... Trying to work with in org-mode with R code blocks attached to persistent s= essions (i.e. adding ':session myRsession' to the code block header ) makes= things start to break again, at least in my hands. I'm going to wait till things settle down before trying to upgrade ESS agai= n. Thanks for the patch anyway. Cheers, Malcolm >-----Original Message----- >From: Cook, Malcolm >Sent: Wednesday, September 17, 2014 6:14 PM >To: 'Rainer M Krug'; 'Charles Berry' >Cc: 'emacs-orgmode@gnu.org' >Subject: RE: [O] [PATCH] WAS Re: Bug: problem w/ R code blocks [8.3beta (= release_8.3beta-362-ga92789 >/usr/local/share/emacs/site-lisp/org/)] > >Hiya, > >Likewise - same problem here is fixed with injection of patch. > >Thanks! > >~ malcolm_cook > > > >-----Original Message----- > >From: emacs-orgmode-bounces+mec=3Dstowers.org@gnu.org [mailto:emacs-org= mode-bounces+mec=3Dstowers.org@gnu.org] On > >Behalf Of Rainer M Krug > >Sent: Wednesday, September 17, 2014 2:26 AM > >To: Charles Berry > >Cc: emacs-orgmode@gnu.org > >Subject: Re: [O] [PATCH] WAS Re: Bug: problem w/ R code blocks [8.3beta= (release_8.3beta-362-ga92789 > >/usr/local/share/emacs/site-lisp/org/)] > > > >Rainer M Krug writes: > > > >Using it, error is gone. > > > >Rainer > > > >> Charles Berry writes: > >> > >>> Charles Berry ucsd.edu> writes: > >>> > >>>> > >>>> Rainer M Krug krugs.de> writes: > >>>> > >>>> > > >>>> > Thanks - you came before me. I get the same error but managed to = work > >>>> > around. > >>>> > > >>>> > This is likely caused by the upgrade of ess, > >>>> > >>>> Likely. > >>>> > >>>> But it may not be an ESS problem per se. > >>>> > >>>> M-x R starts a process that runs asynchronously. In interactive use= there > >>>> is no issue (barring something in .First() that slows the startup f= or > >>>> a very long time). > >>>> > >>>> But, ... > >>>> > >>>> If the (rename-buffer ...) in org-babel-R-initiate-session > >>>> runs before all the setup that ESS performs in the process buffer i= s > >>>> complete, chaos can result. > >>>> > >>>> Not sure what the best way is to fix this. > >>>> > >>> > >>> OK. Looks like (ess-wait-for-process) fixes this. Here is a patch. > >> > >> Thanks. > >> > >> Haven't tried it yet, but I can't imagine any downside of this > >> patch. Could this be committed? > >> > >> Rainer > >> > >>> > >>> Chuck > >>> =3D=3D > >>> > >>> From 89472012d80ce9ad4c8722f304c0d29327efa1fc Mon Sep 17 00:00:00 20= 01 > >>> From: chasberry > >>> Date: Tue, 16 Sep 2014 19:57:59 -0700 > >>> Subject: [PATCH] lisp/ob-R.el: use `ess-wait-for-process' to assure = clean > >>> session startup > >>> > >>> * lisp/ob-R.el (org-babel-R-initiate-session): Make sure that (R) ha= s > >>> finished before `rename-buffer' is run. > >>> > >>> TINYCHANGE > >>> --- > >>> lisp/ob-R.el | 3 +++ > >>> 1 file changed, 3 insertions(+) > >>> > >>> diff --git a/lisp/ob-R.el b/lisp/ob-R.el > >>> index 41b943c..7575acf 100644 > >>> --- a/lisp/ob-R.el > >>> +++ b/lisp/ob-R.el > >>> @@ -35,6 +35,8 @@ > >>> (declare-function inferior-ess-send-input "ext:ess-inf" ()) > >>> (declare-function ess-make-buffer-current "ext:ess-inf" ()) > >>> (declare-function ess-eval-buffer "ext:ess-inf" (vis)) > >>> +(declare-function ess-wait-for-process "ext:ess-inf" > >>> + (&optional proc sec-prompt wait force-redisplay)) > >>> (declare-function org-number-sequence "org-compat" (from &optional = to inc)) > >>> (declare-function org-remove-if-not "org" (predicate seq)) > >>> (declare-function org-every "org" (pred seq)) > >>> @@ -262,6 +264,7 @@ This function is called by `org-babel-execute-sr= c-block'." > >>> ;; Session buffer exists, but with dead process > >>> (set-buffer session)) > >>> (require 'ess) (R) > >>> + (ess-wait-for-process) > >>> (rename-buffer > >>> (if (bufferp session) > >>> (buffer-name session) > > > >-- > >Rainer M. Krug > >email: Rainerkrugsde > >PGP: 0x0F52F982