[ESS] Upgraded to El Capitan (OS X 10.11) and ESS Cannot Find R

[Marc Schwartz]

Rich,

You might consider waiting for a point release update with any bug fixes then, if you are not otherwise in a rush.

I have not really seen anything terrible yet though.

The major operational change I think, other than some aesthetics, is SIP:

   https://en.wikipedia.org/wiki/System_Integrity_Protection

and some apps still need to be updated for it. Many (e.g. MacTeX) were updated during the beta previews over the summer.

Regards,

Marc


> On Oct 1, 2015, at 5:03 PM, Richard M. Heiberger <rmh using temple.edu> wrote:
> 
> I skipped Yosemite entirely.  Is it wise to take El Capitan now, or should I wait a bit longer.  I don't mind bleeding edge on R, but
> I am not interested for the operating system.
> 
> Rich
> 
> On Thu, Oct 1, 2015 at 5:57 PM, Marc Schwartz <marc_schwartz using me.com <mailto:marc_schwartz using me.com>> wrote:
> Hi all,
> 
> Apologies for the delay in my follow up, I got pulled into a meeting.
> 
> The addition of exec-path-from-shell to my .emacs has resolved the problem.
> 
> Vincent, what are the modifications in your distribution to the above?
> 
> Stephen, to your first reply, using 'open -a Emacs' worked to run Emacs.app from within the OS X Terminal.
> 
> R did run in that setting, much as it did when I ran a shell in Emacs and started R from there.
> 
> So there was some nuance in how Emacs was picking up the $PATH. This new addition of exec-path-from-shell will hopefully be more robust moving forward.
> 
> Unlike Vincent's experience, reinstalling R did not seem to reset things, despite doing a clean re-install. So some difference there.
> 
> Thanks to both of your for your rapid assist on this.
> 
> Regards,
> 
> Marc
> 
> 
> > On Oct 1, 2015, at 4:07 PM, Vincent Goulet <vincent.goulet using me.com <mailto:vincent.goulet using me.com>> wrote:
> >
> > Hi Stephen,
> >
> > Great minds think alike! ;-)
> >
> > ;;; import-env-from-shell.el --- Make Emacs use the environment set up by the user's shell
> >
> > ;; Copyright (C) 2013-2014 Vincent Goulet
> >
> > ;; Author: Vincent Goulet
> >
> > ;; This file is a modified version of exec-path-from-shell.el by
> > ;; Steve Purcell <steve using sanityinc.com <mailto:steve using sanityinc.com>>
> > ;; URL: https://github.com/purcell/exec-path-from-shell <https://github.com/purcell/exec-path-from-shell>
> >
> >
> >> Le 1 oct. 2015 à 16:41, Stephen Eglen <S.J.Eglen using damtp.cam.ac.uk <mailto:S.J.Eglen using damtp.cam.ac.uk>> a écrit :
> >>
> >> hi Vincent/Marc,
> >>
> >> Is it worth adding this to the Emacs.app that Vincent kindly bundles?
> >>
> >> https://github.com/purcell/exec-path-from-shell <https://github.com/purcell/exec-path-from-shell>
> >>
> >> (apologies if you already have this).
> >>
> >> Stephen
> >>
> >> On Thu, Oct 01 2015, Vincent Goulet wrote:
> >>
> >>>> Le 1 oct. 2015 à 15:54, Marc Schwartz <marc_schwartz using me.com <mailto:marc_schwartz using me.com>> a écrit :
> >>>>
> >>>> Hi all,
> >>>>
> >>>> Using ess-15.09 with Emacs 24.5, which worked fine on OS X Yosemite until yesterday.
> >>>>
> >>>> I know that this has been reported on prior versions of OS X and have attempted the proposed solutions, but I am at a loss to figure this one out at the moment.
> >>>>
> >>>> I upgraded to the new El Capitan yesterday and now ESS cannot find R. I get the familiar:
> >>>>
> >>>> no such file or directory, R
> >>>>
> >>>> when using M-x R.
> >>>
> >>> Same here.
> >>>
> >>>> I did a re-install of R as well, along with XQuartz.
> >>>
> >>> Reinstalling R 3.2.2 fixed the issue for me. I guess this reinstated the symlink in /usr/local/bin.
> >>>
> >>>> R.app (the standard OS X GUI) finds R without issue and I can run R from the OS X shell (Terminal).
> >>>>
> >>>> When I use:
> >>>>
> >>>> M-x shell
> >>>>
> >>>> in Emacs, I can then run R without issue within the shell. So the $PATH seems to be picked up correctly in those settings to /usr/local/bin/R.
> >>>>
> >>>> I do have the location added to $PATH in my ~/.bash_profile and I have a line in my .emacs:
> >>>>
> >>>> (setenv "PATH" "/usr/texbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin")
> >>>>
> >>>> so the path is set there as as well, so that Emacs will pick up $PATH when run from the dock, which I know has been an issue.
> >>>
> >>> Did you check the Emacs variable exec-path? I think this one is the key. My distribution has a patch to correctly import the shell environment at Emacs startup. For example, I have:
> >>>
> >>> exec-path is a variable defined in `C source code'.
> >>> Its value is
> >>> ("/opt/local/bin/" "/opt/local/sbin/" "~/bin/" "/usr/local/bin/" "/usr/bin/" "/bin/" "/usr/sbin/" "/sbin/" "/opt/X11/bin/" "/Library/TeX/texbin/" "/Applications/Emacs.app/Contents/MacOS/bin-x86_64-10_9/" "/Applications/Emacs.app/Contents/MacOS/libexec-x86_64-10_9/" "/Applications/Emacs.app/Contents/MacOS/libexec/")
> >>>
> >>> Hope this helps!
> >>>
> >>> v.
> >>>
> >>>> Anyone else upgrade yet and/or have recommendations based upon fresh eyes?
> >>>>
> >>>> Thanks!
> >>>>
> >>>> Marc Schwartz
> 
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