[R-SIG-Mac] Yosemite and R

[Benjamin Y Clark]

Update on my issue: Upon reinstalling Xquartz, as suggested, all of my previous issues went away.
-Ben

--
Benjamin Y. Clark, PhD
Assistant Professor of Public Administration (Levin College) &
Assistant Professor of Public Health (CEOMPH)
Cleveland State University

Executive Committee Member
Association for Budgeting and Financial Management (ABFM)

b.y.clark[at]csuohio.edu
bit.ly/BenClark


________________________________________
From: John Fox <jfox at mcmaster.ca>
Sent: Thursday, October 23, 2014 2:15 PM
To: 'Simon Urbanek'
Cc: 'Amos B. Elberg'; 'r-sig-mac'; 'Spencer Mass'; Benjamin Y Clark; 'peter dalgaard'; 'Marc Schwartz'; 'David Winsemius'; 'Hadley Wickham'
Subject: RE: [R-SIG-Mac] Yosemite and R

Dear Simon,

I installed Yosemite a couple of days ago and everything seems to work fine so far, including the tcltk demo that caused problems for Peter, and the Rcmdr package, which gives Tcl/Tk a pretty good workout. I first reinstalled XQuartz, as suggested, and I also reinstalled R and updated all packages, though the latter two steps probably weren't necessary. I figured that it would help to hear positive experiences as well as problems.

The only issue that I've encountered so far is specific to checking packages under RStudio, which doesn't appear to find pdflatex; OTOH, R CMD check runs fine in a terminal window. I haven't yet tried to resolve this problem.

Best,
 John

> -----Original Message-----
> From: Simon Urbanek [mailto:simon.urbanek at r-project.org]
> Sent: Tuesday, October 21, 2014 4:38 PM
> To: John Fox
> Cc: Amos B. Elberg; r-sig-mac; Spencer Mass; Ben Clark; peter dalgaard;
> Marc Schwartz; David Winsemius; Hadley Wickham
> Subject: Re: [R-SIG-Mac] Yosemite and R
>
> I wasn't able to reproduce but I suspect those are all red herrings -
> there are really no subprocesses involved at all in either case.
>
> On Oct 21, 2014, at 4:19 PM, John Fox <jfox at mcmaster.ca> wrote:
> >
> > Dear all,
> >
> > I wonder whether this issue also accounts for the tcltk problems that
> have been reported. (I haven't yet upgraded to Yosemite myself, hoping
> to wait for the wrinkles to be ironed out, though I'll likely do so
> shortly if only to see what happens.)
> >
> > Best,
> > John
> >
> >> -----Original Message-----
> >> From: r-sig-mac-bounces at r-project.org [mailto:r-sig-mac-bounces at r-
> >> project.org] On Behalf Of Amos B. Elberg
> >> Sent: Tuesday, October 21, 2014 12:40 PM
> >> To: David Winsemius; Hadley Wickham
> >> Cc: r-sig-mac; Spencer Mass
> >> Subject: Re: [R-SIG-Mac] Yosemite and R
> >>
> >> If the full environment isn’t getting passed to R-spawned sub-
> >> processes, that might explain an error I’ve been having since the
> >> update:  when R is launched from the command line, calls that should
> >> create an X11 window in the background fail unless an X11 window has
> >> already been created with the width and height specified:
> >>
> >>> plot(rnorm(100))
> >> Error in .External2(C_X11, d$display, d$width, d$height,
> >> d$pointsize,  :
> >>  invalid 'width' or 'height'
> >>> X11()
> >> Error in .External2(C_X11, d$display, d$width, d$height,
> >> d$pointsize,  :
> >>  invalid 'width' or 'height'
> >>> X11(width = 5, height = 5)
> >>> plot(rnorm(100))
> >> [now it  works - and any number of additional windows can be spawned
> >> without repeating the error]
> >> [quitting R and reopening, without quitting XQuartz, and I get the
> same
> >> error calling plot() before X11(width = , height = )
> >>
> >> This does not happen in RStudio.  I don’t use the R.app gui; I
> opened
> >> it just now to test and I got a slew of path-related errors, but
> >> they’re as likely to have to do with my not-maintained R.app as with
> >> anything else.
> >>
> >> I had not reported this already because I wasn’t confident whether
> its
> >> a yosemite issue, an R-patched issue, or just something odd in the
> way
> >> I built R.
> >>
> >> If incomplete-environment-passing is the new normal, is this not
> going
> >> to be a common issue for packages that spawn sub-processes?
> >>
> >>
> >> From: Hadley Wickham <h.wickham at gmail.com>
> >> Reply: Hadley Wickham <h.wickham at gmail.com>>
> >> Date: October 21, 2014 at 10:12:13 AM
> >> To: David Winsemius <dwinsemius at comcast.net>>
> >> Cc: r-sig-mac <r-sig-mac at r-project.org>>, Spencer Mass
> >> <masss at newpaltz.edu>>
> >> Subject:  Re: [R-SIG-Mac] Yosemite and R
> >>
> >>> No, it is not. It is expected that the path in the terminal be
> >>> different to the path in R, it is _not_ expected that the path in R
> >> be
> >>> different to the path in a subprocess started by R.
> >>>
> >>> (Well it is now expected, because this appears to be a new security
> >>> feature in Yosemite)
> >>
> >> The best thread I could find on the problem is here:
> >> https://code.google.com/p/mactlmgr/issues/detail?id=102
> >>
> >> --
> >> http://had.co.nz/
> >>
> >> _______________________________________________
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> >> R-SIG-Mac at r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>
> >>    [[alternative HTML version deleted]]
> >>
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> >