[R-SIG-Mac] Yosemite and R

John Fox jfox at mcmaster.ca
Thu Oct 23 21:12:31 CEST 2014 

Hi Kevin,

Thank you for this.

As I said, I hadn't gotten around to checking into the problem -- not even looking whether someone else had reported it. I expect that the RStudio folks will address the issue, and it's probably best discussed on their website. 

I don't think that the first solution on StackOverflow is appropriate for checking packages using the RStudio Build tab, since a command like system2("pdflatex", "--help", env=paste0("PATH=", Sys.getenv("PATH"))) (adapting the suggestion on StackOverflow) simply invokes pdflatex from the current session, and doesn't modify the path for the package check. The second solution, opening RStudio from a terminal, does work but is of course awkward.

Best,
 John

> -----Original Message-----
> From: Kevin Ushey [mailto:kevinushey at gmail.com]
> Sent: Thursday, October 23, 2014 2:23 PM
> To: Benjamin Y Clark
> Cc: John Fox; Simon Urbanek; r-sig-mac; Spencer Mass
> Subject: Re: [R-SIG-Mac] Yosemite and R
> 
> Hi John,
> 
> Regarding your issue in RStudio and pdflatex -- this is a general
> problem with any applications not launched from the terminal;
> presumedly it would be seen in R.app as well when not launched from
> the terminal (this is related to the forward-PATH-to-subprocesses
> problem discussed earlier)
> 
> There is a prescription available on StackOverflow:
> http://stackoverflow.com/questions/26491934/running-system-command-
> from-r-console-cannot-locate-installed-programs-since-upg
> 
> Cheers,
> Kevin
> 
> On Thu, Oct 23, 2014 at 11:18 AM, Benjamin Y Clark
> <b.y.clark at csuohio.edu> wrote:
> > 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/
> >> >>
> >> >> _______________________________________________
> >> >> R-SIG-Mac mailing list
> >> >> R-SIG-Mac at r-project.org
> >> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >> >>
> >> >>    [[alternative HTML version deleted]]
> >> >>
> >> >> _______________________________________________
> >> >> R-SIG-Mac mailing list
> >> >> R-SIG-Mac at r-project.org
> >> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >> >
> >
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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