[R-SIG-Mac] Yosemite and R

[Kevin Ushey]

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/
>> >>
>> >> _______________________________________________
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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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>> >
>
>
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