[R-SIG-Mac] Yosemite and R

Tue Oct 28 05:21:07 CET 2014

http://xquartz.macosforge.org/ ?

John Maindonald             email: john.maindonald at anu.edu.au
phone : +61 2 (6125)3473    fax  : +61 2(6125)5549
Centre for Mathematics & Its Applications, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National University, Canberra ACT 0200.


On 28 Oct 2014, at 15:03, Richard M. Heiberger <rmh at temple.edu> wrote:

> I just did a workshop for new R users.  the only serious installation problem I
> saw was Macintosh users and tctlk.  From this discussion, I knew to tell both
> people they needed to download quartz.macosforge.org
> and indeed that solved it.
> 
> Is there a place on the package DESCRIPTION file to state that dependency,
> thus triggering the download and installation of quartz?  That would
> take the responsibility for discovering this need away from the end user?
> 
> Rich
> 
> 
> On Thu, Oct 23, 2014 at 2:15 PM, John Fox <jfox at mcmaster.ca> wrote:
>> 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]]
>>>>> 
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>> 
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