[R-SIG-Mac] Yosemite and R

Tue Oct 28 05:36:32 CET 2014

thank you for catching that typo

Rich

On Tue, Oct 28, 2014 at 12:21 AM, John Maindonald
<john.maindonald at anu.edu.au> wrote:
> 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/
>>>>>>
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>>>>>>
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>>>>>
>>>
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