[R-SIG-Mac] Yosemite and R

Tue Oct 28 15:14:12 CET 2014

Dear all,

Brian Ripley has brought it my attention that R 3.1.2, due to be released soon, *does* check that X11 is present and prints an informative error message if it isn't. That's a substantial improvement.

Thanks,
 John

On Tue, 28 Oct 2014 09:43:53 -0400
 "John Fox" <jfox at mcmaster.ca> wrote:
> Dear Rich,
> 
> I've made a similar suggestions before, I believe. It would even help to have tcltk fail less cryptically if X-Windows is unavailable under Mac OS X, suggesting that XQuartz be installed and pointing to the XQuartz website. And it shouldn't be hard to check capabilities()["X11"] when tcltk loads. 
> 
> The large majority of Rcmdr problems about which people write me concern this one issue. There are clear, detailed installation instructions on the Rcmdr website but no way for me to insure that people are aware of them. I spent some time trying to find a way to report the absence of X-Windows at Rcmdr start-up, but the dependency on tcltk causes the Rcmdr to fail to load before an informative message can be printed -- a chicken-and-egg problem. Maybe there's a way to do this that I didn't discover.
> 
> The essential problem here is that naive users don't have an obvious way of avoiding the problem. They install the software and expect it to work. There are similar issues with the system path under Yosemite and with app nap. This leads to repetitious emails to package maintainers and to repetitive questions on the various help lists, etc.
> 
> That said, I think that there is a good solution for teachers of courses, workshops, etc.: Create -- or point to existing -- clear installation instructions that include installing XQuartz under OS X. The less tractable problem is individual users downloading and installing R from CRAN.
> 
> Best,
>  John
> 
> On Tue, 28 Oct 2014 00:03:52 -0400
>  "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