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.cl...@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 <j...@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.urba...@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 <j...@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-boun...@r-project.org [mailto:r-sig-mac-bounces@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.wick...@gmail.com> >> >> Reply: Hadley Wickham <h.wick...@gmail.com>> >> >> Date: October 21, 2014 at 10:12:13 AM >> >> To: David Winsemius <dwinsem...@comcast.net>> >> >> Cc: r-sig-mac <r-sig-mac@r-project.org>>, Spencer Mass >> >> <ma...@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@r-project.org >> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> >> >> >> [[alternative HTML version deleted]] >> >> >> >> _______________________________________________ >> >> R-SIG-Mac mailing list >> >> R-SIG-Mac@r-project.org >> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> > > > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac