JJ, this is unrelated - this is about apps started via LS not using shell profiles. (The issue you refer to has been fixed long time ago on our end).
Cheers, Simon > On Mar 17, 2015, at 6:21 AM, JJ Allaire <[email protected]> wrote: > > Sounds like this may be targeted at fixing the OS X Yosemite bug > wherein some environment variables for GUI applications are > duplicated: > > http://tex.stackexchange.com/questions/208181/why-did-my-tex-related-gui-program-stop-working-in-mac-os-x-yosemite > > Until Apple fixes this issue I think that GUI applications need to > clean the duplicated environment variables received at launch time. > Here's what we do in RStudio: > > https://github.com/rstudio/rstudio/commit/09c9be12 > > > > > On Mon, Mar 16, 2015 at 9:12 PM, John Fox <[email protected]> wrote: >> Dear Simon, >> >>> -----Original Message----- >>> From: Simon Urbanek [mailto:[email protected]] >>> Sent: March-16-15 3:57 PM >>> To: [email protected] >>> Cc: Berend Hasselman; [email protected] >>> Subject: Re: [R-SIG-Mac] checking for pdflatex >>> >>> >>>> On Mar 16, 2015, at 3:43 PM, John Fox <[email protected]> wrote: >>>> >>>> Dear all, >>>> >>>> I've now implemented Simon's solution, setting the path in the .onLoad() >>> function of the Rcmdr package and resetting it to its pre-existing value in >>> .onUnload(). This seems to work fine for me and, I hope, will be a more >>> robust solution. >>>> >>> >>> I don't think messing with PATH of the R process is a good idea - as a user >>> I'd >>> be somewhat unpleasantly surprised if you changed the PATH of my running >>> session. I'm not quite sure what's your intention, but I would suggest using >>> the setting to locate the binary to run it explicitly - that is what R does >>> normally. If you rely on some scripts that you don't control, then I would >>> suggest setting it in the shell that you start the script with, but not in >>> the R >>> process itself. >> >> That occurred to me, but the problem arises when a function in the rmarkdown >> package calls pandoc and pandoc fails to run pdflatex. I don't think that I >> have control over this. >> >> I'm cc'ing J. J. Alaire, the maintainer of the rmarkdown package in case he >> sees a solution in that package. The problem doesn't of course occur when >> rmarkdown is run from RStudio (or a terminal) but only from R.app, as I >> explained initially. (J.J.: Please let me know if this is unclear, and I >> can send you the rest of this thread.) >> >> OTOH, I doubt whether Rcmdr users will care that the package alters the PATH >> of the R process (though it would be better to avoid that). >> >> Best, >> John >> >>> >>> Cheers, >>> Simon >>> >>> >>> >>>> Thanks again to everyone for their help. >>>> >>>> John >>>> >>>>> -----Original Message----- >>>>> From: R-SIG-Mac [mailto:[email protected]] On Behalf Of >>>>> John Fox >>>>> Sent: March-16-15 2:45 PM >>>>> To: 'Berend Hasselman' >>>>> Cc: [email protected] >>>>> Subject: Re: [R-SIG-Mac] checking for pdflatex >>>>> >>>>> Dear Berend and Simon, >>>>> >>>>> I've now tried Berend's solution and it appears to work fine: If >>>>> necessary, I add /usr/texbin to the path when the Rcmdr GUI starts up >>>>> and restore the path to its previous state when it closes. >>>>> >>>>> I agree that Simon's solution will be more flexible since it should >>>>> work if pdflatex is located elsewhere (as long as it's on the path >>>>> reported by path_helper), and I'll give that a try as well. >>>>> >>>>> Thanks again for all the help, >>>>> John >>>>> >>>>>> -----Original Message----- >>>>>> From: Berend Hasselman [mailto:[email protected]] >>>>>> Sent: March-16-15 2:34 PM >>>>>> To: [email protected] >>>>>> Cc: Simon Urbanek; [email protected] >>>>>> Subject: Re: [R-SIG-Mac] checking for pdflatex >>>>>> >>>>>> John, >>>>>> >>>>>>> On 16-03-2015, at 18:53, John Fox <[email protected]> wrote: >>>>>>> >>>>>>> Dear Berend, >>>>>>> …. >>>>>>>> >>>>>>>> For what it’s worth: I have the following code in the .First >>>>>>>> function in >>>>>>>> ~/.Rprofile: >>>>>>>> (R 3.1.3 on OS X Yosemite) >>>>>>>> >>>>>>>> if( .Platform$GUI == "AQUA" ) { >>>>>>>> # this appends /usr/local/bin to what is already in PATH >>>>>>>> # by default this is already in PATH (at least in 10.6.8) >>>>>>>> # so remove any duplicated items >>>>>>>> z <- Sys.getenv("PATH") >>>>>>>> z <- unlist(strsplit(z,.Platform$path.sep,fixed=TRUE)) >>>>>>>> # add path to MacTeX executables for OS X Yosemite (which >>>>>>>> has a >>>>>> bug) >>>>>>>> # in Terminal it is added automatically >>>>>>>> z[length(z)+1] <- "/usr/texbin" >>>>>>>> >>>>>> Sys.setenv(PATH=paste(z[!duplicated(z)],collapse=.Platform$path.sep) >>>>>> ) >>>>>>>> } >>>>>>> >>>>>>> This should work fine if pdflatex is in /usr/texbin, which I now >>>>>>> understand is >>>>>> by far the most common case (and is the case on my Mac). >>>>>>> >>>>>>> Do you mind if I adapt your code for the Rcmdr? I can fix the path >>>>>>> in this >>>>>> manner at startup of the Rcmdr GUI and restore it to its initial >>>>>> value on exit from the GUI. >>>>>>> >>>>>> >>>>>> Go right ahead. Don’t forget it assumes MacTeX. >>>>>> >>>>>> But do also have a look Simon’s suggestion of using path_helper, >>>>>> which seems more flexible than my solution: >>>>>> >>>>>> I tried this in R-GUI >>>>>> >>>>>> system2("/usr/libexec/path_helper","-s", stdout=TRUE) >>>>>> >>>>>> and got this answer >>>>>> >>>>>> [1] >>>>>> "PATH=\"/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/u >>>>>> sr >>>>>> /texbi >>>>>> n\"; export PATH;” >>>>>> >>>>>> which will have to be fiddled with to get something that is usable. >>>>>> >>>>>> Berend >>>>>> >>>>>> >>>>>>> Thanks for this, >>>>>>> John >>>>>>> >>>>>>>> >>>>>>>> Berend >>>>>>> >>>>>>> >>>>>>> --- >>>>>>> This email has been checked for viruses by Avast antivirus software. >>>>>>> http://www.avast.com >>>>>>> >>>>> >>>>> >>>>> --- >>>>> This email has been checked for viruses by Avast antivirus software. >>>>> >>>>> _______________________________________________ >>>>> R-SIG-Mac mailing list >>>>> [email protected] >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>> >>>> >>>> --- >>>> This email has been checked for viruses by Avast antivirus software. >>>> http://www.avast.com >>>> >> >> >> --- >> This email has been checked for viruses by Avast antivirus software. >> http://www.avast.com >> > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
