[R-SIG-Mac] checking for pdflatex

Tue Mar 17 15:41:54 CET 2015

Dear Simon,

Sorry to prolong this, but I have two additional questions:

(1) Is there a reason that R.app uses a different default PATH than R in a terminal window does? That is, why not make them the same? I suspect that there's a consideration that I'm not aware of.

(2) Would it still be objectionable if I reverted to the previous solution of having the Rcmdr package add "/usr/texbin" to the current PATH if it's not already present rather than replacing the PATH? Though that wouldn't be as bullet-proof, it would cover the large majority of cases,  and wouldn't potentially surprise a user by removing a directory from the PATH.

Thanks,
 John

> -----Original Message-----
> From: Simon Urbanek [mailto:simon.urbanek at r-project.org]
> Sent: March-17-15 10:34 AM
> To: JJ Allaire
> Cc: jfox at mcmaster.ca; Berend Hasselman; r-sig-mac at r-project.org
> Subject: Re: [R-SIG-Mac] checking for pdflatex
> 
> 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 <jj at rstudio.com> 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-
> g
> > ui-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 <jfox at mcmaster.ca> wrote:
> >> Dear Simon,
> >>
> >>> -----Original Message-----
> >>> From: Simon Urbanek [mailto:simon.urbanek at r-project.org]
> >>> Sent: March-16-15 3:57 PM
> >>> To: jfox at mcmaster.ca
> >>> Cc: Berend Hasselman; r-sig-mac at r-project.org
> >>> Subject: Re: [R-SIG-Mac] checking for pdflatex
> >>>
> >>>
> >>>> On Mar 16, 2015, at 3:43 PM, John Fox <jfox at mcmaster.ca> 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:r-sig-mac-bounces at r-project.org] On Behalf
> >>>>> Of John Fox
> >>>>> Sent: March-16-15 2:45 PM
> >>>>> To: 'Berend Hasselman'
> >>>>> Cc: r-sig-mac at r-project.org
> >>>>> 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:bhh at xs4all.nl]
> >>>>>> Sent: March-16-15 2:34 PM
> >>>>>> To: jfox at mcmaster.ca
> >>>>>> Cc: Simon Urbanek; r-sig-mac at r-project.org
> >>>>>> Subject: Re: [R-SIG-Mac] checking for pdflatex
> >>>>>>
> >>>>>> John,
> >>>>>>
> >>>>>>> On 16-03-2015, at 18:53, John Fox <jfox at mcmaster.ca> 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.s
> >>>>>> ep)
> >>>>>> )
> >>>>>>>>  }
> >>>>>>>
> >>>>>>> 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
> >>>>>>>
> >>>>>>>
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