[R-SIG-Mac] checking for pdflatex

Simon Urbanek simon.urbanek at r-project.org
Tue Mar 17 15:34:03 CET 2015 

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-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 <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.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
>>>>>>> 
>>>>>>> 
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>>>>> 
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