[R-SIG-Mac] checking for pdflatex

Simon Urbanek simon.urbanek at r-project.org
Tue Mar 17 15:47:57 CET 2015 

> On Mar 17, 2015, at 10:41 AM, John Fox <jfox at mcmaster.ca> wrote:
> 
> 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.
> 

See the FAQ I was pointing to.


> (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.
> 

I guess that would be less disruptive. If the user has picked a custom order at least it would be preserved. But as noted earlier I also think that this should be better fixed in rmarkdown - preferably by using the full path so it doesn't depend on PATH. I'm told RStudio is providing pandoc binaries so I would guess it's easy for them to guarantee the functionality but JJ is included so he can weigh in.

Cheers,
Simon



> 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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