inherit $PATH in R.app ?

[Timothy Bates]

got an error running

> devtools::check("~/bin/umx")

...

* installing the package to build vignettes

* creating vignettes ... ERROR

Error: processing vignette 'umx.Rmd' failed with diagnostics:

pandoc version 1.12.3 or higher is required and was not found.

Execution halted

I have pandoc in my $PATH but R.app seems not to inherit the bash .profile settings

how does get R to inherit the value of $PATH or at least get check working?

# R.app

system("echo $PATH")

/usr/bin:/bin:/usr/sbin:/sbin

by contrast in terminal

echo $PATH

/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/texbin:/usr/local/bin:/Users/tim/bin/:/Users/tim/bin/get_iplayer:/usr/local/bin:/opt/local/bin:/opt/local/sbin

[Winston Chang]

Are you running on OSX 10.10 preview? There was a change in behavior in the inheritance of PATH in this version of OS X.

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[Timothy Bates]

Yes 10.10 Public Beta 5

R version: R version 3.1.1 (2014-07-10)

[Hadley Wickham]

Try the dev version of rmarkdown which has a fix:
https://github.com/rstudio/rmarkdown/commit/49ec20f9491c6099d9a1447f50e2a42336e12ec7

On Thu, Oct 9, 2014 at 10:08 AM, Timothy Bates

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