[R-SIG-Mac] sh: convert: command not found

[peter dalgaard]

On 24 Oct 2014, at 12:55 , Duncan Murdoch <murdoch.duncan at gmail.com> wrote:

> On 24/10/2014, 1:37 AM, Simon Urbanek wrote:
>> 
>> On Oct 24, 2014, at 12:22 AM, Emma Sherratt <emma.sherratt at gmail.com> wrote:
>> 
>>> Dear Mac R community,
>>> 
>>> I wonder if anyone else has come across this issue. After installing the
>>> new Mac OS10.10 Yosemite, I am now having a strange problem.
>>> 
>>> I'm trying to use movie3d and run similar functions based on this I have
>>> written myself.
>>> 
>>> Specifically, when I run
>>> 
>>>> system("convert --version")
>>> sh: convert: command not found
>>> 
>>> yet, it is not a path issue.
>>>> Sys.getenv("PATH")
>>> [1]
>>> "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/git/bin:
>>> */opt/ImageMagick/bin*:/usr/texbin"
>>> 
>> 
>> It is, because Yosemite ignores PATH for processes started from a GUI application. You will see if you run
>> system("echo $PATH")
>> 
>> You have to use full paths in Yosemite for anything that is not on the "sanctioned" PATH -- or use R from the shell.
> 
> What is the best way to find the full path to a command there, since
> Sys.which() sees the same PATH as system() does?
> 
> Alternatively, how do you modify the PATH that system() sees?
> 
> Duncan Murdoch
> 
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Disclaimer: I'm at the office computer right now, still on Mavericks.

In my limited experimentation, I found that you can pass the PATH explicitly as in 

path <- Sys.getenv("PATH")
cmd <- paste("PATH=", path, "; which pdflatex")
system(cmd)

I don't recall needing to export PATH, and there could be complications with the shell flavour (sh, ash, bash, zsh, ...). Also, I think it wants to be two commands with the intervening semicolon, but it might work without it. Anyways, give it a try.

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com