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

[Simon Urbanek]

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.

Cheers,
Simon



> This shows clearly that the imagemagick path is listed  (and so isn't the
> same as the problem in this previous discussion:
> http://r.789695.n4.nabble.com/convert-command-not-found-in-movie3d-rgl-package-in-Mac-OS-X-td4320734.html
> )
> 
> Also, in Terminal,
> 
> echo $PATH
> 
> /usr/local/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/local/git/bin:
> */opt/ImageMagick/bin*:/usr/texbin
> 
> The only way I have been able to get it to work is:
> 
> system("/opt/ImageMagick/bin/convert --version")
> 
> [1] "Version: ImageMagick 6.8.9-8 Q16 x86_64 2014-10-08
> http://www.imagemagick.org"
> 
> [2] "Copyright: Copyright (C) 1999-2014 ImageMagick Studio LLC"
> 
> 
> [3] "Features: DPC OpenCL"
> 
> 
> [4] "Delegates: bzlib fftw jng jpeg lcms lzma png tiff webp xml zlib"
> 
> 
> [5] ""
> 
> 
> However, this workaround does not work for me using movie3d{rgl}
> 
> Any ideas most appreciated
> 
> 
> Emma
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> Emma Sherratt, PhD.
> 
> Lecturer in Zoology,
> Zoology Division, School of Environmental and Rural Science,
> Room L118 Bldg C02,
> University of New England,
> Armidale, NSW, Australia, 2351
> Tel: +61 2 6773 5038
> email: emma.sherratt at une.edu.au
> 
> Caecilians are legless amphibians...
> 
> *                      __
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> 
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