R help - Jan 2012 - convert command not found in movie3d (rgl package) in Mac OS X

Dear list,

I gave up trying to fix my movie3d (rgl library) issue in my PC
(completely black gif/png file) and went ahead and installed MacPorts
and ImageMagick onto my iMac (OSX ver 10.6.8). I think ImageMagick is
successfully installed in its default location (under /opt/local), and
I ran movie3d but I get the following error:

Error in system("convert --version", intern = TRUE) :
? error in running command
sh: convert: command not found

so I'm guessing R can't find the "convert" executable file,
which is
in "/opt/local/bin", in its system search path, which I presume is
"/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin" that I got using
Sys.getenv("PATH").

Does anyone know how I can resolve this? For instance, should I move
or copy the convert executable file to an appropriate directory (which
I don't really know where exactly, i.e. I can't find a folder
"usr" in
the Macintosh HD), or can I add "/opt/local/bin" to the R's search
path?

best regards,
Manabu

-- 
Manabu Sakamoto, PhD
School of Earth Sciences
University of Bristol
manabu.sakamoto at gmail.com

On 12-01-23 8:50 AM, Manabu Sakamoto wrote:
> Dear list,
>
> I gave up trying to fix my movie3d (rgl library) issue in my PC
> (completely black gif/png file) and went ahead and installed MacPorts
> and ImageMagick onto my iMac (OSX ver 10.6.8). I think ImageMagick is
> successfully installed in its default location (under /opt/local), and
> I ran movie3d but I get the following error:
>
> Error in system("convert --version", intern = TRUE) :
>    error in running command
> sh: convert: command not found
>
> so I'm guessing R can't find the "convert" executable
file, which is
> in "/opt/local/bin", in its system search path, which I presume
is
> "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin" that I got using
> Sys.getenv("PATH").
>
> Does anyone know how I can resolve this? For instance, should I move
> or copy the convert executable file to an appropriate directory (which
> I don't really know where exactly, i.e. I can't find a folder
"usr" in
> the Macintosh HD), or can I add "/opt/local/bin" to the R's
search
> path?
I think the latter is easiest.  Just use Sys.setenv to set it, e.g.

Sys.setenv(PATH=paste("/opt/local/bin", Sys.getenv("PATH"),
sep=":")

The setting will only last for the duration of your R session.

Duncan Murdoch

On Jan 23, 2012, at 5:50 AM, Manabu Sakamoto wrote:
> Dear list,
> 
> I gave up trying to fix my movie3d (rgl library) issue in my PC
> (completely black gif/png file) and went ahead and installed MacPorts
> and ImageMagick onto my iMac (OSX ver 10.6.8). I think ImageMagick is
> successfully installed in its default location (under /opt/local),
I'm not sure it has a default location, but if you are using a package
management system, then there might be a default location for all the packages
installed in that manner.
> and
> I ran movie3d but I get the following error:
> 
> Error in system("convert --version", intern = TRUE) :
>   error in running command
> sh: convert: command not found
> 
> so I'm guessing R can't find the "convert" executable
file, which is
> in "Sys.getenv("PATH")", in its system search path,
which I presume is
> "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin" that I got using
> Sys.getenv("PATH").
> 
> Does anyone know how I can resolve this? For instance, should I move
> or copy the convert executable file to an appropriate directory (which
> I don't really know where exactly, i.e. I can't find a folder
"usr" in
> the Macintosh HD),

The /usr/ directory is hidden and not displayed by the default settings of the
Finder.app, but you should be able to change those settings if you da a Google
search and use Terminal.app to start up a bash shell   or you can use
Terminal.app and type these two lines:

cd /
ls
> 
> or can I add "/opt/local/bin" to the R's search
> path?
I'm not sure whether executing:

 Sys.setenv("PATH") <- paste(Sys.getenv("PATH"),
":/opt/local")

... will necessarily cause success with a system()-mediated call, since my
fragile understanding is that the system()-calls use the bash shell which has a
different PATH variable than does R called from R.app which is what I suspect
you are using.

This is probably better addressed to the R-SIG-Mac mailing list and you will
need to subscribe:

r-sig-mac R <r-sig-mac at r-project.org>


> best regards,
> Manabu
> 
> -- 
> Manabu Sakamoto, PhD
> School of Earth Sciences
> University of Bristol
> manabu.sakamoto at gmail.com
> 
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David Winsemius
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