[kepler-users] Installing Kepler on Lion: finding R

[Karin Nadrowski Leipzig]

Adding new paths to the environment.plist solves the problems below. My file now looks like this:

{
        PATH = "$PATH:/usr/local/Cellar/r/2.14.0/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin";
}

It seems to me, that the beginning ($PATH) is not understood by the execution of environment.plist, so that I had to copy from the terminal what is given with 
> echo $PATH 
and then copy paste it to the environment.plist

Cheers, Karin.


On Feb 6, 2012, at 14:18 PM, Karin Nadrowski Leipzig wrote:

> 
> Unfortunately manipulating the environment.plist screws up a whole lot other applications, including my Aquamacs - R functioning (X11 does not start, the help does not start), and the Word Plugin of Mendeley (it does not execute). 
> 
> There is a web page saying that environment.plist does not work with applications launched from spotlight, this applies to all applications launched from the application folder also, I guess. 
> 
> http://www.digitaledgesw.com/node/31
> 
> So the solution given so far does not work for me. As soon as I rename the environment.plist file, the other software are functioning fine again.
> 
> Best, Karin.
> 
> 
> On Jan 26, 2012, at 10:08 AM, Karin Nadrowski wrote:
> 
>> Dear Jing,
>> 
>> thanks, it's running now.
>> 
>> I used the following commands, as I'm not so fluent with vim:
>> $>mkdir .MacOSX
>> $>touch .MacOSX/environment.plist
>> $>pico .MacOSX/environment.plist
>> 
>> Not sure, where to send the mail so that it reaches the archive for others
>> to read.
>> 
>> Best, Karin.
>> 
>> 
>> -----Ursprüngliche Nachricht-----
>> Von: tao [mailto:tao at nceas.ucsb.edu]
>> Gesendet: Thursday, January 26, 2012 2:09 AM
>> An: barseghian at nceas.ucsb.edu
>> Cc: Karin Nadrowski Leipzig; kepler-users at kepler-project.org
>> Betreff: Re: [kepler-users] Installing Kepler on Lion: finding R
>> 
>> Hi, Karin:
>> 
>> How did you add the path of the R to the PATH variable? By modifying the
>> .bash_profile? If you had done this way, it would not work.
>> 
>> Since OS X windows applications receive environment variables from the
>> your environment.plist file, you have to set the R path to PATH in
>> ~/.MacOSX/environment.plist file in order to let Kepler know the R.
>> 
>> If you don't have the ~/.MacOSX/environment.plist  file, you may open a
>> terminal and type:
>> $>mkdir .MacOSX
>> $>touch .MacOSX/environment.plist
>> $>vim .MacOSX/environment.plist
>> Paste the following lines to the file:
>> 
>> {
>>        PATH = "$PATH:your_R_bin_dir";
>> }
>> 
>> If you already have ~/.MacOSX/environment.plist, you may type:
>> $>open .MacOSX/environment.plist
>> In the editor interface, set variable(key) PATH with the value of
>> $PATH:your_R_bin_dir.
>> 
>> Note: please replace your_R_bin_dir by the real value.
>> 
>> More information about editing environment.plist, please see:
>> http://developer.apple.com/qa/qa2001/qa1067.html
>> 
>> After saving the file, you must restart your computer. Then it should
>> work.
>> 
>> Thanks,
>> 
>> Jing
>> 
>> barseghian at nceas.ucsb.edu wrote:
>>> I'm seeing this too.
>>> We'll try to look into it and get a fix out soon.
>>> Thanks for reporting it,
>>> Derik
>>> 
>>> 
>>> On Tue, 24 Jan 2012 22:16:24 +0100, Karin Nadrowski Leipzig
>>> <nadrowski at uni-leipzig.de> wrote:
>>> 
>>>> Hello,
>>>> 
>>>> has anyone experienced problems with installing Kepler on Lion? I have
>>>> installed Keppler 2.3 and 2.2. Added the path to R to the PATH
>> variable.
>>>> 
>>> R
>>> 
>>>> is running from the terminal. I'm using R regularly on the computer.
>> But
>>>> Kepler cannot find it.
>>>> 
>>>> Thanks, Karin.
>>>> _______________________________________________
>>>> Kepler-users mailing list
>>>> Kepler-users at kepler-project.org
>>>> http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>>>> 
>>> _______________________________________________
>>> Kepler-users mailing list
>>> Kepler-users at kepler-project.org
>>> http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>>> 
>> 
> 
> -----------------------------
> Dr. Karin Nadrowski
> -----------------------------
> Institut Biologie I - Special Botany and Functional Biodiversity; University of  Leipzig; Johannisallee 21-23; 04103 Leipzig;  Room 130; phone (0049) 341 - 97-38576; fax (0049) 341 - 97-38549; mobile (0049) 163 8640108; nadrowski at uni-leipzig.de; http://alfresco.uni-leipzig.de/spezbot/~nadrowski
> 
> 
> 
> 
> 

-----------------------------
Dr. Karin Nadrowski
-----------------------------
Institut Biologie I - Special Botany and Functional Biodiversity; University of  Leipzig; Johannisallee 21-23; 04103 Leipzig;  Room 130; phone (0049) 341 - 97-38576; fax (0049) 341 - 97-38549; mobile (0049) 163 8640108; nadrowski at uni-leipzig.de; http://alfresco.uni-leipzig.de/spezbot/~nadrowski





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