[R-SIG-Mac] Help rJava and imaplib.

[Simon Urbanek]

On Aug 17, 2011, at 8:15 AM, Bhima Pandava wrote:

> I am trying to teach myself a little R and recently I found an entry 
> over at R-Bloggers & Expansed, on how to create social graphs from your 
> email 
> <http://expansed.com/2011/08/sna-visualising-an-email-box-with-r/>, that 
> interested me.
> 
> I am using Mac OS Lion, so I installed the R-2.13.1pkg and the R.app 
> R-2.13-patched.  The script requires the Network, rJython, and rJava 
> libraries, so I installed these as binaries.  Mac OS Lion does not come 
> with a Java Development Kit installed,


It does (it will be installed the first time you try to use it). You may want to give it a shot - using MacPorts may be your problem.

Cheers,
Simon


> so I installed one from Mac Ports 
> and then I also tried building it from source based on the 
> instructions.  I then registered the JDK with R using "sudo R CMD 
> javareconf".  The script fails when executed with the following error:
> 
> Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,  :
>   Traceback (most recent call last):
>   File "<string>", line 1, in <module>
>   File 
> "/Library/Frameworks/R.framework/Versions/2.13/Resources/library/rJython/jython.jar/Lib/imaplib.py", 
> line 437, in fetch
>   File 
> "/Library/Frameworks/R.framework/Versions/2.13/Resources/library/rJython/jython.jar/Lib/imaplib.py", 
> line 1055, in _simple_command
>   File 
> "/Library/Frameworks/R.framework/Versions/2.13/Resources/library/rJython/jython.jar/Lib/imaplib.py", 
> line 892, in _command_complete
> imaplib.error: FETCH command error: BAD ['Could not parse command']
> 
> I have tried many, many different things but I simply can not work out 
> how to make this work.  As other people sound like they have run this, 
> it is a mystery to me.  One of the things I have tried was trying the 
> same thing in a virtual instance of Linux running on my Mac and that 
> segfaults.  Another is installing the rJava library as source, so that 
> it would be compiled on my machine.  This fails due to R expecting a 
> different framework version.  The error returned is:
> 
> checking whether JNI programs can be compiled... configure: error: 
> Cannot compile a simple JNI program. See config.log for details.
> 
> and checking the log I find:
> 
> Dyld Error Message:
>   Library not loaded: 
> /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib
>   Referenced from: /Applications/R.app/Contents/MacOS/R
>   Reason: image not found
> 
> I am using Framework version 2.13, so I do not even have a directory for 
> version 2.12.  The file "libR.dylib" is in the right place for 2.13 but 
> I do not know how to configure R.app to use a particular version of the 
> Framework.  Or even if this is actually the root of the problem above.
> 
> If anyone has any suggestions I would appreciate it... or even if 
> someone could try the script Expansed published and see if it works for 
> them, I would appreciate that as well.
> 
> Thanks!
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
>