Re: [R] Incorrect libxml2.2.dylib version on Tiger install

From: Brian Beckage <Brian.Beckage_at_uvm.edu>
Date: Tue 10 May 2005 - 00:51:54 EST

I found the exchange below on the R devel archive and it seems to have solved my problem with R 2.1.0 and Panther...

Brian

>From: stefano iacus <jago_at_mclink.it>
>Date: Thu 08 Jul 2004 - 23:37:39 EST
>
>
>Please remove your copy of libxml2 in /usr/local/lib, you no longer
>need it on Panther and the one included in 10.3.4 is incompatible
>with the one in /usr/local/lib
> stefano
>
> On Jul 7, 2004, at 12:41 PM, theodos@csd.auth.gr wrote:
>
> > Full_Name: Theodosios Theodosiou
>> Version: 1.9.1
>> OS: MAC OS X (10.3.4)
>> Submission from: (NULL) (193.62.199.161)
>>
>>
>> dyld: /usr/bin/open version mismatch for library:
> > /usr/local/lib/libxml2.2.dylib
>> (compatibility version of user: 9.0.0 greater than library's version:
> > 8.0.0)
>>
>> type help.start() to reproduce the problem. Have checked the "Show
> > system error
>> output in R console of the Misc tab at Preferences".
>>

At 10:25 AM -0400 5/9/05, Brian Beckage wrote:
>I encountered a similar problem after installing the new version of
>R (2.1.0) on my Mac OSX 10.3.8--I have not updated to Tiger. The
>error message I get is below. As Steven reported, I do not get this
>error when running R from within the Aqua GUI, but only at the
>command line (which is unfortunately how I use R). Is the solution
>to install the newer version of Xcode (2.0) as suggested in earlier
>emails?
>
>Thanks,
>Brian
>
>
>Error in dyn.load(x, as.logical(local), as.logical(now)) :
> unable to load shared library
>'/Library/Frameworks/R.framework/Resources/library/grDevices/libs/grDevices.so':
> dlcompat: dyld:
>/Library/Frameworks/R.framework/Resources/bin/exec/R version
>mismatch for library: /usr/local/lib/libxml2.2.dylib (compatibility
>version of user: 9.0.0 greater than library's version: 8.0.0)
>Loading required package: grDevices
>Error in dyn.load(x, as.logical(local), as.logical(now)) :
> unable to load shared library
>'/Library/Frameworks/R.framework/Resources/library/grDevices/libs/grDevices.so':
> dlcompat: dyld:
>/Library/Frameworks/R.framework/Resources/bin/exec/R version
>mismatch for library: /usr/local/lib/libxml2.2.dylib (compatibility
>version of user: 9.0.0 greater than library's version: 8.0.0)
>In addition: Warning message:
>package grDevices in options("defaultPackages") was not found
>Error: package 'grDevices' could not be loaded
>
>
>>Sorry to reply to my own post, but I have more info. This probably
>>needs to come to the attention of the Mac R developers.
>>
>>Xcode 2.0 does not have a more recent libxml2.2.dylib.
>>
>>The problem only manifests itself when running R 2.1.0 from the
>>command line, not within the Aqua GUI.
>>
>>Thanks for your patience.
>>
>>On May 7, 2005, at 9:30 AM, Steven Boker wrote:
>>
>>>Hi all,
>>>
>>>I have just installed OSX Server 10.4 and R comes up with the
>>>incompatible libxml library message reported by Dan Kelley a few
>>>messages ago. Xcode 2 does not ship with Tiger Server. I
>>>installed the X-Windows code. I can report that the version of
>>>libxml2.2 that is installed in this case is the version 8.0.0
>>>dylib.
>>>
>>>[6]sboker@munimula:/usr/lib % ls -l libxml2.2*
>>>-rwxr-xr-x 1 root wheel 1061704 Apr 15 23:44 libxml2.2.6.16.dylib*
>>>-rwxr-xr-x 1 root wheel 1061804 May 6 14:15 libxml2.2.dylib*
>>>
>>>I'm working on getting a copy of the Xcode 2 CD. I was surprised
>>>it wasn't in the 10.4 server CD set. I have a production problem
>>>today, though, if anyone can help me with a copy of this library.
>>>
>>>Best,
>>>Steve Boker
>>>
>>>On May 6, 2005, at 12:39 PM, Dan Kelley wrote:
>>>>
>>>> Error in dyn.load(x, as.logical(local), as.logical(now)) :
>>>> unable to load shared library '/Library/Frameworks/
>>>> R.framework/Resources/library/grDevices/libs/grDevices.so':
>>>> dlopen(/Library/Frameworks/R.framework/Resources/library/grDevices/
>>>> libs/grDevices.so, 6): Library not loaded: /usr/lib/libxml2.2.dylib
>>>> Referenced from: /System/Library/Frameworks/AppKit.framework/
>>>> Versions/C/AppKit
>>>> Reason: Incompatible library version: AppKit requires version
>>>> 9.0.0 or later, but libxml2.2.dylib provides version 8.0.0
>>>
>>>---------------------------------------------------------------------
>>> Steven M. Boker 574-339-0735 (cell/page/message)
>>> sboker@nd.edu 574-631-4941 (office)
>>> http://www.nd.edu/~sboker/ 574-631-8883 (fax)
>>> Dept. of Psychology, University of Notre Dame, Notre Dame, IN 46556
>>>
>>>______________________________________________
>>>R-help@stat.math.ethz.ch mailing list
>>>https://stat.ethz.ch/mailman/listinfo/r-help
>>>PLEASE do read the posting guide!
>>>http://www.R-project.org/posting-guide.html
>>>
>>---------------------------------------------------------------------
>> Steven M. Boker 574-339-0735 (cell/page/message)
>> sboker@nd.edu 574-631-4941 (office)
>> http://www.nd.edu/~sboker/ 574-631-8883 (fax)
>> Dept. of Psychology, University of Notre Dame, Notre Dame, IN 46556
>>
>>______________________________________________
>>R-help@stat.math.ethz.ch mailing list
>>https://stat.ethz.ch/mailman/listinfo/r-help
>>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
>
>--
>*********************************************************************
>Brian Beckage
>Department of Botany
>University of Vermont
>Marsh Life Science Building
>Burlington, VT 05405
>
>Phone: 802 656-0197
>Fax : 802 656-0440
>email: Brian.Beckage@uvm.edu
>web : www.uvm.edu/~bbeckage
>
>______________________________________________
>R-help@stat.math.ethz.ch mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

-- 
*********************************************************************
Brian Beckage
Department of Botany
University of Vermont
Marsh Life Science Building
Burlington, VT 05405

Phone:  802 656-0197
Fax  :  802 656-0440
email:  Brian.Beckage@uvm.edu
web  :  www.uvm.edu/~bbeckage
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Received on Tue May 10 01:00:34 2005

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