[R-SIG-Mac] Problems loading Rcmdr on a Mac 10.7.2 and a Mac 10.6.8

Simon Urbanek urbanek at research.att.com
Thu Sep 19 15:10:52 CEST 2013 

On Sep 19, 2013, at 4:04 AM, David Winsemius wrote:

> 
> On Sep 18, 2013, at 8:47 PM, John Fox wrote:
> 
>> Dear Sarah,
>> 
>> It seems likely from the message that you reported that the problem isn't directly related to the Rcmdr package, but rather to the tcltk package on which the Rcmdr depends. Your student (and the other students who are experiencing problems) can verify this by trying to load the tcltk package directly, via library(tcltk), to see whether he gets the same error. 
>> 
>> It also seems apparent from the error message that there's a mismatch between the version of Tcl/Tk, presumably the one supplied with the R distribution, and the version of X-Windows.
> 
> That is not what I am reading. libfreetype.6 version 13 is the reported problem with  a need to update to version 14.
> 
>> I'm not sure why that happened, and there was a previous message about a similar problem on the list. I suggested that the user install the current version of X-Quartz, but you student apparently already has done that. Is it possible that there's an old version of X-Windows on the student's computer?
>> 
>> I assume that your students have been following the Rcmdr installation instructions for Mac OS X at <http://socserv.socsci.mcmaster.ca/jfox/Misc/Rcmdr/installation-notes.html>. Have any of them been successful? Are all the problems identical? You mentioned that another student installed a version of Tcl/Tk independently of R. I suppose that this could cause problems if the wrong Tcl/Tk is invoked.
> 
> I'm not really a student but maybe this will be useful anyway. There is a version of Tk at:
> 
> http://r.research.att.com/src/tk8.6.0-src.tar.gz
> 

Those are the sources - not very useful to end-users ;).

R 3.0.1 comes with the necessary binary so there is no need to download anything else.


> ... which appears to be the most up-to-date version. I'm actually running version 8.5 with OSX 10.7.5
> 
>> From the Unix cmd line one can execute:
> 
> echo "puts [info tclversion]" | tclsh
> 
> ... for find the installed version.
> 
> My XQuartz.app in the Utilities folder reports version 2.7.4
> 

Note that we don't use XQuartz - the default is to use system X11 (hence the /usr/X11 path). If XQuartz replaces the system X11 (by symlinking into /usr/X11) then it is used, but that is only the default on OS X versions that don't come with X11 at all.


> In the R64.app console:
> 
>> help(package='tcltk')
>> install.packages("Rcmdr")  
> 
> # I have 1.9.4 before installing version 2.0-0 which is what the CRAN gods are delivering for my system.
> 
> trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/contrib/3.0/Rcmdr_2.0-0.tgz'
> Content type 'application/x-gzip' length 3945755 bytes (3.8 Mb)
> opened URL
> ==================================================
> downloaded 3.8 Mb
> 
> 
> The downloaded binary packages are in
> 	/var/folders/yq/m3j1jqtj6hq6s5mq_v0jn3s80000gn/T//RtmptEudZq/downloaded_packages
>> library(Rcmdr)
> Loading required package: knitr
> Loading required package: markdown
> 
> Rcmdr Version 2.0-0
> 
> And the GUI panel pops up.
> 
> The error message below says that libfreetype.6 is an old version and that you need version 14.0 for libtk8.6
> 
>> From Unix cmd line:
> 
> otool -L /opt/local/lib/libfreetype.6.dylib
> 

^^-- this is irrelevant - TclTk uses /usr/X11:

$ otool -L /usr/X11/lib/libfreetype.6.dylib
/usr/X11/lib/libfreetype.6.dylib:
	/usr/X11/lib/libfreetype.6.dylib (compatibility version 14.0.0, current version 14.2.0)

Cheers,
Simon


> # ---- reports ___________
> /opt/local/lib/libfreetype.6.dylib:
> 	/opt/local/lib/libfreetype.6.dylib (compatibility version 16.0.0, current version 16.0.0)
> 	/opt/local/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.7)
> 	/opt/local/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.6)
> 	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 125.2.11)
> 
> 
>> 
>> I too am teaching with the Rcmdr this Fall, and about half the students in my (small) class have Macs. None have experienced problems with the tcltk package or version 2.0-1 of the Rcmdr under R 3.0.1. Nor have I on my Mac,  running OS X 10.8.5 and XQuartz 2.7.4
>> 
>> Like you, I'm not terribly knowledgeable about Mac OS X. I expect that someone else on the list will be able to offer better help, and I've taken the liberty of copying this response to Simon Urbanek.
>> 
>> I'm sorry that you're experiencing this problem.
>> 
>> John
>> 
>> On Wed, 18 Sep 2013 21:46:00 -0400
>> Sarah Hardy <sarah.hardy at maine.edu> wrote:
>>> I myself am not a Mac user, but I have about 6 students with Macs all
>>> having the same (or similar) problem loading Rcmdr 2.0.1 on their Mac (but
>>> have successfully installed R 3.0.1).
>>> 
>>> One student has a Mac 10.7.2. I know he installed XQuartz-2.7.4.dmg and
>>> then completely logged out and back in.
>>> Before he did that he ran the "Repair Disk Permissions" in "Disk Utility".
>>> Afterwards I checked "Verify Disk Permissions" and I didn't see any
>>> warnings. When installing Rcmdr there are no unusual messages. The message
>>> he gets in R when attempting to load Rcmdr  is:
>>> 
>>> R version 3.0.1 (2013-05-16) -- "Good Sport"
>>> Copyright (C) 2013 The R Foundation for Statistical Computing
>>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>> 
>>> ...
>>> 
>>> 
>>>> library(Rcmdr)
>>> Loading required package: splines
>>> Error : .onLoad failed in loadNamespace() for 'tcltk', details:
>>> call: dyn.load(file, DLLpath = DLLpath, ...)
>>> error: unable to load shared object
>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/tcltk/libs/tcltk.so':
>>> 
>>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/tcltk/libs/tcltk.so,
>>> 10): Library not loaded: /usr/X11/lib/libfreetype.6.dylib
>>> Referenced from: /usr/local/lib/libtk8.6.dylib
>>>  Reason: Incompatible library version: libtk8.6.dylib requires version
>>> 14.0.0 or later, but libfreetype.6.dylib provides version 13.0.0
>>> Error: package or namespace load failed for ‘Rcmdr’
>>> 
>>> I'm not sure if this provides any clues, but I also ran this system
>>> function:
>>> .
>>>> system("ls -ld /usr/local /usr/local/lib /usr/local/lib/libtcl*")
>>> drwxr-xr-x   7 root  wheel      238 Mar 29 20:36 /usr/local
>>> drwxr-xr-x  27 root  wheel      918 Sep 17 16:55 /usr/local/lib
>>> -r-xr-xr-x   1 root  wheel  4820229 Oct 21  2008
>>> /usr/local/lib/libtcl8.5.dylib
>>> -r-xr-xr-x   1 root  wheel  1419604 Mar 29 20:35/usr/local/lib/libtcl8.6.dylib
>>> -rw-r--r--   1 root  wheel    11072 Oct 21  2008
>>> /usr/local/lib/libtclstub8.5.a
>>> -rwxr-xr-x   1 root  wheel     4824 Mar 29 20:35/usr/local/lib/libtclstub8.6.a
>>> 
>>> Another student with identical messages has a Mac 10.6.8. I think she
>>> installed tcltk-8.5.5-x11.dmg.
>>> 
>>> Any tips or suggestions on how to proceed would be greatly appreciated.
>>> 
>>> Thank you,
>>> Sarah Hardy
>>> 
>>> -- 
>>> 
>>> Sarah Hardy, PhD
>>> Associate Professor of Mathematics
>>> University of Maine Farmington
>>> 207-778-7124    Office: Brinkman 100
>>> 
>>> 	[[alternative HTML version deleted]]
>>> 
>> 
>> ------------------------------------------------
>> John Fox
>> McMaster University
>> Hamilton, Ontario, Canada
>> http://socserv.mcmaster.ca/jfox/
>> 
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> David Winsemius
> Alameda, CA, USA
> 
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