I wonder if this is related.  Package 'rgl' failed to load in an error  
similar to one I've had previously.  It was working for a while and  
now it is not working again.  R output attached

Mark Grimes

 > library (rgl)
Error : .onLoad failed in loadNamespace() for 'rgl', details:
   call: dyn.load(file, DLLpath = DLLpath, ...)
   error: unable to load shared object '/Library/Frameworks/ 
R.framework/Versions/2.15/Resources/library/rgl/libs/x86_64/aglrgl.so':
   dlopen(/Library/Frameworks/R.framework/Versions/2.15/Resources/ 
library/rgl/libs/x86_64/aglrgl.so, 6): Symbol not found:  
__ZN3gui13OSXGUIFactory12hasEventLoopEv
   Referenced from: /Library/Frameworks/R.framework/Versions/2.15/ 
Resources/library/rgl/libs/x86_64/aglrgl.so
   Expected in: dynamic lookup

Error: package/namespace load failed for ‘rgl’
 > install.packages("rgl")
--- Please select a CRAN mirror for use in this session ---
trying URL 'http://cran.stat.sfu.ca/bin/macosx/leopard/contrib/2.15/rgl_0.92.892.tgz'
Content type 'application/x-gzip' length 7774197 bytes (7.4 Mb)
opened URL
==================================================
downloaded 7.4 Mb


The downloaded binary packages are in
	/var/folders/p3/vs342gm97msfg0y_fsx79x880000gn/T//RtmpYZqfh1/ 
downloaded_packages
 > library(rgl)
Error in get(Info[i, 1], envir = env) :
   internal error -3 in R_decompress1
Error: package/namespace load failed for ‘rgl’
 > library("rgl")
Error in get(Info[i, 1], envir = env) :
   internal error -3 in R_decompress1
Error: package/namespace load failed for ‘rgl’
 > sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid      splines   stats     graphics  grDevices utils      
datasets  methods   base

other attached packages:
  [1] gplots_2.11.0        KernSmooth_2.23-8    caTools_1.13          
bitops_1.0-4.1       gdata_2.11.0         gtools_2.7.0          
tsne_0.1-2           vegan_2.0-4          permute_0.7-0         
RUnit_0.4.26         bio3d_1.1-3
[12] RCytoscape_1.6.5     XMLRPC_0.2-4         graph_1.34.0          
org.Hs.eg.db_2.7.1   RSQLite_0.11.1       DBI_0.2-5             
AnnotationDbi_1.18.1 Biobase_2.16.0       BiocGenerics_0.2.0    
adegenet_1.3-4       ade4_1.4-17
[23] MASS_7.3-19          cluster_1.14.2       Hmisc_3.9-3           
survival_2.36-14     plyr_1.7.1

loaded via a namespace (and not attached):
[1] IRanges_1.14.4 lattice_0.20-6 RCurl_1.91-1   stats4_2.15.1   
tools_2.15.1   XML_3.9-4
 >

On Jul 17, 2012, at 1:25 PM, Duncan Murdoch wrote:

> On 17/07/2012 2:33 PM, peter dalgaard wrote:
>> On Jul 17, 2012, at 19:31 , Davor Cubranic wrote:
>>
>> > On 2012-07-17, at 10:05 AM, Duncan Murdoch wrote:
>> >
>> >> The aglrgl.so library is built from osxgui.mm and osxlib.cpp.   
>> I'd been assuming the problem was an API change in recent OSX 64  
>> bit, but maybe it's a problem with the makefiles or the compiler.   
>> If you can suggest any fixes for this, I'd appreciate it.  (The  
>> newest OSX that I have is 10.6.8.)
>> >
>> > BTW, I see osxgui.o being of wrong architecture during an install  
>> on 10.6.8 as well...
>> >
>> > But I think this is caused by object files being left in the  
>> tar.gz:
>> >
>> > $ tar xzf rgl_0.92.880.tar.gz
>> > $ find rgl -name \*.o |xargs file
>> > rgl/src/AGL/x11gui.o: Mach-O object i386
>> > rgl/src/AGL/x11lib.o: Mach-O object i386
>> > rgl/src/osx/osxgui.o: Mach-O object i386
>> > rgl/src/osx/osxlib.o: Mach-O object i386
>> >
>> > Davor
>>
>> Yay, nice catch!
>>
>> This allows me to build an rgl that loads in R.app:
>>
>> tar xvfz rgl_0.92.880.tar.gz
>> rm `find rgl -name \*.o`
>> R64 CMD INSTALL --configure-args=--with-gl-libs=/usr/X11/lib rgl
>>
>> I still have some issues with the 32 bit version, but I believe  
>> those are unrelated. (MacPorts seems to be interfering....)
>>
>
> Yes, nice catch indeed.   If you get the tarball from R-forge,  
> you'll get a slightly newer version, and no *.o files included. I'll  
> send that one to CRAN.
>
> Duncan Murdoch
>
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> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac


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