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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