[R-SIG-Mac] rgl configure error: "missing required library GL"

peter dalgaard pdalgd at gmail.com
Mon Jul 23 20:31:47 CEST 2012 

On Jul 23, 2012, at 19:13 , Duncan Murdoch wrote:

> On 23/07/2012 12:55 PM, Grimes Mark wrote:
>> 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
> 
> I think that's a different problem.  The original one in this thread (which should now be fixed) caused R to fail to build.  This one causes it to fail to run on some newer MacOSX systems.  (Newer than what I have, anyway.)  This is probably caused by Apple changing their API; I don't know a fix, but a workaround is to delete the aglrgl.so library mentioned in the error message.  rgl will fall back to the X11 library, which still works.
> 

I think they are somewhat related. I managed to build an rgl package that loaded neatly into R.app and ran without requiring X (somewhat smoother than the X version, I might add). However, some attempts along the way gave symptoms with missing symbols. The generic issue seems to be that when you build the binary package, there may be warnings about missing support libraries but aglrgl.so is still created. The final step of the package build is to test whether the package can be loaded, but since the build is from the command line, the X11 route is taken, and that may well work in spite of a broken aglrgl.so. 

In my note from July 17, I mentioned that I had trouble on 32 bit, and that was exactly because some of my libs were 64 bit only. Those were MacPort builds, but I don't think it actually matters. Simon does things slightly differently, but I would conjecture that there might be a lib that is found in 32 bit only on the build machine.

- Peter

> Duncan Murdoch
> 
>> 
>> 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
>> >
>> > _______________________________________________
>> > R-SIG-Mac mailing list
>> > R-SIG-Mac at r-project.org
>> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
>> 
> 

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com

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