[R] rgl_0.92.879 package broke with R 2.15

Fri Apr 13 22:08:15 CEST 2012

Duncan

Brilliant.  This solved the problem.  Library (rgl) is now  
accessiible, and the plot3d function works fine in X11 (which I think  
is how it worked before anyway).  Whatever I may be missing, I don't  
think I'll notice.

Best,

Mark

On Apr 13, 2012, at 11:08 AM, Duncan Murdoch wrote:

> On 13/04/2012 11:44 AM, Duncan Murdoch wrote:
>> There were no changes to that code (the OSXGUIFactory) between  
>> 0.92.861
>> and 0.92.879, so I'd have to assume it's a difference between the
>> systems used to build it.  All I can suggest is that you go back to  
>> the
>> older one if you can't do a build yourself.
>
> I've had some discussions offline with another user who had this  
> problem.  For him, the workaround was to delete the aglrgl.so  
> library (full path given in the error message).  This will cause rgl  
> to fall back to using X11 for graphics.  It doesn't look as nice as  
> the native window, but as long as you have X11 working, it should  
> work.
>
> Duncan Murdoch
>
>> Duncan Murdoch
>>
>> On 12/04/2012 5:27 PM, Grimes Mark wrote:
>> >  Dear All
>> >
>> >  I am unhappy to report that rgl_0.92.879 gives the following  
>> error:
>> >  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’
>> >  >sessionInfo()
>> >  R version 2.15.0 (2012-03-30)
>> >  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] splines   stats     graphics  grDevices utils     datasets
>> >  methods   base
>> >
>> >  other attached packages:
>> >   [1] RUnit_0.4.26         bio3d_1.1-3          RCytoscape_1.6.2
>> >  XMLRPC_0.2-4         graph_1.34.0         org.Hs.eg.db_2.7.1
>> >  RSQLite_0.11.1       DBI_0.2-5            AnnotationDbi_1.18.0
>> >  [10] Biobase_2.16.0       BiocGenerics_0.2.0   adegenet_1.3-4
>> >  ade4_1.4-17          MASS_7.3-17          cluster_1.14.2
>> >  Hmisc_3.9-3          survival_2.36-12     plyr_1.7.1
>> >
>> >  loaded via a namespace (and not attached):
>> >  [1] grid_2.15.0    IRanges_1.14.2 lattice_0.20-6 RCurl_1.91-1
>> >  stats4_2.15.0  tools_2.15.0   XML_3.9-4
>> >  >
>> >  I don't understand how this happens or how to fix it.  Doesn't  
>> matter
>> >  if I use CRAN or R CMD INSTALL from terminal.  Terminal gave me no
>> >  errors when I installed in this way:
>> >  ~¤  R CMD INSTALL /Users/Mark/R_/Packages/rgl_0.92.879.tar
>> >  * installing to library
>> >  ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’
>> >  * installing *binary* package ‘rgl’ ...
>> >
>> >  * DONE (rgl)
>> >  ~ ¤
>> >  Mark
>> >
>> >  On Apr 5, 2012, at 5:06 PM, Grimes Mark wrote:
>> >
>> >>  Dear David, Duncan, and Jochen, and everyone
>> >>
>> >>  I am happy to report that  with R version 2.15.0, rgl_0.92.861  
>> now
>> >>  loads properly.  To whoever fixed this, thank you!
>> >>
>> >>  Mark
>> >>
>> >>
>> >>>  Below some more observations that might help you locate the  
>> problem.
>> >>>
>> >>>  Also sorry for ignoring the posting rules in my last post. I was
>> >>>  still on 2.14.1, and installing from source from the GUI  
>> version of
>> >>>  R64. Installing from source from R64 GUI still works after the
>> >>>  upgrade to R 2.14.2, .
>> >>>
>> >>>  The 32 bit versions of R don't work for me anymore, probably  
>> because
>> >>>  I have only installed the 64 bit versions of some libraries  
>> under
>> >>>  Lion. I have never noticed before, since after the problem  
>> discussed
>> >>>  in this thread
>> >>>  https://stat.ethz.ch/pipermail/r-sig-mac/2010-July/007609.html I
>> >>>  have been using R64 exclusively.
>> >>>
>> >>>  Also note that installing from the command line (Terminal)  
>> version
>> >>>  of either R32 or R64 gives the error
>> >>>
>> >>>>  checking for glEnd in -lGL... no
>> >>>>  configure: error: missing required library GL
>> >>>
>> >>>  Presumably, something is wrong with my bash environment and the
>> >>>  configure script is picking up the wrong gl libraries.
>> >>>  Installing from source does work after downloading and  
>> unzipping the
>> >>>  rgl tarball with
>> >>>
>> >>>  ./configure --with-gl-libs=/usr/X11/lib
>> >>>  --with-gl-includes=/usr/X11/include
>> >>>
>> >>>
>> >>>  Jochen
>> >>>
>> >>>  On Mar 28, 2012, at 10:15 AM, Duncan Murdoch wrote:
>> >>>
>> >>>>  On 12-03-27 6:31 PM, Grimes Mark wrote:
>> >>>>>  Dear People
>> >>>>>
>> >>>>>   I can't figure out how to fix this problem: rgl won't run  
>> under R
>> >>>>>  2.14.2 (it was working for me before under 2.14.0). The  
>> error message
>> >>>>>  is:
>> >>>>
>> >>>>  rgl is currently changing fairly rapidly.  I'd suggest trying  
>> to
>> >>>>  install again (the current version, as of yesterday, is  
>> 0.92.861).
>> >>>>   If that's not enough, I'd install a binary build (which may  
>> be a
>> >>>>  little old, but at least it built successfully...).
>> >>>>
>> >>>>  Duncan Murdoch
>> >>>
>> >>>  Thanks for your continued efforts Duncan. I had tried  
>> compiling that
>> >>>  version from source and gotten an error but when I attempted to
>> >>>  install from the current binary image which is now  
>> rgl_0.92.861.tgz,
>> >>>  I got apparent success, it loads without error, and the  
>> example in
>> >>>  ?rgl runs.
>> >>>
>> >>>  -- >>>
>> >>>  David Winsemius, MD
>> >>>  West Hartford, CT
>> >>>
>> >>
>> >
>>
>