Re: [R] rgl_0.92.879 package broke with R 2.15

Grimes Mark Fri, 13 Apr 2012 13:10:47 -0700

Duncan

Brilliant. This solved the problem. Library (rgl) is nowaccessiible, and the plot3d function works fine in X11 (which I thinkis how it worked before anyway). Whatever I may be missing, I don'tthink 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) between0.92.861
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 tothe
older one if you can't do a build yourself.
I've had some discussions offline with another user who had thisproblem. For him, the workaround was to delete the aglrgl.solibrary (full path given in the error message). This will cause rglto fall back to using X11 for graphics. It doesn't look as nice asthe native window, but as long as you have X11 working, it shouldwork.
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 followingerror:
>  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'tmatter
>  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_0.92.861now
>>  loads properly.  To whoever fixed this, thank you!
>>
>>  Mark
>>
>>
>>> Below some more observations that might help you locate theproblem.
>>>
>>>  Also sorry for ignoring the posting rules in my last post. I was
>>> still on 2.14.1, and installing from source from the GUIversion 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, probablybecause>>> I have only installed the 64 bit versions of some librariesunder>>> Lion. I have never noticed before, since after the problemdiscussed
>>>  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 andunzipping 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 rununder R>>>>> 2.14.2 (it was working for me before under 2.14.0). Theerror message
>>>>>  is:
>>>>
>>>> rgl is currently changing fairly rapidly. I'd suggest tryingto>>>> install again (the current version, as of yesterday, is0.92.861).>>>> If that's not enough, I'd install a binary build (which maybe a
>>>>  little old, but at least it built successfully...).
>>>>
>>>>  Duncan Murdoch
>>>
>>> Thanks for your continued efforts Duncan. I had triedcompiling that
>>>  version from source and gotten an error but when I attempted to
>>> install from the current binary image which is nowrgl_0.92.861.tgz,>>> I got apparent success, it loads without error, and theexample in
>>>  ?rgl runs.
>>>
>>>  -- >>>
>>>  David Winsemius, MD
>>>  West Hartford, CT
>>>
>>
>


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