[R-SIG-Mac] [R] rgl package broke with R 2.14.2

jochen laubrock jochen.laubrock at gmail.com
Sat Mar 31 15:10:28 CEST 2012 

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


=== broken: R64  === 
> sessionInfo()
R version 2.14.2 (2012-02-29)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

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

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

loaded via a namespace (and not attached):
[1] tcltk_2.14.2 tools_2.14.2

> configure: error: missing required library GL
> ERROR: configuration failed for package ‘rgl’



=== working: R.app  === 

> sessionInfo()
R version 2.14.2 (2012-02-29)
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] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] tools_2.14.2

> install.packages("rgl", type="source", lib=.libPaths()[2])

> [...] ** testing if installed package can be loaded
> * DONE (rgl)




On Mar 28, 2012, at 6:30 , David Winsemius wrote:

> 
> On Mar 27, 2012, at 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:
> 
> I'm having basically the same problem (at least to the extent that the error message on attempted loading is the same), but would add that rgl _was_ working with R 2.14.2 until I updated to the current version from rgl 0.87 in a failed effort at answering posting on StackOverflow. (I have tried reverting to rgl 0.87 without success.) I have had problems in th past related to difference in freetype and libpng This is, however, probably a Mac specific issue and should get posted to the Mac list rather than the general R help list. I am alternate-posting (correct term doubtful) this and do not think it appropriate to respond to further replies on R-help.
> 
> I generally run the Mac R GUI 64 bit and installed both from binary and source (with Xcode installed) using the Package Installer, and get the same error message at the point of loading. I get the following warnings during installation from source using teh Mac GUI Package Installer with a target of rgl 0.92.861 and with the version that was current as a couple of days ago 0.92.858 :
> 
> -----
> ld warning: in /opt/local/lib/libpng12.dylib, file is not of required architecture
> ld warning: in /opt/local/lib/libX11.dylib, file is not of required architecture
> ld warning: in /opt/local/lib/libfreetype.dylib, file is not of required architecture
> ld warning: in /opt/local/lib/libz.dylib, file is not of required architecture
> mkdir Temp
> mv x11*.o Temp
> mkdir -p AGL
> mv AGL/* .
> MAKINGAGL=TRUE /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB  -o aglrgl.so *.cpp *.c \
> 		osx/*.mm osx/*.cpp
> mv: rename AGL/* to ./*: No such file or directory
> make: [aglrgl.so] Error 1 (ignored)
> 
> ------
> 
> 
> 
> sessionInfo()
> R version 2.14.2 (2012-02-29)
> 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     grDevices utils     datasets  graphics  methods   base
> 
> other attached packages:
> [1] rms_3.4-0        Hmisc_3.9-2      survival_2.36-12 sos_1.3-1        brew_1.0-6       lattice_0.20-0
> 
> loaded via a namespace (and not attached):
> [1] cluster_1.14.2 grid_2.14.2    tools_2.14.2
> > require(rgl)
> Loading required package: 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/2.14/Resources/library/rgl/libs/x86_64/aglrgl.so':
>  dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library/rgl/libs/x86_64/aglrgl.so, 6): Symbol not found: __ZN3gui13OSXGUIFactory12hasEventLoopEv
>  Referenced from: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/rgl/libs/x86_64/aglrgl.so
>  Expected in: dynamic lookup
> 
> 
>> 
>>> 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/2.14/Resources/library/rgl/libs/x86_64/aglrgl.so':
>>  dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/
>> library/rgl/libs/x86_64/aglrgl.so, 6): Symbol not found:
>> __ZN3gui13OSXGUIFactory12hasEventLoopEv
>>  Referenced from: /Library/Frameworks/R.framework/Versions/2.14/
>> Resources/library/rgl/libs/x86_64/aglrgl.so
>>  Expected in: dynamic lookup
>> 
>> Error: package/namespace load failed for ‘rgl’
>> 
>> I tried re-installing the package several ways, including from R, both
>> binary and type='source', and from Terminal using R CMD INSTALL
>> rgl_0.92.858.tar.
>> 
>> I found some threads with this error but no solutions that I could
>> understand.  I am an R user, not a developer.  Do you have any idea
>> how to fix this?
>> 
>> Thanks for your help,
>> 
>> Mark
>> 
>>> sessionInfo()
>> R version 2.14.2 (2012-02-29)
>> 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] bio3d_1.1-3           RCytoscape_1.4.4
>> XMLRPC_0.2-4          graph_1.32.0          org.Hs.eg.db_2.6.4
>> [6] RSQLite_0.11.1        DBI_0.2-5
>> AnnotationDbi_1.16.19 Biobase_2.14.0        adegenet_1.3-4
>> [11] ade4_1.4-17           MASS_7.3-17           cluster_1.14.2
>> Hmisc_3.9-2           survival_2.36-12
>> [16] plyr_1.7.1
>> 
>> loaded via a namespace (and not attached):
>> [1] grid_2.14.2    IRanges_1.12.6 lattice_0.20-6 RCurl_1.91-1
>> tools_2.14.2   XML_3.9-4
>> 
>> 
>> 	[[alternative HTML version deleted]]
>> 
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
> 
> David Winsemius, MD
> West Hartford, CT
> 
> _______________________________________________
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> R-SIG-Mac at r-project.org
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