[R-SIG-Mac] library problem (leopard v. tiger)

Andrew Beckerman a.beckerman at sheffield.ac.uk
Wed Jan 9 11:07:59 CET 2008 

Simon -

Many thanks for the advice.  I've re-installed 2.6.1 with the GNU  
fortran with it.  GeneticsPed 1.1.0 installed and loads fine now.   
Don't quite know what happened before.

Do I need to remove the HPC fortran/GCC stuff now?  Is that prudent?

Cheers
andrew


---------------------------------------------------------------------------------
Dr. Andrew Beckerman
Department of Animal and Plant Sciences, University of Sheffield,
Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
ph +44 (0)114 222 0026; fx +44 (0)114 222 0002
http://www.beckslab.staff.shef.ac.uk/
----------------------------------------------------------------------------------


On 8 Jan 2008, at 15:59, Simon Urbanek wrote:

> Andrew,
>
> On Jan 7, 2008, at 10:57 AM, Andrew Beckerman wrote:
>
>> 10.5.1, R 2.6.1.
>>
>> I am trying to get a biocinductor package called GeneticsPed to  
>> work with leopard and R2.6.1.  It worked on Tiger with 2.5.
>>
>> I have tried to install via Bioconductor, via the binary as a  
>> download, and as a source file.
>>
>> Before documenting the behaviours, please note, that I have the  
>> latest Xcode installed, and also the latest GCC and gfortran  
>> installed through HPC.
>>
>
> HPC fortran doesn't work (it has several problems but the main one  
> is that it is not universal). You'll have to use a universal   
> fortran compiler and we strongly recommend the use of the one we  
> supply. (See also http://r.research.att.com/tools/ for details).
>
>
>> 1) Bioconductor can't find it, and that's ok, because it only exists
>> now in the Devel version.
>>
>> 2) When I try and load the installed binary, I get the following  
>> error
>> (note that it appeast to be built against 2.5?).
>>
>
> Are you sure it's not a problem on your end pulling packages from  
> the wrong place (see .libPaths())? It is the most common mistake to  
> forget to wipe old 2.5 packages from custom lib paths.
>
> I'm not building BioC packages anymore, but I have checked the  
> binary from http://www.bioconductor.org/packages/2.2/bioc/bin/macosx/universal/contrib/2.7/GeneticsPed_1.1.0.tgz
> and that works just fine:
> i386/GeneticsPed.so:
> 	GeneticsPed.so (compatibility version 0.0.0, current version 0.0.0)
> 	/Library/Frameworks/R.framework/Versions/2.6/Resources/lib/ 
> libgfortran.2.dylib (compatibility version 3.0.0, current version  
> 3.0.0)
>
> ppc/GeneticsPed.so:
> 	GeneticsPed.so (compatibility version 0.0.0, current version 0.0.0)
> 	/Library/Frameworks/R.framework/Versions/2.6/Resources/lib/ 
> libgfortran.2.dylib (compatibility version 3.0.0, current version  
> 3.0.0)
>
>
>>> library(GeneticsPed)
>> Loading required package: gdata
>>
>> Attaching package: 'gdata'
>>
>>
>> 	The following object(s) are masked from package:Hmisc :
>>
>> 	 combine,
>> 	 reorder.factor
>>
>> Error in dyn.load(file, ...) :
>>  unable to load shared library '/Library/Frameworks/R.framework/
>> Resources/library/GeneticsPed/libs/i386/GeneticsPed.so':
>>  dlopen(/Library/Frameworks/R.framework/Resources/library/
>> GeneticsPed/libs/i386/GeneticsPed.so, 6): Library not loaded: / 
>> Library/
>> Frameworks/R.framework/Versions/2.5/Resources/lib/libgfortran.2.dylib
>>  Referenced from: /Library/Frameworks/R.framework/Resources/library/
>> GeneticsPed/libs/i386/GeneticsPed.so
>>  Reason: image not found
>> Error: package/namespace load failed for 'GeneticsPed'
>>>
>>
>> 3) When I try and install via source, I get the following error
>> (indicating use of the 10.4SDK?):
>>
>
> Yes, the R you are using is a Tiger build, so it makes sure  
> everything stays Tiger-compatible.
>
>
>> /Library/Frameworks/R.framework/Resources/library
>> * Installing *source* package 'GeneticsPed' ...
>> ** libs
>> ** arch - i386
>> g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-
>> version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/
>> Resources/include -I/Library/Frameworks/R.framework/Resources/ 
>> include/
>> i386  -msse3    -fPIC  -g -O2 -march=nocona -c ainverse.cc -o  
>> ainverse.o
>> g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-
>> version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/
>> Resources/include -I/Library/Frameworks/R.framework/Resources/ 
>> include/
>> i386  -msse3    -fPIC  -g -O2 -march=nocona -c eibd.cc -o eibd.o
>> gfortran -arch i386  -isysroot /Developer/SDKs/MacOSX10.4u.sdk   -
>> fPIC  -g -O2 -march=nocona -c ggmatmult.f -o ggmatmult.o
>> ** arch - ppc
>> g++ -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-
>> version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/
>> Resources/include -I/Library/Frameworks/R.framework/Resources/ 
>> include/
>> ppc  -I/usr/local/include    -fPIC  -g -O2 -c ainverse.cc -o  
>> ainverse.o
>> f951: error: unrecognized command line option "-arch"
>> make: *** [ggmatmult.o] Error 1
>
> Problem with HPC fortran - please use the GNU Fortran that comes  
> with R.
>
> Cheers,
> Simon
>
>
>> chmod: /Library/Frameworks/R.framework/Resources/library/GeneticsPed/
>> libs/i386/*: No such file or directory
>> g++ -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-
>> version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/
>> Resources/include -I/Library/Frameworks/R.framework/Resources/ 
>> include/
>> ppc  -I/usr/local/include    -fPIC  -g -O2 -c eibd.cc -o eibd.o
>> gfortran -arch ppc  -isysroot /Developer/SDKs/MacOSX10.4u.sdk   -fPIC
>> -g -O2 -c ggmatmult.f -o ggmatmult.o
>> ** Removing '/Library/Frameworks/R.framework/Resources/library/
>> GeneticsPed'
>> ** Restoring previous '/Library/Frameworks/R.framework/Resources/
>> library/GeneticsPed'
>> f951: error: unrecognized command line option "-arch"
>> make: *** [ggmatmult.o] Error 1
>> chmod: /Library/Frameworks/R.framework/Resources/library/GeneticsPed/
>> libs/ppc/*: No such file or directory
>> ERROR: compilation failed for package 'GeneticsPed'
>>
>> Any advice or obvious comments on what to do?
>>
>> Cheers
>> andrew
>> ---------------------------------------------------------------------------------
>> Dr. Andrew Beckerman
>> Department of Animal and Plant Sciences, University of Sheffield,
>> Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
>> ph +44 (0)114 222 0026; fx +44 (0)114 222 0002
>> http://www.beckslab.staff.shef.ac.uk/
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>>
>

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