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 >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> >> > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
