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Package 410/467HostnameOS / ArchBUILDCHECKBUILD BIN
seqbias 1.0.0
Daniel Jones
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/seqbias
Last Changed Rev: 54800 / Revision: 59457
Last Changed Date: 2011-04-13 15:27:35 -0700 (Wed, 13 Apr 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK [ OK ]

Summary

Package: seqbias
Version: 1.0.0
Command: rm -rf seqbias.buildbin-libdir && mkdir seqbias.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh seqbias_1.0.0.tar.gz /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R seqbias.buildbin-libdir
StartedAt: 2011-10-20 18:31:42 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 18:35:03 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 201.4 seconds
RetCode: 0
Status:  OK 
PackageFile: seqbias_1.0.0.tgz
PackageFileSize: 1.544 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --library=seqbias.buildbin-libdir seqbias_1.0.0.tar.gz'
>>>>>>> 

* installing *source* package 'seqbias' ...
** libs
*** arch - i386
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c sequencing_bias.cpp -o sequencing_bias.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c kmers.cpp -o kmers.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c miscmath.cpp -o miscmath.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c common.cpp -o common.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -pedantic -c table.c -o table.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -pedantic -c logger.c -o logger.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c seqbias.cpp -o seqbias.o
seqbias.cpp: In function 'SEXPREC* seqbias_predict(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
seqbias.cpp:132: warning: 'c_seqbias' may be used uninitialized in this function
seqbias.cpp: In function 'SEXPREC* seqbias_save(SEXPREC*, SEXPREC*)':
seqbias.cpp:81: warning: 'c_seqbias' may be used uninitialized in this function
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/aliascontent.cpp -o yaml-cpp/aliascontent.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/map.cpp -o yaml-cpp/map.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/node.cpp -o yaml-cpp/node.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/null.cpp -o yaml-cpp/null.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/parserstate.cpp -o yaml-cpp/parserstate.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/scalar.cpp -o yaml-cpp/scalar.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/sequence.cpp -o yaml-cpp/sequence.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
g++-4.2 -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o seqbias.so sequencing_bias.o kmers.o miscmath.o common.o table.o logger.o seqbias.o yaml-cpp/aliascontent.o yaml-cpp/conversion.o yaml-cpp/emitter.o yaml-cpp/emitterstate.o yaml-cpp/emitterutils.o yaml-cpp/exp.o yaml-cpp/iterator.o yaml-cpp/map.o yaml-cpp/node.o yaml-cpp/null.o yaml-cpp/ostream.o yaml-cpp/parser.o yaml-cpp/parserstate.o yaml-cpp/regex.o yaml-cpp/scalar.o yaml-cpp/scanner.o yaml-cpp/scanscalar.o yaml-cpp/scantag.o yaml-cpp/scantoken.o yaml-cpp/sequence.o yaml-cpp/simplekey.o yaml-cpp/stream.o yaml-cpp/tag.o -L/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/usrlib/i386 -lbam -lbcf -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/seqbias.buildbin-libdir/seqbias/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (seqbias)


>>>>>>> 
>>>>>>> FIXING LINKS FOR seqbias.buildbin-libdir/seqbias/libs/i386/seqbias.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgcc_s.1.dylib" "seqbias.buildbin-libdir/seqbias/libs/i386/seqbias.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "seqbias.buildbin-libdir/seqbias/libs/i386/seqbias.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib" "seqbias.buildbin-libdir/seqbias/libs/i386/seqbias.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "seqbias.buildbin-libdir/seqbias/libs/i386/seqbias.so"


>>>>>>> 
>>>>>>> INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --preclean --library=seqbias.buildbin-libdir --libs-only seqbias_1.0.0.tar.gz'
>>>>>>> 

* installing *source* package 'seqbias' ...
** libs
*** arch - ppc
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c sequencing_bias.cpp -o sequencing_bias.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c kmers.cpp -o kmers.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c miscmath.cpp -o miscmath.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c common.cpp -o common.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -pedantic -c table.c -o table.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -pedantic -c logger.c -o logger.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c seqbias.cpp -o seqbias.o
seqbias.cpp: In function 'SEXPREC* seqbias_predict(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
seqbias.cpp:132: warning: 'c_seqbias' may be used uninitialized in this function
seqbias.cpp: In function 'SEXPREC* seqbias_save(SEXPREC*, SEXPREC*)':
seqbias.cpp:81: warning: 'c_seqbias' may be used uninitialized in this function
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/aliascontent.cpp -o yaml-cpp/aliascontent.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/map.cpp -o yaml-cpp/map.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/node.cpp -o yaml-cpp/node.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/null.cpp -o yaml-cpp/null.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/parserstate.cpp -o yaml-cpp/parserstate.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/scalar.cpp -o yaml-cpp/scalar.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/sequence.cpp -o yaml-cpp/sequence.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
g++-4.2 -arch ppc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o seqbias.so sequencing_bias.o kmers.o miscmath.o common.o table.o logger.o seqbias.o yaml-cpp/aliascontent.o yaml-cpp/conversion.o yaml-cpp/emitter.o yaml-cpp/emitterstate.o yaml-cpp/emitterutils.o yaml-cpp/exp.o yaml-cpp/iterator.o yaml-cpp/map.o yaml-cpp/node.o yaml-cpp/null.o yaml-cpp/ostream.o yaml-cpp/parser.o yaml-cpp/parserstate.o yaml-cpp/regex.o yaml-cpp/scalar.o yaml-cpp/scanner.o yaml-cpp/scanscalar.o yaml-cpp/scantag.o yaml-cpp/scantoken.o yaml-cpp/sequence.o yaml-cpp/simplekey.o yaml-cpp/stream.o yaml-cpp/tag.o -L/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/usrlib/ppc -lbam -lbcf -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/seqbias.buildbin-libdir/seqbias/libs/ppc

* DONE (seqbias)


>>>>>>> 
>>>>>>> FIXING LINKS FOR seqbias.buildbin-libdir/seqbias/libs/ppc/seqbias.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgcc_s.1.dylib" "seqbias.buildbin-libdir/seqbias/libs/ppc/seqbias.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "seqbias.buildbin-libdir/seqbias/libs/ppc/seqbias.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib" "seqbias.buildbin-libdir/seqbias/libs/ppc/seqbias.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "seqbias.buildbin-libdir/seqbias/libs/ppc/seqbias.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --library=seqbias.buildbin-libdir --libs-only seqbias_1.0.0.tar.gz'
>>>>>>> 

* installing *source* package 'seqbias' ...
** libs
*** arch - x86_64
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c sequencing_bias.cpp -o sequencing_bias.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c kmers.cpp -o kmers.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c miscmath.cpp -o miscmath.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c common.cpp -o common.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -pedantic -c table.c -o table.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -pedantic -c logger.c -o logger.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c seqbias.cpp -o seqbias.o
seqbias.cpp: In function 'SEXPREC* seqbias_predict(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
seqbias.cpp:132: warning: 'c_seqbias' may be used uninitialized in this function
seqbias.cpp: In function 'SEXPREC* seqbias_save(SEXPREC*, SEXPREC*)':
seqbias.cpp:81: warning: 'c_seqbias' may be used uninitialized in this function
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/aliascontent.cpp -o yaml-cpp/aliascontent.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/map.cpp -o yaml-cpp/map.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/node.cpp -o yaml-cpp/node.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/null.cpp -o yaml-cpp/null.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/parserstate.cpp -o yaml-cpp/parserstate.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/scalar.cpp -o yaml-cpp/scalar.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/sequence.cpp -o yaml-cpp/sequence.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/include"  -Wall -D_GNU_SOURCE -fPIC  -g -O2 -Wall -fasm-blocks -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o seqbias.so sequencing_bias.o kmers.o miscmath.o common.o table.o logger.o seqbias.o yaml-cpp/aliascontent.o yaml-cpp/conversion.o yaml-cpp/emitter.o yaml-cpp/emitterstate.o yaml-cpp/emitterutils.o yaml-cpp/exp.o yaml-cpp/iterator.o yaml-cpp/map.o yaml-cpp/node.o yaml-cpp/null.o yaml-cpp/ostream.o yaml-cpp/parser.o yaml-cpp/parserstate.o yaml-cpp/regex.o yaml-cpp/scalar.o yaml-cpp/scanner.o yaml-cpp/scanscalar.o yaml-cpp/scantag.o yaml-cpp/scantoken.o yaml-cpp/sequence.o yaml-cpp/simplekey.o yaml-cpp/stream.o yaml-cpp/tag.o -L/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rsamtools/usrlib/x86_64 -lbam -lbcf -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/seqbias.buildbin-libdir/seqbias/libs/x86_64

* DONE (seqbias)


>>>>>>> 
>>>>>>> FIXING LINKS FOR seqbias.buildbin-libdir/seqbias/libs/x86_64/seqbias.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgcc_s.1.dylib" "seqbias.buildbin-libdir/seqbias/libs/x86_64/seqbias.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "seqbias.buildbin-libdir/seqbias/libs/x86_64/seqbias.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib" "seqbias.buildbin-libdir/seqbias/libs/x86_64/seqbias.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "seqbias.buildbin-libdir/seqbias/libs/x86_64/seqbias.so"