* installing *source* package ‘kebabs’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c ByteStringVector.c -o ByteStringVector.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c ExplicitRepC.cpp -o ExplicitRepC.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c GappyPairC.cpp -o GappyPairC.o
GappyPairC.cpp: In function ‘void getKMPosDistGappy(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, int, bool, bool, bool, bool, Rcpp::NumericVector, int, alphaInfo*) [with T = unsigned char]’:
GappyPairC.cpp:3474: instantiated from here
GappyPairC.cpp:1555: warning: comparison between signed and unsigned integer expressions
GappyPairC.cpp: In function ‘void getKMStdAnnGappy(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, bool, int, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = unsigned char]’:
GappyPairC.cpp:3480: instantiated from here
GappyPairC.cpp:932: warning: comparison between signed and unsigned integer expressions
GappyPairC.cpp: In function ‘void getKMPosDistGappy(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, int, bool, bool, bool, bool, Rcpp::NumericVector, int, alphaInfo*) [with T = short unsigned int]’:
GappyPairC.cpp:3492: instantiated from here
GappyPairC.cpp:1555: warning: comparison between signed and unsigned integer expressions
GappyPairC.cpp: In function ‘void getKMStdAnnGappy(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, bool, int, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = short unsigned int]’:
GappyPairC.cpp:3498: instantiated from here
GappyPairC.cpp:932: warning: comparison between signed and unsigned integer expressions
GappyPairC.cpp: In function ‘void getKMPosDistGappy(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, int, bool, bool, bool, bool, Rcpp::NumericVector, int, alphaInfo*) [with T = unsigned int]’:
GappyPairC.cpp:3511: instantiated from here
GappyPairC.cpp:1555: warning: comparison between signed and unsigned integer expressions
GappyPairC.cpp: In function ‘void getKMStdAnnGappy(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, bool, int, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = unsigned int]’:
GappyPairC.cpp:3517: instantiated from here
GappyPairC.cpp:932: warning: comparison between signed and unsigned integer expressions
GappyPairC.cpp: In function ‘void getKMPosDistGappy(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, int, bool, bool, bool, bool, Rcpp::NumericVector, int, alphaInfo*) [with T = long long unsigned int]’:
GappyPairC.cpp:3529: instantiated from here
GappyPairC.cpp:1555: warning: comparison between signed and unsigned integer expressions
GappyPairC.cpp: In function ‘void getKMStdAnnGappy(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, bool, int, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = long long unsigned int]’:
GappyPairC.cpp:3535: instantiated from here
GappyPairC.cpp:932: warning: comparison between signed and unsigned integer expressions
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c KernelUtils.cpp -o KernelUtils.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c MismatchC.cpp -o MismatchC.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c MotifC.cpp -o MotifC.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c PredictionC.cpp -o PredictionC.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c PredictionProfileC.cpp -o PredictionProfileC.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c R_init_kebabs.cpp -o R_init_kebabs.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c SparseMatrixHash.cpp -o SparseMatrixHash.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c SpectrumC.cpp -o SpectrumC.o
SpectrumC.cpp: In function ‘void getKMPosDistSpec(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, bool, bool, bool, bool, Rcpp::NumericVector, int, alphaInfo*) [with T = unsigned char]’:
SpectrumC.cpp:3222: instantiated from here
SpectrumC.cpp:1134: warning: comparison between signed and unsigned integer expressions
SpectrumC.cpp: In function ‘void getKMStdAnnSpec(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, bool, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = unsigned char]’:
SpectrumC.cpp:3228: instantiated from here
SpectrumC.cpp:612: warning: comparison between signed and unsigned integer expressions
SpectrumC.cpp: In function ‘void getKMPosDistSpec(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, bool, bool, bool, bool, Rcpp::NumericVector, int, alphaInfo*) [with T = short unsigned int]’:
SpectrumC.cpp:3240: instantiated from here
SpectrumC.cpp:1134: warning: comparison between signed and unsigned integer expressions
SpectrumC.cpp: In function ‘void getKMStdAnnSpec(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, bool, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = short unsigned int]’:
SpectrumC.cpp:3246: instantiated from here
SpectrumC.cpp:612: warning: comparison between signed and unsigned integer expressions
SpectrumC.cpp: In function ‘void getKMPosDistSpec(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, bool, bool, bool, bool, Rcpp::NumericVector, int, alphaInfo*) [with T = unsigned int]’:
SpectrumC.cpp:3259: instantiated from here
SpectrumC.cpp:1134: warning: comparison between signed and unsigned integer expressions
SpectrumC.cpp: In function ‘void getKMStdAnnSpec(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, bool, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = unsigned int]’:
SpectrumC.cpp:3265: instantiated from here
SpectrumC.cpp:612: warning: comparison between signed and unsigned integer expressions
SpectrumC.cpp: In function ‘void getKMPosDistSpec(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, bool, bool, bool, bool, Rcpp::NumericVector, int, alphaInfo*) [with T = long long unsigned int]’:
SpectrumC.cpp:3277: instantiated from here
SpectrumC.cpp:1134: warning: comparison between signed and unsigned integer expressions
SpectrumC.cpp: In function ‘void getKMStdAnnSpec(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, bool, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = long long unsigned int]’:
SpectrumC.cpp:3283: instantiated from here
SpectrumC.cpp:612: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c SymmetricPairC.cpp -o SymmetricPairC.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c Utils.cpp -o Utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o kebabs.so Biostrings_stubs.o ByteStringVector.o ExplicitRepC.o FeatureWeightsPosDepC.o GappyPairC.o IRanges_stubs.o KernelUtils.o MismatchC.o MotifC.o PredictionC.o PredictionProfileC.o R_init_kebabs.o SparseMatrixHash.o SpectrumC.o SymmetricPairC.o Utils.o XVector_stubs.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/kebabs.Rcheck/kebabs/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (kebabs)