>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GRENITS.buildbin-libdir GRENITS_1.10.0.tar.gz'
>>>>>>>
* installing *source* package 'GRENITS' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RcppArmadillo/include" -fPIC -g -O2 -Wall -fasm-blocks -c AR1_Gauss_biocond.cc -o AR1_Gauss_biocond.o
AR1_Gauss_biocond.cc: In function 'void Error_Gauss_c(std::string&, arma::mat&, arma::colvec&, arma::mat&)':
AR1_Gauss_biocond.cc:49: warning: unused variable 'numDiag'
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RcppArmadillo/include" -fPIC -g -O2 -Wall -fasm-blocks -c AR1_Student_biocond.cc -o AR1_Student_biocond.o
AR1_Student_biocond.cc: In function 'void Error_Student_c(std::string&, arma::mat&, arma::colvec&, arma::mat&)':
AR1_Student_biocond.cc:49: warning: unused variable 'numDiag'
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RcppArmadillo/include" -fPIC -g -O2 -Wall -fasm-blocks -c AR1_biocond.cc -o AR1_biocond.o
AR1_biocond.cc: In function 'void AR1_c(std::string&, arma::mat&, arma::colvec&, arma::mat&)':
AR1_biocond.cc:48: warning: unused variable 'numDiag'
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RcppArmadillo/include" -fPIC -g -O2 -Wall -fasm-blocks -c PSplines_biocond.cc -o PSplines_biocond.o
PSplines_biocond.cc: In function 'void PSplines_c(std::string&, arma::mat&, arma::colvec&, arma::mat&)':
PSplines_biocond.cc:45: warning: unused variable 'numDiag'
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RcppArmadillo/include" -fPIC -g -O2 -Wall -fasm-blocks -c R_C_interface.cpp -o R_C_interface.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RcppArmadillo/include" -fPIC -g -O2 -Wall -fasm-blocks -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RcppArmadillo/include" -fPIC -g -O2 -Wall -fasm-blocks -c commonFunctions.cc -o commonFunctions.o
commonFunctions.cc: In function 'void random_intSequence(arma::ucolvec&)':
commonFunctions.cc:270: warning: comparison between signed and unsigned integer expressions
commonFunctions.cc: In function 'void processFixedGammas(arma::mat&, int&, int&, arma::umat&, arma::umat&, arma::ucolvec&, arma::umat&, arma::uvec&, arma::uvec&)':
commonFunctions.cc:377: warning: comparison between signed and unsigned integer expressions
commonFunctions.cc:380: warning: comparison between signed and unsigned integer expressions
commonFunctions.cc: In function 'void updateCoefficients_reg(arma::mat&, const int&, const arma::urowvec&, const arma::mat&, const arma::rowvec&, const arma::ucolvec&)':
commonFunctions.cc:440: warning: unused variable 'num_on'
commonFunctions.cc: In function 'void updateCoefficients(arma::mat&, const int&, const arma::urowvec&, const arma::mat&, const arma::rowvec&)':
commonFunctions.cc:482: warning: unused variable 'num_on'
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RcppArmadillo/include" -fPIC -g -O2 -Wall -fasm-blocks -c functionsErrorModel.cc -o functionsErrorModel.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RcppArmadillo/include" -fPIC -g -O2 -Wall -fasm-blocks -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RcppArmadillo/include" -fPIC -g -O2 -Wall -fasm-blocks -c updateFunctions_AR1.cc -o updateFunctions_AR1.o
updateFunctions_AR1.cc: In function 'void updateCoeffAndGibbsVars(arma::mat&, arma::umat&, const arma::colvec&, const arma::mat&, const arma::mat&, const arma::mat&, const double&, const unsigned int&)':
updateFunctions_AR1.cc:128: warning: comparison between signed and unsigned integer expressions
updateFunctions_AR1.cc:134: warning: comparison between signed and unsigned integer expressions
updateFunctions_AR1.cc: In function 'void updateCoeffAndGibbsVars_reg(arma::mat&, arma::umat&, const arma::colvec&, const arma::mat&, const arma::mat&, double, const double&, const unsigned int&, arma::umat&, arma::ucolvec&, arma::umat&)':
updateFunctions_AR1.cc:186: warning: comparison between signed and unsigned integer expressions
updateFunctions_AR1.cc: In function 'void calc_logMVPDF_withLinks(double&, const arma::mat&, const arma::rowvec&, arma::urowvec&)':
updateFunctions_AR1.cc:264: warning: unused variable 'num_on'
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RcppArmadillo/include" -fPIC -g -O2 -Wall -fasm-blocks -c updateFunctions_Splines.cc -o updateFunctions_Splines.o
updateFunctions_Splines.cc: In function 'void updateTaus_reg(arma::mat&, arma::colvec&, const arma::mat&, arma::urowvec&, const arma::mat&, double, double, int, double, double, double, double, int, double, arma::uvec)':
updateFunctions_Splines.cc:296: warning: comparison between signed and unsigned integer expressions
updateFunctions_Splines.cc: In function 'void updateGammaAndB_row_i_reg(arma::mat&, arma::umat&, const arma::mat&, const arma::rowvec&, const arma::colvec&, int, int, int, arma::urowvec&, const arma::ucolvec&, const arma::urowvec&, const arma::ucolvec&, const arma::uvec&)':
updateFunctions_Splines.cc:478: warning: comparison between signed and unsigned integer expressions
updateFunctions_Splines.cc: In function 'void fixedBasesFromFixedRegs(arma::umat&, arma::umat&, arma::ucolvec&, int)':
updateFunctions_Splines.cc:714: warning: comparison between signed and unsigned integer expressions
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GRENITS.so AR1_Gauss_biocond.o AR1_Student_biocond.o AR1_biocond.o PSplines_biocond.o R_C_interface.o ReadMCMCFiles.o commonFunctions.o functionsErrorModel.o matrixManipulationFunctions.o updateFunctions_AR1.o updateFunctions_Splines.o /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/lib/i386/libRcpp.a -L/Library/Frameworks/R.framework/Resources/lib/i386 -lRlapack -L/Library/Frameworks/R.framework/Resources/lib/i386 -lRblas -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/GRENITS.buildbin-libdir/GRENITS/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'GRENITS_package.Rnw'
** testing if installed package can be loaded
* DONE (GRENITS)
>>>>>>>
>>>>>>> FIXING LINKS FOR GRENITS.buildbin-libdir/GRENITS/libs/i386/GRENITS.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgcc_s.1.dylib" "GRENITS.buildbin-libdir/GRENITS/libs/i386/GRENITS.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "GRENITS.buildbin-libdir/GRENITS/libs/i386/GRENITS.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.5.2.dylib" "GRENITS.buildbin-libdir/GRENITS/libs/i386/GRENITS.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "GRENITS.buildbin-libdir/GRENITS/libs/i386/GRENITS.so"
>>>>>>>
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=GRENITS.buildbin-libdir --libs-only GRENITS_1.10.0.tar.gz'
>>>>>>>
* installing *source* package 'GRENITS' ...
** libs
*** arch - x86_64
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RcppArmadillo/include" -fPIC -g -O2 -Wall -fasm-blocks -c AR1_Gauss_biocond.cc -o AR1_Gauss_biocond.o
AR1_Gauss_biocond.cc: In function 'void Error_Gauss_c(std::string&, arma::mat&, arma::colvec&, arma::mat&)':
AR1_Gauss_biocond.cc:49: warning: unused variable 'numDiag'
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RcppArmadillo/include" -fPIC -g -O2 -Wall -fasm-blocks -c AR1_Student_biocond.cc -o AR1_Student_biocond.o
AR1_Student_biocond.cc: In function 'void Error_Student_c(std::string&, arma::mat&, arma::colvec&, arma::mat&)':
AR1_Student_biocond.cc:49: warning: unused variable 'numDiag'
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RcppArmadillo/include" -fPIC -g -O2 -Wall -fasm-blocks -c AR1_biocond.cc -o AR1_biocond.o
AR1_biocond.cc: In function 'void AR1_c(std::string&, arma::mat&, arma::colvec&, arma::mat&)':
AR1_biocond.cc:48: warning: unused variable 'numDiag'
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RcppArmadillo/include" -fPIC -g -O2 -Wall -fasm-blocks -c PSplines_biocond.cc -o PSplines_biocond.o
PSplines_biocond.cc: In function 'void PSplines_c(std::string&, arma::mat&, arma::colvec&, arma::mat&)':
PSplines_biocond.cc:45: warning: unused variable 'numDiag'
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RcppArmadillo/include" -fPIC -g -O2 -Wall -fasm-blocks -c R_C_interface.cpp -o R_C_interface.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RcppArmadillo/include" -fPIC -g -O2 -Wall -fasm-blocks -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RcppArmadillo/include" -fPIC -g -O2 -Wall -fasm-blocks -c commonFunctions.cc -o commonFunctions.o
commonFunctions.cc: In function 'void random_intSequence(arma::ucolvec&)':
commonFunctions.cc:270: warning: comparison between signed and unsigned integer expressions
commonFunctions.cc: In function 'void processFixedGammas(arma::mat&, int&, int&, arma::umat&, arma::umat&, arma::ucolvec&, arma::umat&, arma::uvec&, arma::uvec&)':
commonFunctions.cc:377: warning: comparison between signed and unsigned integer expressions
commonFunctions.cc:380: warning: comparison between signed and unsigned integer expressions
commonFunctions.cc: In function 'void updateCoefficients_reg(arma::mat&, const int&, const arma::urowvec&, const arma::mat&, const arma::rowvec&, const arma::ucolvec&)':
commonFunctions.cc:440: warning: unused variable 'num_on'
commonFunctions.cc: In function 'void updateCoefficients(arma::mat&, const int&, const arma::urowvec&, const arma::mat&, const arma::rowvec&)':
commonFunctions.cc:482: warning: unused variable 'num_on'
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RcppArmadillo/include" -fPIC -g -O2 -Wall -fasm-blocks -c functionsErrorModel.cc -o functionsErrorModel.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RcppArmadillo/include" -fPIC -g -O2 -Wall -fasm-blocks -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RcppArmadillo/include" -fPIC -g -O2 -Wall -fasm-blocks -c updateFunctions_AR1.cc -o updateFunctions_AR1.o
updateFunctions_AR1.cc: In function 'void updateCoeffAndGibbsVars(arma::mat&, arma::umat&, const arma::colvec&, const arma::mat&, const arma::mat&, const arma::mat&, const double&, const unsigned int&)':
updateFunctions_AR1.cc:128: warning: comparison between signed and unsigned integer expressions
updateFunctions_AR1.cc:134: warning: comparison between signed and unsigned integer expressions
updateFunctions_AR1.cc: In function 'void updateCoeffAndGibbsVars_reg(arma::mat&, arma::umat&, const arma::colvec&, const arma::mat&, const arma::mat&, double, const double&, const unsigned int&, arma::umat&, arma::ucolvec&, arma::umat&)':
updateFunctions_AR1.cc:186: warning: comparison between signed and unsigned integer expressions
updateFunctions_AR1.cc: In function 'void calc_logMVPDF_withLinks(double&, const arma::mat&, const arma::rowvec&, arma::urowvec&)':
updateFunctions_AR1.cc:264: warning: unused variable 'num_on'
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RcppArmadillo/include" -fPIC -g -O2 -Wall -fasm-blocks -c updateFunctions_Splines.cc -o updateFunctions_Splines.o
updateFunctions_Splines.cc: In function 'void updateTaus_reg(arma::mat&, arma::colvec&, const arma::mat&, arma::urowvec&, const arma::mat&, double, double, int, double, double, double, double, int, double, arma::uvec)':
updateFunctions_Splines.cc:296: warning: comparison between signed and unsigned integer expressions
updateFunctions_Splines.cc: In function 'void updateGammaAndB_row_i_reg(arma::mat&, arma::umat&, const arma::mat&, const arma::rowvec&, const arma::colvec&, int, int, int, arma::urowvec&, const arma::ucolvec&, const arma::urowvec&, const arma::ucolvec&, const arma::uvec&)':
updateFunctions_Splines.cc:478: warning: comparison between signed and unsigned integer expressions
updateFunctions_Splines.cc: In function 'void fixedBasesFromFixedRegs(arma::umat&, arma::umat&, arma::ucolvec&, int)':
updateFunctions_Splines.cc:714: warning: comparison between signed and unsigned integer expressions
Error in tools:::file_path_as_absolute(base:::system.file(..., package = "Rcpp")) :
file '' does not exist
Calls: <Anonymous> ... RcppLdFlags -> RcppLdPath -> Rcpp.system.file -> <Anonymous>
Execution halted
g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GRENITS.so AR1_Gauss_biocond.o AR1_Student_biocond.o AR1_biocond.o PSplines_biocond.o R_C_interface.o ReadMCMCFiles.o commonFunctions.o functionsErrorModel.o matrixManipulationFunctions.o updateFunctions_AR1.o updateFunctions_Splines.o -L/Library/Frameworks/R.framework/Resources/lib/x86_64 -lRlapack -L/Library/Frameworks/R.framework/Resources/lib/x86_64 -lRblas -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Error in tools:::file_path_as_absolute(base:::system.file(..., package = "Rcpp")) :
file '' does not exist
Calls: <Anonymous> ... RcppLdFlags -> RcppLdPath -> Rcpp.system.file -> <Anonymous>
Execution halted
installing to /Users/biocbuild/bbs-2.11-bioc/meat/GRENITS.buildbin-libdir/GRENITS/libs/x86_64
* DONE (GRENITS)
>>>>>>>
>>>>>>> FIXING LINKS FOR GRENITS.buildbin-libdir/GRENITS/libs/x86_64/GRENITS.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgcc_s.1.dylib" "GRENITS.buildbin-libdir/GRENITS/libs/x86_64/GRENITS.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "GRENITS.buildbin-libdir/GRENITS/libs/x86_64/GRENITS.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.5.2.dylib" "GRENITS.buildbin-libdir/GRENITS/libs/x86_64/GRENITS.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "GRENITS.buildbin-libdir/GRENITS/libs/x86_64/GRENITS.so"