############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf miloR.buildbin-libdir && mkdir miloR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh miloR_2.3.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R miloR.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=miloR.buildbin-libdir miloR_2.3.0.tar.gz' >>>>>>> * installing *source* package ‘miloR’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c computeMatrices.cpp -o computeMatrices.o computeMatrices.cpp:246:9: warning: variable 'stot' set but not used [-Wunused-but-set-variable] int stot = 0; ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c fitGeneticPLGlmm.cpp -o fitGeneticPLGlmm.o fitGeneticPLGlmm.cpp:113:12: warning: variable '_intercept' set but not used [-Wunused-but-set-variable] double _intercept = constval; // intercept for HE regression ^ fitGeneticPLGlmm.cpp:200:10: warning: unused variable '_phi_est' [-Wunused-variable] bool _phi_est = true; // control if we re-estimate phi or not ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c fitPLGlmm.cpp -o fitPLGlmm.o fitPLGlmm.cpp:106:12: warning: variable '_intercept' set but not used [-Wunused-but-set-variable] double _intercept = constval; // intercept for HE regression?? need a better estimate. ^ fitPLGlmm.cpp:172:10: warning: unused variable '_phi_est' [-Wunused-variable] bool _phi_est = true; // control if we re-estimate phi or not ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c inference.cpp -o inference.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c invertPseudoVar.cpp -o invertPseudoVar.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c multiP.cpp -o multiP.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c paramEst.cpp -o paramEst.o paramEst.cpp:36:33: warning: left operand of comma operator has no effect [-Wunused-value] double rhs = 0.5 * mid1[0, 0]; ^ paramEst.cpp:172:12: warning: unused variable 'lambda' [-Wunused-variable] double lambda = 1e-1; ^ paramEst.cpp:173:12: warning: unused variable 'lambda_step' [-Wunused-variable] double lambda_step = 10; ^ paramEst.cpp:174:12: warning: unused variable '_illcond_eps' [-Wunused-variable] double _illcond_eps = 1e-6; ^ paramEst.cpp:175:12: warning: unused variable '_lcond_target' [-Wunused-variable] double _lcond_target = 1e-5; ^ paramEst.cpp:241:19: warning: unused variable 'nsq' [-Wunused-variable] unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix, no diag ^ paramEst.cpp:242:18: warning: unused variable 'i' [-Wunused-variable] unsigned int i, j; // Declare loop variables i and j for OpenMP ^ paramEst.cpp:242:21: warning: unused variable 'j' [-Wunused-variable] unsigned int i, j; // Declare loop variables i and j for OpenMP ^ paramEst.cpp:243:12: warning: unused variable '_ycovij' [-Wunused-variable] double _ycovij; // Declare temp_value ^ paramEst.cpp:276:19: warning: unused variable 'nsq' [-Wunused-variable] unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix ^ paramEst.cpp:277:18: warning: unused variable 'i' [-Wunused-variable] unsigned int i, j; // Declare loop variables i and j for OpenMP ^ paramEst.cpp:277:21: warning: unused variable 'j' [-Wunused-variable] unsigned int i, j; // Declare loop variables i and j for OpenMP ^ paramEst.cpp:278:12: warning: unused variable '_ycovij' [-Wunused-variable] double _ycovij; // Declare temp_value ^ paramEst.cpp:342:19: warning: unused variable 'nsq' [-Wunused-variable] unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix ^ paramEst.cpp:409:19: warning: unused variable 'nsq' [-Wunused-variable] unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix ^ paramEst.cpp:410:18: warning: unused variable 'i' [-Wunused-variable] unsigned int i, j; // Declare loop variables i and j for OpenMP ^ paramEst.cpp:410:21: warning: unused variable 'j' [-Wunused-variable] unsigned int i, j; // Declare loop variables i and j for OpenMP ^ paramEst.cpp:442:19: warning: unused variable 'nsq' [-Wunused-variable] unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix ^ paramEst.cpp:443:18: warning: unused variable 'i' [-Wunused-variable] unsigned int i, j; // Declare loop variables i and j for OpenMP ^ paramEst.cpp:443:21: warning: unused variable 'j' [-Wunused-variable] unsigned int i, j; // Declare loop variables i and j for OpenMP ^ paramEst.cpp:774:12: warning: unused variable 'half_logli' [-Wunused-variable] double half_logli = nbLogLik(mu, disp/2.0, y) - normlihood; ^ paramEst.cpp:779:10: warning: unused variable 'comp_vals' [-Wunused-variable] bool comp_vals = false; ^ 22 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c pseudovarPartial.cpp -o pseudovarPartial.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c solveQP.cpp -o solveQP.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c utils.cpp -o utils.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o miloR.so RcppExports.o computeMatrices.o fitGeneticPLGlmm.o fitPLGlmm.o inference.o invertPseudoVar.o multiP.o paramEst.o pseudovarPartial.o solveQP.o utils.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.21-bioc/meat/miloR.buildbin-libdir/00LOCK-miloR/00new/miloR/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘graph’ in package ‘miloR’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (miloR) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR miloR.buildbin-libdir/miloR/libs/miloR.so >>>>>>> >>>>>>> Paths before fix: miloR.buildbin-libdir/miloR/libs/miloR.so: miloR.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.5.0, current version 4.5.0) /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "miloR.buildbin-libdir/miloR/libs/miloR.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "miloR.buildbin-libdir/miloR/libs/miloR.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "miloR.buildbin-libdir/miloR/libs/miloR.so" install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "miloR.buildbin-libdir/miloR/libs/miloR.so" install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "miloR.buildbin-libdir/miloR/libs/miloR.so" >>>>>>> Paths after fix: miloR.buildbin-libdir/miloR/libs/miloR.so: miloR.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.5.0, current version 4.5.0) /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)