############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf RNAdecay.buildbin-libdir && mkdir RNAdecay.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh RNAdecay_1.24.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R RNAdecay.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=RNAdecay.buildbin-libdir RNAdecay_1.24.0.tar.gz' >>>>>>> * installing *source* package ‘RNAdecay’ ... ** using staged installation rm -rf *o ** libs /Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_dExp_1sse.cpp',safebounds=FALSE,safeunload=FALSE)" using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_dExp_1sse -DCPPAD_FRAMEWORK -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general_dExp_1sse.cpp -o general_dExp_1sse.o In file included from general_dExp_1sse.cpp:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include/TMB.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] Index count = 0; ^ In file included from general_dExp_1sse.cpp:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include/TMB.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_dExp_1sse.so general_dExp_1sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation [1] 0 /Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_Exp_1sse.cpp',safebounds=FALSE,safeunload=FALSE)" using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_Exp_1sse -DCPPAD_FRAMEWORK -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general_Exp_1sse.cpp -o general_Exp_1sse.o In file included from general_Exp_1sse.cpp:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include/TMB.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] Index count = 0; ^ In file included from general_Exp_1sse.cpp:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include/TMB.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_Exp_1sse.so general_Exp_1sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation [1] 0 /Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_dExp_2sse.cpp',safebounds=FALSE,safeunload=FALSE)" using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_dExp_2sse -DCPPAD_FRAMEWORK -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general_dExp_2sse.cpp -o general_dExp_2sse.o In file included from general_dExp_2sse.cpp:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include/TMB.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] Index count = 0; ^ In file included from general_dExp_2sse.cpp:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include/TMB.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_dExp_2sse.so general_dExp_2sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation [1] 0 /Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_Exp_2sse.cpp',safebounds=FALSE,safeunload=FALSE)" using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_Exp_2sse -DCPPAD_FRAMEWORK -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general_Exp_2sse.cpp -o general_Exp_2sse.o In file included from general_Exp_2sse.cpp:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include/TMB.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] Index count = 0; ^ In file included from general_Exp_2sse.cpp:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include/TMB.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_Exp_2sse.so general_Exp_2sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation [1] 0 /Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_dExp_3sse.cpp',safebounds=FALSE,safeunload=FALSE)" using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_dExp_3sse -DCPPAD_FRAMEWORK -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general_dExp_3sse.cpp -o general_dExp_3sse.o In file included from general_dExp_3sse.cpp:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include/TMB.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] Index count = 0; ^ In file included from general_dExp_3sse.cpp:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include/TMB.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_dExp_3sse.so general_dExp_3sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation [1] 0 /Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_Exp_3sse.cpp',safebounds=FALSE,safeunload=FALSE)" using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_Exp_3sse -DCPPAD_FRAMEWORK -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general_Exp_3sse.cpp -o general_Exp_3sse.o In file included from general_Exp_3sse.cpp:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include/TMB.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] Index count = 0; ^ In file included from general_Exp_3sse.cpp:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include/TMB.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_Exp_3sse.so general_Exp_3sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation [1] 0 /Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_dExp_4sse.cpp',safebounds=FALSE,safeunload=FALSE)" using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_dExp_4sse -DCPPAD_FRAMEWORK -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general_dExp_4sse.cpp -o general_dExp_4sse.o In file included from general_dExp_4sse.cpp:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include/TMB.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] Index count = 0; ^ In file included from general_dExp_4sse.cpp:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include/TMB.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_dExp_4sse.so general_dExp_4sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation [1] 0 /Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_Exp_4sse.cpp',safebounds=FALSE,safeunload=FALSE)" using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_Exp_4sse -DCPPAD_FRAMEWORK -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general_Exp_4sse.cpp -o general_Exp_4sse.o In file included from general_Exp_4sse.cpp:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include/TMB.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] Index count = 0; ^ In file included from general_Exp_4sse.cpp:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/TMB/include/TMB.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_Exp_4sse.so general_Exp_4sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation [1] 0 installing to /Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/RNAdecay.buildbin-libdir/00LOCK-RNAdecay/00new/RNAdecay/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** 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 (RNAdecay) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_1sse.so >>>>>>> >>>>>>> Paths before fix: RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_1sse.so: general_Exp_1sse.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_1sse.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_1sse.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_1sse.so" >>>>>>> Paths after fix: RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_1sse.so: general_Exp_1sse.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_2sse.so >>>>>>> >>>>>>> Paths before fix: RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_2sse.so: general_Exp_2sse.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_2sse.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_2sse.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_2sse.so" >>>>>>> Paths after fix: RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_2sse.so: general_Exp_2sse.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_3sse.so >>>>>>> >>>>>>> Paths before fix: RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_3sse.so: general_Exp_3sse.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_3sse.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_3sse.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_3sse.so" >>>>>>> Paths after fix: RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_3sse.so: general_Exp_3sse.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_4sse.so >>>>>>> >>>>>>> Paths before fix: RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_4sse.so: general_Exp_4sse.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_4sse.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_4sse.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_4sse.so" >>>>>>> Paths after fix: RNAdecay.buildbin-libdir/RNAdecay/libs/general_Exp_4sse.so: general_Exp_4sse.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_1sse.so >>>>>>> >>>>>>> Paths before fix: RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_1sse.so: general_dExp_1sse.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_1sse.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_1sse.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_1sse.so" >>>>>>> Paths after fix: RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_1sse.so: general_dExp_1sse.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_2sse.so >>>>>>> >>>>>>> Paths before fix: RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_2sse.so: general_dExp_2sse.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_2sse.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_2sse.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_2sse.so" >>>>>>> Paths after fix: RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_2sse.so: general_dExp_2sse.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_3sse.so >>>>>>> >>>>>>> Paths before fix: RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_3sse.so: general_dExp_3sse.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_3sse.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_3sse.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_3sse.so" >>>>>>> Paths after fix: RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_3sse.so: general_dExp_3sse.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_4sse.so >>>>>>> >>>>>>> Paths before fix: RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_4sse.so: general_dExp_4sse.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_4sse.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_4sse.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_4sse.so" >>>>>>> Paths after fix: RNAdecay.buildbin-libdir/RNAdecay/libs/general_dExp_4sse.so: general_dExp_4sse.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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)