* installing *source* package ‘HDPenReg’ ... ** package ‘HDPenReg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/HDPenReg/src' /usr/local/clang15/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CppFlags()"` -I'/data/gannet/ripley/R/test-clang/rtkore/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang15/include `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CxxFlags()"` -fopenmp -fpic -O3 -Wall -pedantic -frtti -c EMPenModels.cpp -o EMPenModels.o /usr/local/clang15/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CppFlags()"` -I'/data/gannet/ripley/R/test-clang/rtkore/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang15/include -fpic -O3 -Wall -pedantic -c init.c -o init.o /usr/local/clang15/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CppFlags()"` -I'/data/gannet/ripley/R/test-clang/rtkore/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang15/include `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CxxFlags()"` -fopenmp -fpic -O3 -Wall -pedantic -frtti -c larsR.cpp -o larsR.o (cd ./HDPenReg && make all) make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/HDPenReg/src/HDPenReg' (make -f lassoModels.mk) make[3]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/HDPenReg/src/HDPenReg' /usr/local/clang15/bin/clang++ -std=gnu++11 `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CxxFlags()"` -fopenmp -fpic -O3 -Wall -pedantic -frtti -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CppFlags()"` -I'/data/gannet/ripley/R/test-clang/rtkore/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang15/include lassoModels/LassoSolver.cpp -c -o lassoModels/LassoSolver.o /usr/local/clang15/bin/clang++ -std=gnu++11 `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CxxFlags()"` -fopenmp -fpic -O3 -Wall -pedantic -frtti -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CppFlags()"` -I'/data/gannet/ripley/R/test-clang/rtkore/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang15/include lassoModels/FusedLassoPenalty.cpp -c -o lassoModels/FusedLassoPenalty.o In file included from lassoModels/LassoSolver.cpp:35: In file included from lassoModels/LassoSolver.h:39: In file included from lassoModels/IPenalizedSolver.h:39: In file included from lassoModels/IPenalty.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:156: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Arrays.h:93: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Arrays/include/STK_Display.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ExportToCsv.h:40: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ReadWriteCsv.h:42: /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_Variable.h:247:11: warning: variable 'code' set but not used [-Wunused-but-set-variable] { int code = baseIdx; ^ In file included from lassoModels/LassoSolver.cpp:35: In file included from lassoModels/LassoSolver.h:39: In file included from lassoModels/IPenalizedSolver.h:39: In file included from lassoModels/IPenalty.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:162: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Algebra.h:82: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_MultiLeastSquare.h:39: /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_ILeastSquare.h:97:39: warning: returning reference to local temporary object [-Wreturn-stack-address] Real const& rank() const { return rank_;} ^~~~~ lassoModels/LassoSolver.cpp:154:9: warning: unused variable 'cgiter' [-Wunused-variable] int cgiter = cgsolver_.run(); ^ In file included from lassoModels/FusedLassoPenalty.cpp:35: In file included from lassoModels/FusedLassoPenalty.h:39: In file included from lassoModels/PenalizedModels.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:156: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Arrays.h:93: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Arrays/include/STK_Display.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ExportToCsv.h:40: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ReadWriteCsv.h:42: /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_Variable.h:247:11: warning: variable 'code' set but not used [-Wunused-but-set-variable] { int code = baseIdx; ^ In file included from lassoModels/FusedLassoPenalty.cpp:35: In file included from lassoModels/FusedLassoPenalty.h:39: In file included from lassoModels/PenalizedModels.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:162: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Algebra.h:82: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_MultiLeastSquare.h:39: /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_ILeastSquare.h:97:39: warning: returning reference to local temporary object [-Wreturn-stack-address] Real const& rank() const { return rank_;} ^~~~~ 2 warnings generated. 3 warnings generated. /usr/local/clang15/bin/clang++ -std=gnu++11 `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CxxFlags()"` -fopenmp -fpic -O3 -Wall -pedantic -frtti -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CppFlags()"` -I'/data/gannet/ripley/R/test-clang/rtkore/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang15/include lassoModels/FusedLassoSolver.cpp -c -o lassoModels/FusedLassoSolver.o /usr/local/clang15/bin/clang++ -std=gnu++11 `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CxxFlags()"` -fopenmp -fpic -O3 -Wall -pedantic -frtti -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CppFlags()"` -I'/data/gannet/ripley/R/test-clang/rtkore/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang15/include lassoModels/LogisticLassoSolver.cpp -c -o lassoModels/LogisticLassoSolver.o /usr/local/clang15/bin/clang++ -std=gnu++11 `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CxxFlags()"` -fopenmp -fpic -O3 -Wall -pedantic -frtti -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CppFlags()"` -I'/data/gannet/ripley/R/test-clang/rtkore/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang15/include lassoModels/LogisticFusedLassoSolver.cpp -c -o lassoModels/LogisticFusedLassoSolver.o /usr/local/clang15/bin/clang++ -std=gnu++11 `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CxxFlags()"` -fopenmp -fpic -O3 -Wall -pedantic -frtti -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CppFlags()"` -I'/data/gannet/ripley/R/test-clang/rtkore/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang15/include lassoModels/CV.cpp -c -o lassoModels/CV.o In file included from lassoModels/FusedLassoSolver.cpp:35: In file included from lassoModels/FusedLassoSolver.h:39: In file included from lassoModels/IPenalizedSolver.h:39: In file included from lassoModels/IPenalty.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:156: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Arrays.h:93: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Arrays/include/STK_Display.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ExportToCsv.h:40: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ReadWriteCsv.h:42: /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_Variable.h:247:11: warning: variable 'code' set but not used [-Wunused-but-set-variable] { int code = baseIdx; ^ In file included from lassoModels/FusedLassoSolver.cpp:35: In file included from lassoModels/FusedLassoSolver.h:39: In file included from lassoModels/IPenalizedSolver.h:39: In file included from lassoModels/IPenalty.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:162: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Algebra.h:82: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_MultiLeastSquare.h:39: /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_ILeastSquare.h:97:39: warning: returning reference to local temporary object [-Wreturn-stack-address] Real const& rank() const { return rank_;} ^~~~~ lassoModels/FusedLassoSolver.cpp:186:9: warning: unused variable 'cgiter' [-Wunused-variable] int cgiter = cgsolver_.run(); ^ In file included from lassoModels/LogisticLassoSolver.cpp:36: In file included from lassoModels/LogisticLassoSolver.h:39: In file included from lassoModels/IPenalizedSolver.h:39: In file included from lassoModels/IPenalty.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:156: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Arrays.h:93: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Arrays/include/STK_Display.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ExportToCsv.h:40: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ReadWriteCsv.h:42: /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_Variable.h:247:11: warning: variable 'code' set but not used [-Wunused-but-set-variable] { int code = baseIdx; ^ In file included from lassoModels/LogisticLassoSolver.cpp:36: In file included from lassoModels/LogisticLassoSolver.h:39: In file included from lassoModels/IPenalizedSolver.h:39: In file included from lassoModels/IPenalty.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:162: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Algebra.h:82: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_MultiLeastSquare.h:39: /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_ILeastSquare.h:97:39: warning: returning reference to local temporary object [-Wreturn-stack-address] Real const& rank() const { return rank_;} ^~~~~ In file included from lassoModels/LogisticFusedLassoSolver.cpp:37: In file included from lassoModels/LogisticFusedLassoSolver.h:40: In file included from lassoModels/IPenalizedSolver.h:39: In file included from lassoModels/IPenalty.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:156: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Arrays.h:93: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Arrays/include/STK_Display.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ExportToCsv.h:40: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ReadWriteCsv.h:42: /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_Variable.h:247:11: warning: variable 'code' set but not used [-Wunused-but-set-variable] { int code = baseIdx; ^ In file included from lassoModels/CV.cpp:36: In file included from lassoModels/CV.h:39: In file included from lassoModels/IAlgo.h:39: In file included from lassoModels/PenalizedModels.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:156: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Arrays.h:93: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Arrays/include/STK_Display.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ExportToCsv.h:40: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ReadWriteCsv.h:42: /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_Variable.h:247:11: warning: variable 'code' set but not used [-Wunused-but-set-variable] { int code = baseIdx; ^ lassoModels/LogisticLassoSolver.cpp:148:9: warning: unused variable 'cgiter' [-Wunused-variable] int cgiter = cgsolver_.run(); ^ In file included from lassoModels/LogisticFusedLassoSolver.cpp:37: In file included from lassoModels/LogisticFusedLassoSolver.h:40: In file included from lassoModels/IPenalizedSolver.h:39: In file included from lassoModels/IPenalty.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:162: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Algebra.h:82: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_MultiLeastSquare.h:39: /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_ILeastSquare.h:97:39: warning: returning reference to local temporary object [-Wreturn-stack-address] Real const& rank() const { return rank_;} ^~~~~ In file included from lassoModels/CV.cpp:36: In file included from lassoModels/CV.h:39: In file included from lassoModels/IAlgo.h:39: In file included from lassoModels/PenalizedModels.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:162: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Algebra.h:82: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_MultiLeastSquare.h:39: /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_ILeastSquare.h:97:39: warning: returning reference to local temporary object [-Wreturn-stack-address] Real const& rank() const { return rank_;} ^~~~~ lassoModels/LogisticFusedLassoSolver.cpp:185:9: warning: unused variable 'cgiter' [-Wunused-variable] int cgiter = cgsolver_.run(); ^ /usr/local/clang15/bin/clang++ -std=gnu++11 `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CxxFlags()"` -fopenmp -fpic -O3 -Wall -pedantic -frtti -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CppFlags()"` -I'/data/gannet/ripley/R/test-clang/rtkore/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang15/include EMmain.cpp -c -o EMmain.o 3 warnings generated. /usr/local/clang15/bin/clang++ -std=gnu++11 `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CxxFlags()"` -fopenmp -fpic -O3 -Wall -pedantic -frtti -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CppFlags()"` -I'/data/gannet/ripley/R/test-clang/rtkore/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang15/include EMCVmain.cpp -c -o EMCVmain.o 2 warnings generated. 3 warnings generated. 3 warnings generated. In file included from EMmain.cpp:1: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:156: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Arrays.h:93: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Arrays/include/STK_Display.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ExportToCsv.h:40: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ReadWriteCsv.h:42: /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_Variable.h:247:11: warning: variable 'code' set but not used [-Wunused-but-set-variable] { int code = baseIdx; ^ In file included from EMmain.cpp:1: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:162: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Algebra.h:82: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_MultiLeastSquare.h:39: /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_ILeastSquare.h:97:39: warning: returning reference to local temporary object [-Wreturn-stack-address] Real const& rank() const { return rank_;} ^~~~~ EMmain.cpp:238:8: warning: unused variable 'interceptC' [-Wunused-variable] bool interceptC=as(intercept); ^ In file included from EMCVmain.cpp:1: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:156: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Arrays.h:93: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Arrays/include/STK_Display.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ExportToCsv.h:40: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ReadWriteCsv.h:42: /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_Variable.h:247:11: warning: variable 'code' set but not used [-Wunused-but-set-variable] { int code = baseIdx; ^ In file included from EMCVmain.cpp:1: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:162: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Algebra.h:82: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_MultiLeastSquare.h:39: /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_ILeastSquare.h:97:39: warning: returning reference to local temporary object [-Wreturn-stack-address] Real const& rank() const { return rank_;} ^~~~~ 3 warnings generated. 2 warnings generated. ar -r lib/libHD.a lassoModels/LassoSolver.o lassoModels/FusedLassoPenalty.o lassoModels/FusedLassoSolver.o lassoModels/LogisticLassoSolver.o lassoModels/LogisticFusedLassoSolver.o lassoModels/CV.o EMmain.o EMCVmain.o ar: creating lib/libHD.a make[3]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/HDPenReg/src/HDPenReg' (make -f lars.mk) make[3]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/HDPenReg/src/HDPenReg' /usr/local/clang15/bin/clang++ -std=gnu++11 `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CxxFlags()"` -fopenmp -fpic -O3 -Wall -pedantic -frtti -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CppFlags()"` -I'/data/gannet/ripley/R/test-clang/rtkore/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang15/include -DSTKBASEARRAYS=1 lars/Lars.cpp -c -o lars/Lars.o /usr/local/clang15/bin/clang++ -std=gnu++11 `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CxxFlags()"` -fopenmp -fpic -O3 -Wall -pedantic -frtti -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CppFlags()"` -I'/data/gannet/ripley/R/test-clang/rtkore/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang15/include -DSTKBASEARRAYS=1 lars/Path.cpp -c -o lars/Path.o In file included from lars/Lars.cpp:35: In file included from lars/../larsRmain.h:4: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:156: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Arrays.h:93: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Arrays/include/STK_Display.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ExportToCsv.h:40: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ReadWriteCsv.h:42: /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_Variable.h:247:11: warning: variable 'code' set but not used [-Wunused-but-set-variable] { int code = baseIdx; ^ In file included from lars/Lars.cpp:35: In file included from lars/../larsRmain.h:4: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:162: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Algebra.h:82: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_MultiLeastSquare.h:39: /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_ILeastSquare.h:97:39: warning: returning reference to local temporary object [-Wreturn-stack-address] Real const& rank() const { return rank_;} ^~~~~ /usr/local/clang15/bin/clang++ -std=gnu++11 `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CxxFlags()"` -fopenmp -fpic -O3 -Wall -pedantic -frtti -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CppFlags()"` -I'/data/gannet/ripley/R/test-clang/rtkore/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang15/include -DSTKBASEARRAYS=1 lars/PathState.cpp -c -o lars/PathState.o In file included from lars/Path.cpp:35: In file included from lars/../larsRmain.h:4: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:156: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Arrays.h:93: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Arrays/include/STK_Display.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ExportToCsv.h:40: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ReadWriteCsv.h:42: /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_Variable.h:247:11: warning: variable 'code' set but not used [-Wunused-but-set-variable] { int code = baseIdx; ^ In file included from lars/Path.cpp:35: In file included from lars/../larsRmain.h:4: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:162: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Algebra.h:82: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_MultiLeastSquare.h:39: /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_ILeastSquare.h:97:39: warning: returning reference to local temporary object [-Wreturn-stack-address] Real const& rank() const { return rank_;} ^~~~~ 2 warnings generated. /usr/local/clang15/bin/clang++ -std=gnu++11 `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CxxFlags()"` -fopenmp -fpic -O3 -Wall -pedantic -frtti -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CppFlags()"` -I'/data/gannet/ripley/R/test-clang/rtkore/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang15/include -DSTKBASEARRAYS=1 lars/functions.cpp -c -o lars/functions.o In file included from lars/PathState.cpp:35: In file included from lars/../larsRmain.h:4: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:156: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Arrays.h:93: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Arrays/include/STK_Display.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ExportToCsv.h:40: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ReadWriteCsv.h:42: /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_Variable.h:247:11: warning: variable 'code' set but not used [-Wunused-but-set-variable] { int code = baseIdx; ^ In file included from lars/PathState.cpp:35: In file included from lars/../larsRmain.h:4: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:162: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Algebra.h:82: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_MultiLeastSquare.h:39: /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_ILeastSquare.h:97:39: warning: returning reference to local temporary object [-Wreturn-stack-address] Real const& rank() const { return rank_;} ^~~~~ 2 warnings generated. /usr/local/clang15/bin/clang++ -std=gnu++11 `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CxxFlags()"` -fopenmp -fpic -O3 -Wall -pedantic -frtti -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CppFlags()"` -I'/data/gannet/ripley/R/test-clang/rtkore/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang15/include -DSTKBASEARRAYS=1 lars/Fusion.cpp -c -o lars/Fusion.o 2 warnings generated. In file included from lars/functions.cpp:35: In file included from lars/../larsRmain.h:4: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:156: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Arrays.h:93: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Arrays/include/STK_Display.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ExportToCsv.h:40: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ReadWriteCsv.h:42: /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_Variable.h:247:11: warning: variable 'code' set but not used [-Wunused-but-set-variable] { int code = baseIdx; ^ In file included from lars/functions.cpp:35: In file included from lars/../larsRmain.h:4: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:162: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Algebra.h:82: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_MultiLeastSquare.h:39: /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_ILeastSquare.h:97:39: warning: returning reference to local temporary object [-Wreturn-stack-address] Real const& rank() const { return rank_;} ^~~~~ /usr/local/clang15/bin/clang++ -std=gnu++11 `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CxxFlags()"` -fopenmp -fpic -O3 -Wall -pedantic -frtti -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CppFlags()"` -I'/data/gannet/ripley/R/test-clang/rtkore/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang15/include -DSTKBASEARRAYS=1 lars/Cvlars.cpp -c -o lars/Cvlars.o 2 warnings generated. /usr/local/clang15/bin/clang++ -std=gnu++11 `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CxxFlags()"` -fopenmp -fpic -O3 -Wall -pedantic -frtti -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `/data/gannet/ripley/R/R-clang/bin/Rscript -e "rtkore:::CppFlags()"` -I'/data/gannet/ripley/R/test-clang/rtkore/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang15/include -DSTKBASEARRAYS=1 larsRmain.cpp -c -o larsRmain.o In file included from lars/Fusion.cpp:35: In file included from lars/../larsRmain.h:4: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:156: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Arrays.h:93: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Arrays/include/STK_Display.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ExportToCsv.h:40: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ReadWriteCsv.h:42: /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_Variable.h:247:11: warning: variable 'code' set but not used [-Wunused-but-set-variable] { int code = baseIdx; ^ In file included from lars/Fusion.cpp:35: In file included from lars/../larsRmain.h:4: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:162: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Algebra.h:82: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_MultiLeastSquare.h:39: /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_ILeastSquare.h:97:39: warning: returning reference to local temporary object [-Wreturn-stack-address] Real const& rank() const { return rank_;} ^~~~~ lars/Fusion.cpp:52:23: warning: field 'maxSteps_' is uninitialized when used here [-Wuninitialized] , path_(maxSteps_) ^ In file included from lars/Cvlars.cpp:35: In file included from lars/../larsRmain.h:4: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:156: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Arrays.h:93: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Arrays/include/STK_Display.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ExportToCsv.h:40: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ReadWriteCsv.h:42: /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_Variable.h:247:11: warning: variable 'code' set but not used [-Wunused-but-set-variable] { int code = baseIdx; ^ In file included from lars/Cvlars.cpp:35: In file included from lars/../larsRmain.h:4: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:162: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Algebra.h:82: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_MultiLeastSquare.h:39: /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_ILeastSquare.h:97:39: warning: returning reference to local temporary object [-Wreturn-stack-address] Real const& rank() const { return rank_;} ^~~~~ 3 warnings generated. In file included from larsRmain.cpp:1: In file included from ./larsRmain.h:4: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:156: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Arrays.h:93: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Arrays/include/STK_Display.h:39: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ExportToCsv.h:40: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_ReadWriteCsv.h:42: /data/gannet/ripley/R/test-clang/rtkore/projects/DManager/include/STK_Variable.h:247:11: warning: variable 'code' set but not used [-Wunused-but-set-variable] { int code = baseIdx; ^ In file included from larsRmain.cpp:1: In file included from ./larsRmain.h:4: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKpp.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/RTKppForward.h:41: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/STKpp.h:162: In file included from /data/gannet/ripley/R/test-clang/rtkore/include/Algebra.h:82: In file included from /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_MultiLeastSquare.h:39: /data/gannet/ripley/R/test-clang/rtkore/projects/Algebra/include/STK_ILeastSquare.h:97:39: warning: returning reference to local temporary object [-Wreturn-stack-address] Real const& rank() const { return rank_;} ^~~~~ 2 warnings generated. 2 warnings generated. ar -r lib/libEM.a lars/Lars.o lars/Path.o lars/PathState.o lars/functions.o lars/Fusion.o lars/Cvlars.o larsRmain.o ar: creating lib/libEM.a make[3]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/HDPenReg/src/HDPenReg' make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/HDPenReg/src/HDPenReg' (cd ./HDPenReg && make clean) make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/HDPenReg/src/HDPenReg' (rm -f lassoModels/*.o) (rm -f ./*.o) (rm -f lars/*.o) make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/HDPenReg/src/HDPenReg' /usr/local/clang15/bin/clang++ -std=gnu++11 -shared -L/usr/local/clang/lib64 -L/usr/local/clang15/lib -L/usr/local/lib64 -o HDPenReg.so EMPenModels.o init.o larsR.o ./HDPenReg/lib/libHD.a ./HDPenReg/lib/libEM.a -fopenmp -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lgfortran -lm -lquadmath make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/HDPenReg/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/HDPenReg/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/HDPenReg/src' installing to /data/gannet/ripley/R/packages/tests-clang/HDPenReg.Rcheck/00LOCK-HDPenReg/00new/HDPenReg/libs ** R ** 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 (HDPenReg)