* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’ * installing *source* package ‘Cyclops’ ... ** package ‘Cyclops’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘Debian clang version 18.1.4 (1)’ make[1]: Entering directory '/tmp/RtmpazIWrA/R.INSTALL8c16c38a3a8da/Cyclops/src' clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c cyclops/CcdInterface.cpp -o cyclops/CcdInterface.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c cyclops/CompressedDataMatrix.cpp -o cyclops/CompressedDataMatrix.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c cyclops/CyclicCoordinateDescent.cpp -o cyclops/CyclicCoordinateDescent.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c cyclops/ModelData.cpp -o cyclops/ModelData.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c cyclops/Timer.cpp -o cyclops/Timer.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c cyclops/drivers/AbstractCrossValidationDriver.cpp -o cyclops/drivers/AbstractCrossValidationDriver.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c cyclops/drivers/AbstractDriver.cpp -o cyclops/drivers/AbstractDriver.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c cyclops/drivers/AbstractSelector.cpp -o cyclops/drivers/AbstractSelector.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c cyclops/drivers/AutoSearchCrossValidationDriver.cpp -o cyclops/drivers/AutoSearchCrossValidationDriver.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c cyclops/drivers/BootstrapDriver.cpp -o cyclops/drivers/BootstrapDriver.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c cyclops/drivers/BootstrapSelector.cpp -o cyclops/drivers/BootstrapSelector.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c cyclops/drivers/CrossValidationSelector.cpp -o cyclops/drivers/CrossValidationSelector.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c cyclops/drivers/WeightBasedSelector.cpp -o cyclops/drivers/WeightBasedSelector.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c cyclops/drivers/GridSearchCrossValidationDriver.cpp -o cyclops/drivers/GridSearchCrossValidationDriver.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c cyclops/drivers/HierarchyAutoSearchCrossValidationDriver.cpp -o cyclops/drivers/HierarchyAutoSearchCrossValidationDriver.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c cyclops/drivers/HierarchyGridSearchCrossValidationDriver.cpp -o cyclops/drivers/HierarchyGridSearchCrossValidationDriver.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c cyclops/drivers/ProportionSelector.cpp -o cyclops/drivers/ProportionSelector.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c cyclops/engine/AbstractModelSpecifics.cpp -o cyclops/engine/AbstractModelSpecifics.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c utils/HParSearch.cpp -o utils/HParSearch.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c IsSorted.cpp -o IsSorted.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:29: In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Sparse:26: In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/SparseCore:61: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 273 | Index count = 0; | ^ In file included from RcppExports.cpp:4: In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:29: In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Sparse:29: In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/SparseLU:35: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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] 78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree | ^ /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree | ^ In file included from RcppExports.cpp:4: In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:31: In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 72 | Index replacements = 0; | ^ In file included from RcppExports.cpp:4: In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25: In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:37: In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 246 | int count = 0; | ^ 5 warnings generated. clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c RcppModelData.cpp -o RcppModelData.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c RcppCyclopsInterface.cpp -o RcppCyclopsInterface.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c RcppIsSorted.cpp -o RcppIsSorted.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c cyclops/priors/CovariatePrior.cpp -o cyclops/priors/CovariatePrior.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -Icyclops -DR_BUILD -DDOUBLE_PRECISION -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g1 -fpic -g -O3 -Wall -pedantic -c cyclops/io/InputReader.cpp -o cyclops/io/InputReader.o clang++-18 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o Cyclops.so cyclops/CcdInterface.o cyclops/CompressedDataMatrix.o cyclops/CyclicCoordinateDescent.o cyclops/ModelData.o cyclops/Timer.o cyclops/drivers/AbstractCrossValidationDriver.o cyclops/drivers/AbstractDriver.o cyclops/drivers/AbstractSelector.o cyclops/drivers/AutoSearchCrossValidationDriver.o cyclops/drivers/BootstrapDriver.o cyclops/drivers/BootstrapSelector.o cyclops/drivers/CrossValidationSelector.o cyclops/drivers/WeightBasedSelector.o cyclops/drivers/GridSearchCrossValidationDriver.o cyclops/drivers/HierarchyAutoSearchCrossValidationDriver.o cyclops/drivers/HierarchyGridSearchCrossValidationDriver.o cyclops/drivers/ProportionSelector.o cyclops/engine/AbstractModelSpecifics.o utils/HParSearch.o IsSorted.o RcppExports.o RcppModelData.o RcppCyclopsInterface.o RcppIsSorted.o cyclops/priors/CovariatePrior.o cyclops/io/InputReader.o -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR make[1]: Leaving directory '/tmp/RtmpazIWrA/R.INSTALL8c16c38a3a8da/Cyclops/src' make[1]: Entering directory '/tmp/RtmpazIWrA/R.INSTALL8c16c38a3a8da/Cyclops/src' make[1]: Leaving directory '/tmp/RtmpazIWrA/R.INSTALL8c16c38a3a8da/Cyclops/src' installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-Cyclops/00new/Cyclops/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 * creating tarball packaged installation of ‘Cyclops’ as ‘Cyclops_3.4.0_R_x86_64-pc-linux-gnu.tar.gz’ * DONE (Cyclops)