* installing *source* package ‘PCMBaseCpp’ ... ** package ‘PCMBaseCpp’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-13 (GCC) 13.2.0’ using C++11 make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/PCMBaseCpp/src' g++-13 -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include -DARMA_DONT_USE_OPENMP -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c Rcpp.cpp -o Rcpp.o In file included from QuadraticPoly.h:27, from QuadraticPolyWhite.h:28, from Rcpp.cpp:30: SPLITT.h:2053: warning: ignoring '#pragma omp simd' [-Wunknown-pragmas] 2053 | _PRAGMA_OMP_SIMD | SPLITT.h:2071: warning: ignoring '#pragma omp simd' [-Wunknown-pragmas] 2071 | _PRAGMA_OMP_SIMD | SPLITT.h:2084: warning: ignoring '#pragma omp simd' [-Wunknown-pragmas] 2084 | _PRAGMA_OMP_SIMD | SPLITT.h:2096: warning: ignoring '#pragma omp simd' [-Wunknown-pragmas] 2096 | _PRAGMA_OMP_SIMD | SPLITT.h:2106: warning: ignoring '#pragma omp simd' [-Wunknown-pragmas] 2106 | _PRAGMA_OMP_SIMD | SPLITT.h:2132: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2132 | #pragma omp parallel | SPLITT.h:2134: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 2134 | _PRAGMA_OMP_FOR_SIMD | SPLITT.h:2145: warning: ignoring '#pragma omp barrier' [-Wunknown-pragmas] 2145 | #pragma omp barrier | SPLITT.h:2148: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 2148 | _PRAGMA_OMP_FOR_SIMD | SPLITT.h:2159: warning: ignoring '#pragma omp barrier' [-Wunknown-pragmas] 2159 | #pragma omp barrier | SPLITT.h:2162: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 2162 | _PRAGMA_OMP_FOR_SIMD | SPLITT.h:2178: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2178 | #pragma omp parallel | SPLITT.h:2187: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 2187 | _PRAGMA_OMP_FOR_SIMD | SPLITT.h:2197: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 2197 | _PRAGMA_OMP_FOR_SIMD | SPLITT.h:2223: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2223 | #pragma omp parallel | SPLITT.h:2263: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2263 | #pragma omp parallel | SPLITT.h:2265: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 2265 | _PRAGMA_OMP_FOR_SIMD | SPLITT.h:2276: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 2276 | _PRAGMA_OMP_FOR_SIMD | SPLITT.h:2290: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2290 | #pragma omp parallel | SPLITT.h:2292: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 2292 | _PRAGMA_OMP_FOR_SIMD | SPLITT.h:2300: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 2300 | _PRAGMA_OMP_FOR_SIMD | SPLITT.h:2311: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2311 | #pragma omp parallel | SPLITT.h:2320: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 2320 | _PRAGMA_OMP_FOR_SIMD | SPLITT.h:2331: warning: ignoring '#pragma omp barrier' [-Wunknown-pragmas] 2331 | #pragma omp barrier | SPLITT.h:2334: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 2334 | _PRAGMA_OMP_FOR_SIMD | SPLITT.h:2343: warning: ignoring '#pragma omp simd' [-Wunknown-pragmas] 2343 | _PRAGMA_OMP_SIMD | SPLITT.h:2357: warning: ignoring '#pragma omp simd' [-Wunknown-pragmas] 2357 | _PRAGMA_OMP_SIMD | SPLITT.h:2375: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2375 | #pragma omp parallel | SPLITT.h:2384: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 2384 | _PRAGMA_OMP_FOR_SIMD | SPLITT.h:2395: warning: ignoring '#pragma omp barrier' [-Wunknown-pragmas] 2395 | #pragma omp barrier | SPLITT.h:2398: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 2398 | _PRAGMA_OMP_FOR_SIMD | SPLITT.h:2408: warning: ignoring '#pragma omp simd' [-Wunknown-pragmas] 2408 | _PRAGMA_OMP_SIMD | SPLITT.h:2423: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2423 | #pragma omp parallel | SPLITT.h:2432: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 2432 | _PRAGMA_OMP_FOR_SIMD | SPLITT.h:2442: warning: ignoring '#pragma omp barrier' [-Wunknown-pragmas] 2442 | #pragma omp barrier | SPLITT.h:2445: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 2445 | _PRAGMA_OMP_FOR_SIMD | SPLITT.h:2463: warning: ignoring '#pragma omp simd' [-Wunknown-pragmas] 2463 | _PRAGMA_OMP_SIMD | SPLITT.h:2607: warning: ignoring '#pragma omp simd' [-Wunknown-pragmas] 2607 | _PRAGMA_OMP_SIMD | SPLITT.h:2621: warning: ignoring '#pragma omp simd' [-Wunknown-pragmas] 2621 | _PRAGMA_OMP_SIMD | SPLITT.h:2630: warning: ignoring '#pragma omp simd' [-Wunknown-pragmas] 2630 | _PRAGMA_OMP_SIMD | SPLITT.h:2638: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2638 | #pragma omp parallel | SPLITT.h:2647: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 2647 | _PRAGMA_OMP_FOR_SIMD | SPLITT.h:2656: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 2656 | _PRAGMA_OMP_FOR_SIMD | QuadraticPoly.h: In instantiation of 'bool PCMBaseCpp::IsDiagonal(const MatType&) [with MatType = arma::Mat]': QuadraticPoly.h:94:16: required from 'void PCMBaseCpp::DecomposeH(MatEigvalType&, CubeEigvecType&, CubeEigvecType&, const CubeHType&, arma::uword, double) [with MatEigvalType = arma::Mat >; CubeEigvecType = arma::Cube >; CubeHType = arma::Cube; arma::uword = unsigned int]' QuadraticPolyOU.h:152:17: required from 'arma::uword PCMBaseCpp::CondGaussianOU::SetParameter(const std::vector&, arma::uword) [with TreeType = SPLITT::OrderedTree; DataType = PCMBaseCpp::NumericTraitData; arma::uword = unsigned int]' QuadraticPolyOU.h:203:28: required from here QuadraticPoly.h:47:20: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 47 | for(int i = 0; i < X.n_rows; ++i) { | ~~^~~~~~~~~~ QuadraticPoly.h:48:26: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare] 48 | for(int j = i + 1; j < X.n_cols; ++j) { | ~~^~~~~~~~~~ SPLITT.h: In instantiation of 'void SPLITT::PostOrderTraversal::TraverseTreeMultiThreadLoopVisits() [with TraversalSpecification = PCMBaseCpp::White]': SPLITT.h:1930:46: required from 'void SPLITT::PostOrderTraversal::TraverseTree(ModeType) [with TraversalSpecification = PCMBaseCpp::White; ModeType = SPLITT::PostOrderMode]' SPLITT.h:623:28: required from 'SPLITT::TraversalTask::StateType SPLITT::TraversalTask::TraverseTree(const ParameterType&, SPLITT::uint) [with TraversalSpecification = PCMBaseCpp::White; StateType = arma::Col; ParameterType = std::vector; SPLITT::uint = unsigned int]' QuadraticPolyCommon.h:128:31: required from 'std::string PCMBaseCpp::TraversalTaskWrapper::TraverseTree(const ParameterType&, PCMBaseCpp::uint) [with TraversalSpec = PCMBaseCpp::White; std::string = std::__cxx11::basic_string; ParameterType = std::vector; PCMBaseCpp::uint = unsigned int]' Rcpp.cpp:265:53: required from here SPLITT.h:2180:8: warning: variable 'tid' set but not used [-Wunused-but-set-variable] 2180 | uint tid; | ^~~ SPLITT.h: In instantiation of 'void SPLITT::PostOrderTraversal::TraverseTreeMultiThreadLoopVisits() [with TraversalSpecification = PCMBaseCpp::BM]': SPLITT.h:1930:46: required from 'void SPLITT::PostOrderTraversal::TraverseTree(ModeType) [with TraversalSpecification = PCMBaseCpp::BM; ModeType = SPLITT::PostOrderMode]' SPLITT.h:623:28: required from 'SPLITT::TraversalTask::StateType SPLITT::TraversalTask::TraverseTree(const ParameterType&, SPLITT::uint) [with TraversalSpecification = PCMBaseCpp::BM; StateType = arma::Col; ParameterType = std::vector; SPLITT::uint = unsigned int]' QuadraticPolyCommon.h:128:31: required from 'std::string PCMBaseCpp::TraversalTaskWrapper::TraverseTree(const ParameterType&, PCMBaseCpp::uint) [with TraversalSpec = PCMBaseCpp::BM; std::string = std::__cxx11::basic_string; ParameterType = std::vector; PCMBaseCpp::uint = unsigned int]' Rcpp.cpp:335:48: required from here SPLITT.h:2180:8: warning: variable 'tid' set but not used [-Wunused-but-set-variable] SPLITT.h: In instantiation of 'void SPLITT::PostOrderTraversal::TraverseTreeMultiThreadLoopVisits() [with TraversalSpecification = PCMBaseCpp::BM1D]': SPLITT.h:1930:46: required from 'void SPLITT::PostOrderTraversal::TraverseTree(ModeType) [with TraversalSpecification = PCMBaseCpp::BM1D; ModeType = SPLITT::PostOrderMode]' SPLITT.h:623:28: required from 'SPLITT::TraversalTask::StateType SPLITT::TraversalTask::TraverseTree(const ParameterType&, SPLITT::uint) [with TraversalSpecification = PCMBaseCpp::BM1D; StateType = arma::Col; ParameterType = std::vector; SPLITT::uint = unsigned int]' QuadraticPolyCommon.h:128:31: required from 'std::string PCMBaseCpp::TraversalTaskWrapper::TraverseTree(const ParameterType&, PCMBaseCpp::uint) [with TraversalSpec = PCMBaseCpp::BM1D; std::string = std::__cxx11::basic_string; ParameterType = std::vector; PCMBaseCpp::uint = unsigned int]' Rcpp.cpp:407:52: required from here SPLITT.h:2180:8: warning: variable 'tid' set but not used [-Wunused-but-set-variable] SPLITT.h: In instantiation of 'void SPLITT::PostOrderTraversal::TraverseTreeMultiThreadLoopVisits() [with TraversalSpecification = PCMBaseCpp::OU]': SPLITT.h:1930:46: required from 'void SPLITT::PostOrderTraversal::TraverseTree(ModeType) [with TraversalSpecification = PCMBaseCpp::OU; ModeType = SPLITT::PostOrderMode]' SPLITT.h:623:28: required from 'SPLITT::TraversalTask::StateType SPLITT::TraversalTask::TraverseTree(const ParameterType&, SPLITT::uint) [with TraversalSpecification = PCMBaseCpp::OU; StateType = arma::Col; ParameterType = std::vector; SPLITT::uint = unsigned int]' QuadraticPolyCommon.h:128:31: required from 'std::string PCMBaseCpp::TraversalTaskWrapper::TraverseTree(const ParameterType&, PCMBaseCpp::uint) [with TraversalSpec = PCMBaseCpp::OU; std::string = std::__cxx11::basic_string; ParameterType = std::vector; PCMBaseCpp::uint = unsigned int]' Rcpp.cpp:477:48: required from here SPLITT.h:2180:8: warning: variable 'tid' set but not used [-Wunused-but-set-variable] SPLITT.h: In instantiation of 'void SPLITT::PostOrderTraversal::TraverseTreeMultiThreadLoopVisits() [with TraversalSpecification = PCMBaseCpp::OU1D]': SPLITT.h:1930:46: required from 'void SPLITT::PostOrderTraversal::TraverseTree(ModeType) [with TraversalSpecification = PCMBaseCpp::OU1D; ModeType = SPLITT::PostOrderMode]' SPLITT.h:623:28: required from 'SPLITT::TraversalTask::StateType SPLITT::TraversalTask::TraverseTree(const ParameterType&, SPLITT::uint) [with TraversalSpecification = PCMBaseCpp::OU1D; StateType = arma::Col; ParameterType = std::vector; SPLITT::uint = unsigned int]' QuadraticPolyCommon.h:128:31: required from 'std::string PCMBaseCpp::TraversalTaskWrapper::TraverseTree(const ParameterType&, PCMBaseCpp::uint) [with TraversalSpec = PCMBaseCpp::OU1D; std::string = std::__cxx11::basic_string; ParameterType = std::vector; PCMBaseCpp::uint = unsigned int]' Rcpp.cpp:546:52: required from here SPLITT.h:2180:8: warning: variable 'tid' set but not used [-Wunused-but-set-variable] SPLITT.h: In instantiation of 'void SPLITT::PostOrderTraversal::TraverseTreeMultiThreadLoopVisits() [with TraversalSpecification = PCMBaseCpp::JOU]': SPLITT.h:1930:46: required from 'void SPLITT::PostOrderTraversal::TraverseTree(ModeType) [with TraversalSpecification = PCMBaseCpp::JOU; ModeType = SPLITT::PostOrderMode]' SPLITT.h:623:28: required from 'SPLITT::TraversalTask::StateType SPLITT::TraversalTask::TraverseTree(const ParameterType&, SPLITT::uint) [with TraversalSpecification = PCMBaseCpp::JOU; StateType = arma::Col; ParameterType = std::vector; SPLITT::uint = unsigned int]' QuadraticPolyCommon.h:128:31: required from 'std::string PCMBaseCpp::TraversalTaskWrapper::TraverseTree(const ParameterType&, PCMBaseCpp::uint) [with TraversalSpec = PCMBaseCpp::JOU; std::string = std::__cxx11::basic_string; ParameterType = std::vector; PCMBaseCpp::uint = unsigned int]' Rcpp.cpp:620:49: required from here SPLITT.h:2180:8: warning: variable 'tid' set but not used [-Wunused-but-set-variable] SPLITT.h: In instantiation of 'void SPLITT::PostOrderTraversal::TraverseTreeMultiThreadLoopVisits() [with TraversalSpecification = PCMBaseCpp::DOU]': SPLITT.h:1930:46: required from 'void SPLITT::PostOrderTraversal::TraverseTree(ModeType) [with TraversalSpecification = PCMBaseCpp::DOU; ModeType = SPLITT::PostOrderMode]' SPLITT.h:623:28: required from 'SPLITT::TraversalTask::StateType SPLITT::TraversalTask::TraverseTree(const ParameterType&, SPLITT::uint) [with TraversalSpecification = PCMBaseCpp::DOU; StateType = arma::Col; ParameterType = std::vector; SPLITT::uint = unsigned int]' QuadraticPolyCommon.h:128:31: required from 'std::string PCMBaseCpp::TraversalTaskWrapper::TraverseTree(const ParameterType&, PCMBaseCpp::uint) [with TraversalSpec = PCMBaseCpp::DOU; std::string = std::__cxx11::basic_string; ParameterType = std::vector; PCMBaseCpp::uint = unsigned int]' Rcpp.cpp:689:49: required from here SPLITT.h:2180:8: warning: variable 'tid' set but not used [-Wunused-but-set-variable] SPLITT.h: In instantiation of 'void SPLITT::PostOrderTraversal::TraverseTreeMultiThreadLoopVisits() [with TraversalSpecification = PCMBaseCpp::MixedGaussian]': SPLITT.h:1930:46: required from 'void SPLITT::PostOrderTraversal::TraverseTree(ModeType) [with TraversalSpecification = PCMBaseCpp::MixedGaussian; ModeType = SPLITT::PostOrderMode]' SPLITT.h:623:28: required from 'SPLITT::TraversalTask::StateType SPLITT::TraversalTask::TraverseTree(const ParameterType&, SPLITT::uint) [with TraversalSpecification = PCMBaseCpp::MixedGaussian; StateType = arma::Col; ParameterType = std::vector; SPLITT::uint = unsigned int]' QuadraticPolyCommon.h:128:31: required from 'std::string PCMBaseCpp::TraversalTaskWrapper::TraverseTree(const ParameterType&, PCMBaseCpp::uint) [with TraversalSpec = PCMBaseCpp::MixedGaussian; std::string = std::__cxx11::basic_string; ParameterType = std::vector; PCMBaseCpp::uint = unsigned int]' Rcpp.cpp:762:61: required from here SPLITT.h:2180:8: warning: variable 'tid' set but not used [-Wunused-but-set-variable] SPLITT.h: In instantiation of 'void SPLITT::PostOrderTraversal::TraverseTreeMultiThreadLoopVisits() [with TraversalSpecification = PCMBaseCpp::MixedGaussian1D]': SPLITT.h:1930:46: required from 'void SPLITT::PostOrderTraversal::TraverseTree(ModeType) [with TraversalSpecification = PCMBaseCpp::MixedGaussian1D; ModeType = SPLITT::PostOrderMode]' SPLITT.h:623:28: required from 'SPLITT::TraversalTask::StateType SPLITT::TraversalTask::TraverseTree(const ParameterType&, SPLITT::uint) [with TraversalSpecification = PCMBaseCpp::MixedGaussian1D; StateType = arma::Col; ParameterType = std::vector; SPLITT::uint = unsigned int]' QuadraticPolyCommon.h:128:31: required from 'std::string PCMBaseCpp::TraversalTaskWrapper::TraverseTree(const ParameterType&, PCMBaseCpp::uint) [with TraversalSpec = PCMBaseCpp::MixedGaussian1D; std::string = std::__cxx11::basic_string; ParameterType = std::vector; PCMBaseCpp::uint = unsigned int]' Rcpp.cpp:834:63: required from here SPLITT.h:2180:8: warning: variable 'tid' set but not used [-Wunused-but-set-variable] g++-13 -std=gnu++11 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o PCMBaseCpp.so Rcpp.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/PCMBaseCpp/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/PCMBaseCpp/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/PCMBaseCpp/src' installing to /data/gannet/ripley/R/packages/tests-devel/PCMBaseCpp.Rcheck/00LOCK-PCMBaseCpp/00new/PCMBaseCpp/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 (PCMBaseCpp)