* installing *source* package ‘nimble’ ... ** package ‘nimble’ successfully unpacked and MD5 sums checked ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++-13 -std=gnu++17 accepts -g... yes working on eigen checking how to run the C++ preprocessor... g++-13 -std=gnu++17 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking Eigen/Dense usability... no checking Eigen/Dense presence... no checking for Eigen/Dense... no Using the version of Eigen provided with NIMBLE ENABLE_LIB=true configure: creating ./config.status config.status: creating inst/make/Makevars config.status: creating inst/make/Makevars_lib config.status: creating R/config.R config.status: creating src/Makevars removing debugging flags make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/nimble/inst/CppCode' /data/gannet/ripley/R/R-devel/bin/Rscript --vanilla ./customizeMakeconf.R make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/nimble/inst/CppCode' Building libnimble make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/nimble/inst/CppCode' g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 nimDerivs_atomic_dyn_ind.cpp -o nimDerivs_atomic_dyn_ind.o nimDerivs_atomic_dyn_ind.cpp: In member function 'virtual bool atomic_dyn_ind_set_class::for_type(const CppAD::vector&, const CppAD::vector&, CppAD::vector&)': nimDerivs_atomic_dyn_ind.cpp:149:10: warning: unused variable 'nx' [-Wunused-variable] 149 | size_t nx = length_x-2; | ^~ nimDerivs_atomic_dyn_ind.cpp: In member function 'virtual bool atomic_dyn_ind_set_class::rev_depend(const CppAD::vector&, const CppAD::vector&, CppAD::vector&, const CppAD::vector&)': nimDerivs_atomic_dyn_ind.cpp:178:10: warning: unused variable 'nx' [-Wunused-variable] 178 | size_t nx = length_x-2; | ^~ g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 nodeFun.cpp -o nodeFun.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 accessorClasses.cpp -o accessorClasses.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 nimbleCppAD.cpp -o nimbleCppAD.o In file included from ../include/nimble/EigenTypedefs.h:28, from ../include/nimble/nimbleCppAD.h:38, from nimbleCppAD.cpp:1: In destructor 'virtual pointedToBase::~pointedToBase()', inlined from 'void pointedToBase::removeWatcher()' at ../include/nimble/smartPtrs.h:144:14, inlined from 'void pointedToBase::removeWatcher()' at ../include/nimble/smartPtrs.h:132:8, inlined from 'nimSmartPtr::~nimSmartPtr() [with T = NIMBLE_ADCLASS]' at ../include/nimble/smartPtrs.h:116:29: ../include/nimble/smartPtrs.h:147:29: warning: 'void operator delete(void*, std::size_t)' called on pointer '*this.nimSmartPtr::realPtr' with nonzero offset 56 [-Wfree-nonheap-object] 147 | virtual ~pointedToBase() {}; | ^ In destructor 'virtual pointedToBase::~pointedToBase()', inlined from 'void pointedToBase::removeWatcher()' at ../include/nimble/smartPtrs.h:144:14, inlined from 'void pointedToBase::removeWatcher()' at ../include/nimble/smartPtrs.h:132:8, inlined from 'nimSmartPtr::~nimSmartPtr() [with T = NIMBLE_ADCLASS]' at ../include/nimble/smartPtrs.h:116:29, inlined from 'nimSmartPtr::~nimSmartPtr() [with T = NIMBLE_ADCLASS]' at ../include/nimble/smartPtrs.h:117:3: ../include/nimble/smartPtrs.h:147:29: warning: 'void operator delete(void*, std::size_t)' called on pointer '*this.nimSmartPtr::realPtr' with nonzero offset 56 [-Wfree-nonheap-object] 147 | virtual ~pointedToBase() {}; | ^ In destructor 'virtual pointedToBase::~pointedToBase()', inlined from 'void pointedToBase::removeWatcher()' at ../include/nimble/smartPtrs.h:144:14, inlined from 'void pointedToBase::removeWatcher()' at ../include/nimble/smartPtrs.h:132:8, inlined from 'void nimSmartPtr::setPtrFromT(T*&) [with T = NIMBLE_ADCLASS]' at ../include/nimble/smartPtrs.h:55:39, inlined from 'void nimSmartPtr::setPtrFromVoidPtr(void*&) [with T = NIMBLE_ADCLASS]' at ../include/nimble/smartPtrs.h:64:16: ../include/nimble/smartPtrs.h:147:29: warning: 'void operator delete(void*, std::size_t)' called on pointer '*this.nimSmartPtr::realPtr' with nonzero offset 56 [-Wfree-nonheap-object] 147 | virtual ~pointedToBase() {}; | ^ In destructor 'virtual pointedToBase::~pointedToBase()', inlined from 'void pointedToBase::removeWatcher()' at ../include/nimble/smartPtrs.h:144:14, inlined from 'void pointedToBase::removeWatcher()' at ../include/nimble/smartPtrs.h:132:8, inlined from 'nimSmartPtr::~nimSmartPtr() [with T = NIMBLE_ADCLASS]' at ../include/nimble/smartPtrs.h:116:29, inlined from 'nimSmartPtr nimDerivs_calculate(NodeVectorClassNew_derivs&, const NimArr<1, double>&)' at nimbleCppAD.cpp:115:1: ../include/nimble/smartPtrs.h:147:29: warning: 'void operator delete(void*, std::size_t)' called on pointer '*.nimSmartPtr::realPtr' with nonzero offset 56 [-Wfree-nonheap-object] 147 | virtual ~pointedToBase() {}; | ^ g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 RcppUtils.cpp -o RcppUtils.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 EigenTypedefs.cpp -o EigenTypedefs.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 eigenUsingClasses.cpp -o eigenUsingClasses.o In file included from ../include/Eigen/Core:337, from ../include/Eigen/Dense:1, from ../include/nimble/EigenTypedefs.h:24, from eigenUsingClasses.cpp:22: ../include/Eigen/src/Core/products/SelfadjointMatrixVector.h: In function 'static void Eigen::internal::selfadjoint_product_impl::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Block, -1, 1, false>; Lhs = Eigen::Block, -1, -1, false>; int LhsMode = 17; Rhs = Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Block, -1, 1, true>, -1, 1, false> >]': ../include/Eigen/src/Core/products/SelfadjointMatrixVector.h:229:7: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 227 | internal::selfadjoint_matrix_vector_product::Flags&RowMajorBit) ? RowMajor : ColMajor, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 228 | int(LhsUpLo), bool(LhsBlasTraits::NeedToConjugate), bool(RhsBlasTraits::NeedToConjugate)>::run | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 229 | ( | ^ 230 | lhs.rows(), // size | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 231 | &lhs.coeffRef(0,0), lhs.outerStride(), // lhs info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 232 | actualRhsPtr, // rhs info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 233 | actualDestPtr, // result info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 234 | actualAlpha // scale factor | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 235 | ); | ~ ../include/Eigen/src/Core/products/SelfadjointMatrixVector.h:41:6: note: by argument 4 of type 'const double*' to 'static void Eigen::internal::selfadjoint_matrix_vector_product::run(Index, const Scalar*, Index, const Scalar*, Scalar*, Scalar) [with Scalar = double; Index = long int; int StorageOrder = 0; int UpLo = 1; bool ConjugateLhs = false; bool ConjugateRhs = false; int Version = 0]' declared here 41 | void selfadjoint_matrix_vector_product::run( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../include/Eigen/Core:341: ../include/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': ../include/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ ../include/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 RcppNimbleUtils.cpp -o RcppNimbleUtils.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 Utils.cpp -o Utils.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 NamedObjects.cpp -o NamedObjects.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 ModelClassUtils.cpp -o ModelClassUtils.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 dists.cpp -o dists.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 nimDists.cpp -o nimDists.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 dllFinalizer.cpp -o dllFinalizer.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 nimbleGraph.cpp -o nimbleGraph.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 smartPtrs.cpp -o smartPtrs.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 predefinedNimbleLists.cpp -o predefinedNimbleLists.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 nimOptim.cpp -o nimOptim.o In file included from ../include/nimble/predefinedNimbleLists.h:7, from ../include/nimble/nimOptim.h:26, from nimOptim.cpp:23: In destructor 'virtual pointedToBase::~pointedToBase()', inlined from 'void pointedToBase::removeWatcher()' at ../include/nimble/smartPtrs.h:144:14, inlined from 'void pointedToBase::removeWatcher()' at ../include/nimble/smartPtrs.h:132:8, inlined from 'nimSmartPtr::~nimSmartPtr() [with T = OptimResultNimbleList]' at ../include/nimble/smartPtrs.h:116:29: ../include/nimble/smartPtrs.h:147:29: warning: 'void operator delete(void*, std::size_t)' called on pointer '*this.nimSmartPtr::realPtr' with nonzero offset 56 [-Wfree-nonheap-object] 147 | virtual ~pointedToBase() {}; | ^ In destructor 'virtual pointedToBase::~pointedToBase()', inlined from 'void pointedToBase::removeWatcher()' at ../include/nimble/smartPtrs.h:144:14, inlined from 'void pointedToBase::removeWatcher()' at ../include/nimble/smartPtrs.h:132:8, inlined from 'nimSmartPtr::~nimSmartPtr() [with T = OptimControlNimbleList]' at ../include/nimble/smartPtrs.h:116:29: ../include/nimble/smartPtrs.h:147:29: warning: 'void operator delete(void*, std::size_t)' called on pointer '*this.nimSmartPtr::realPtr' with nonzero offset 56 [-Wfree-nonheap-object] 147 | virtual ~pointedToBase() {}; | ^ In destructor 'virtual pointedToBase::~pointedToBase()', inlined from 'void pointedToBase::removeWatcher()' at ../include/nimble/smartPtrs.h:144:14, inlined from 'void pointedToBase::removeWatcher()' at ../include/nimble/smartPtrs.h:132:8, inlined from 'nimSmartPtr::~nimSmartPtr() [with T = OptimControlNimbleList]' at ../include/nimble/smartPtrs.h:116:29, inlined from 'nimSmartPtr::~nimSmartPtr() [with T = OptimControlNimbleList]' at ../include/nimble/smartPtrs.h:117:3: ../include/nimble/smartPtrs.h:147:29: warning: 'void operator delete(void*, std::size_t)' called on pointer '*this.nimSmartPtr::realPtr' with nonzero offset 56 [-Wfree-nonheap-object] 147 | virtual ~pointedToBase() {}; | ^ In destructor 'virtual pointedToBase::~pointedToBase()', inlined from 'void pointedToBase::removeWatcher()' at ../include/nimble/smartPtrs.h:144:14, inlined from 'void pointedToBase::removeWatcher()' at ../include/nimble/smartPtrs.h:132:8, inlined from 'nimSmartPtr::~nimSmartPtr() [with T = OptimResultNimbleList]' at ../include/nimble/smartPtrs.h:116:29, inlined from 'nimSmartPtr::~nimSmartPtr() [with T = OptimResultNimbleList]' at ../include/nimble/smartPtrs.h:117:3: ../include/nimble/smartPtrs.h:147:29: warning: 'void operator delete(void*, std::size_t)' called on pointer '*this.nimSmartPtr::realPtr' with nonzero offset 56 [-Wfree-nonheap-object] 147 | virtual ~pointedToBase() {}; | ^ In destructor 'virtual pointedToBase::~pointedToBase()', inlined from 'void pointedToBase::removeWatcher()' at ../include/nimble/smartPtrs.h:144:14, inlined from 'void pointedToBase::removeWatcher()' at ../include/nimble/smartPtrs.h:132:8, inlined from 'void nimSmartPtr::setPtrFromT(T*&) [with T = OptimResultNimbleList]' at ../include/nimble/smartPtrs.h:55:39, inlined from 'void nimSmartPtr::setPtrFromVoidPtr(void*&) [with T = OptimResultNimbleList]' at ../include/nimble/smartPtrs.h:64:16: ../include/nimble/smartPtrs.h:147:29: warning: 'void operator delete(void*, std::size_t)' called on pointer '*this.nimSmartPtr::realPtr' with nonzero offset 56 [-Wfree-nonheap-object] 147 | virtual ~pointedToBase() {}; | ^ In destructor 'virtual pointedToBase::~pointedToBase()', inlined from 'void pointedToBase::removeWatcher()' at ../include/nimble/smartPtrs.h:144:14, inlined from 'void pointedToBase::removeWatcher()' at ../include/nimble/smartPtrs.h:132:8, inlined from 'void nimSmartPtr::setPtrFromT(T*&) [with T = OptimControlNimbleList]' at ../include/nimble/smartPtrs.h:55:39, inlined from 'void nimSmartPtr::setPtrFromVoidPtr(void*&) [with T = OptimControlNimbleList]' at ../include/nimble/smartPtrs.h:64:16: ../include/nimble/smartPtrs.h:147:29: warning: 'void operator delete(void*, std::size_t)' called on pointer '*this.nimSmartPtr::realPtr' with nonzero offset 56 [-Wfree-nonheap-object] 147 | virtual ~pointedToBase() {}; | ^ g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 nimIntegrate.cpp -o nimIntegrate.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 nimDerivs_atomic_classes.cpp -o nimDerivs_atomic_classes.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 nimDerivs_atomic_matmult.cpp -o nimDerivs_atomic_matmult.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 nimDerivs_atomic_matinverse.cpp -o nimDerivs_atomic_matinverse.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 nimDerivs_atomic_backsolve.cpp -o nimDerivs_atomic_backsolve.o nimDerivs_atomic_backsolve.cpp: In function 'void atomic_backsolve(const MatrixXd_CppAD&, const MatrixXd_CppAD&, MatrixXd_CppAD&)': nimDerivs_atomic_backsolve.cpp:290:15: warning: comparison of integer expressions of different signedness: 'Eigen::Index' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 290 | if(A.cols() != n1) | ~~~~~~~~~^~~~~ nimDerivs_atomic_backsolve.cpp:292:15: warning: comparison of integer expressions of different signedness: 'Eigen::Index' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 292 | if(B.rows() != n1) | ~~~~~~~~~^~~~~ g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 nimDerivs_atomic_forwardsolve.cpp -o nimDerivs_atomic_forwardsolve.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 nimDerivs_atomic_cholesky.cpp -o nimDerivs_atomic_cholesky.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 nimDerivs_atomic_solve_base.cpp -o nimDerivs_atomic_solve_base.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 nimDerivs_atomic_pow_int.cpp -o nimDerivs_atomic_pow_int.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 nimDerivs_atomic_zround.cpp -o nimDerivs_atomic_zround.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 nimDerivs_atomic_log_pow_int.cpp -o nimDerivs_atomic_log_pow_int.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -fpic -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 nimDerivs_atomic_probit.cpp -o nimDerivs_atomic_probit.o linking libnimble.so Linux g++-13 -std=gnu++17 -shared -o libnimble.so nimDerivs_atomic_dyn_ind.o nodeFun.o accessorClasses.o nimbleCppAD.o RcppUtils.o EigenTypedefs.o eigenUsingClasses.o RcppNimbleUtils.o Utils.o NamedObjects.o ModelClassUtils.o dists.o nimDists.o dllFinalizer.o nimbleGraph.o smartPtrs.o predefinedNimbleLists.o nimOptim.o nimIntegrate.o nimDerivs_atomic_classes.o nimDerivs_atomic_matmult.o nimDerivs_atomic_matinverse.o nimDerivs_atomic_backsolve.o nimDerivs_atomic_forwardsolve.o nimDerivs_atomic_cholesky.o nimDerivs_atomic_solve_base.o nimDerivs_atomic_pow_int.o nimDerivs_atomic_zround.o nimDerivs_atomic_log_pow_int.o nimDerivs_atomic_probit.o rm *.o make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/nimble/inst/CppCode' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/nimble/inst/CppCode' rm -f Makeconf make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/nimble/inst/CppCode' ** libs using C++ compiler: ‘g++-13 (GCC) 13.2.0’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/nimble/src' g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I../inst/include -I/usr/local/include -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 RcppUtils.cpp -o RcppUtils.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I../inst/include -I/usr/local/include -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 dists.cpp -o dists.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I../inst/include -I/usr/local/include -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 eigenUsingClasses.cpp -o eigenUsingClasses.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I../inst/include -I/usr/local/include -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 nimble.cpp -o nimble.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DR_NO_REMAP -I../inst/include -I/usr/local/include -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 nimbleGraph.cpp -o nimbleGraph.o In file included from ../inst/include/Eigen/Core:337, from ../inst/include/Eigen/Dense:1, from ../inst/include/nimble/EigenTypedefs.h:24, from eigenUsingClasses.cpp:22: ../inst/include/Eigen/src/Core/products/SelfadjointMatrixVector.h: In function 'static void Eigen::internal::selfadjoint_product_impl::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Block, -1, 1, false>; Lhs = Eigen::Block, -1, -1, false>; int LhsMode = 17; Rhs = Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Block, -1, 1, true>, -1, 1, false> >]': ../inst/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:229:7: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 227 | internal::selfadjoint_matrix_vector_product::Flags&RowMajorBit) ? RowMajor : ColMajor, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 228 | int(LhsUpLo), bool(LhsBlasTraits::NeedToConjugate), bool(RhsBlasTraits::NeedToConjugate)>::run | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 229 | ( | ^ 230 | lhs.rows(), // size | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 231 | &lhs.coeffRef(0,0), lhs.outerStride(), // lhs info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 232 | actualRhsPtr, // rhs info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 233 | actualDestPtr, // result info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 234 | actualAlpha // scale factor | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 235 | ); | ~ ../inst/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:41:6: note: by argument 4 of type 'const double*' to 'static void Eigen::internal::selfadjoint_matrix_vector_product::run(Index, const Scalar*, Index, const Scalar*, Scalar*, Scalar) [with Scalar = double; Index = long int; int StorageOrder = 0; int UpLo = 1; bool ConjugateLhs = false; bool ConjugateRhs = false; int Version = 0]' declared here 41 | void selfadjoint_matrix_vector_product::run( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/Eigen/Core:341: ../inst/include/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': ../inst/include/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ ../inst/include/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o nimble.so RcppUtils.o dists.o eigenUsingClasses.o nimble.o nimbleGraph.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/nimble/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/nimble/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/nimble/src' installing to /data/gannet/ripley/R/packages/tests-devel/nimble.Rcheck/00LOCK-nimble/00new/nimble/libs ** R ** 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 * DONE (nimble)