* 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<double>&, const CppAD::vector<CppAD::ad_type_enum>&, CppAD::vector<CppAD::ad_type_enum>&)':
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<double>&, const CppAD::vector<CppAD::ad_type_enum>&, CppAD::vector<bool>&, const CppAD::vector<bool>&)':
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<T>::~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<NIMBLE_ADCLASS>::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<T>::~nimSmartPtr() [with T = NIMBLE_ADCLASS]' at ../include/nimble/smartPtrs.h:116:29,
inlined from 'nimSmartPtr<T>::~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<NIMBLE_ADCLASS>::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<T>::setPtrFromT(T*&) [with T = NIMBLE_ADCLASS]' at ../include/nimble/smartPtrs.h:55:39,
inlined from 'void nimSmartPtr<T>::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<NIMBLE_ADCLASS>::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<T>::~nimSmartPtr() [with T = NIMBLE_ADCLASS]' at ../include/nimble/smartPtrs.h:116:29,
inlined from 'nimSmartPtr<NIMBLE_ADCLASS> 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 '*<return-value>.nimSmartPtr<NIMBLE_ADCLASS>::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<Lhs, LhsMode, false, Rhs, 0, true>::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Block<Eigen::Matrix<double, -1, 1>, -1, 1, false>; Lhs = Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>; int LhsMode = 17; Rhs = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, -1, 1> >, const Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1>, -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<Scalar, Index, (internal::traits<ActualLhsTypeCleaned>::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<Scalar, Index, StorageOrder, UpLo, ConjugateLhs, ConjugateRhs, Version>::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<Scalar,Index,StorageOrder,UpLo,ConjugateLhs,ConjugateRhs,Version>::run(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../include/Eigen/Core:341:
../include/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector<Mode, 1>::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<const Eigen::Block<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose<Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1, 1, -1, -1>, 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 | <Index,Mode,
| ~~~~~~~~~~~~
329 | LhsScalar, LhsBlasTraits::NeedToConjugate,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
330 | RhsScalar, RhsBlasTraits::NeedToConjugate,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
331 | RowMajor>
| ~~~~~~~~~
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<Index, Mode, LhsScalar, ConjLhs, RhsScalar, ConjRhs, 1, Version>::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<Index,Mode,LhsScalar,ConjLhs,RhsScalar,ConjRhs,RowMajor,Version>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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<T>::~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<OptimResultNimbleList>::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<T>::~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<OptimControlNimbleList>::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<T>::~nimSmartPtr() [with T = OptimControlNimbleList]' at ../include/nimble/smartPtrs.h:116:29,
inlined from 'nimSmartPtr<T>::~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<OptimControlNimbleList>::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<T>::~nimSmartPtr() [with T = OptimResultNimbleList]' at ../include/nimble/smartPtrs.h:116:29,
inlined from 'nimSmartPtr<T>::~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<OptimResultNimbleList>::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<T>::setPtrFromT(T*&) [with T = OptimResultNimbleList]' at ../include/nimble/smartPtrs.h:55:39,
inlined from 'void nimSmartPtr<T>::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<OptimResultNimbleList>::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<T>::setPtrFromT(T*&) [with T = OptimControlNimbleList]' at ../include/nimble/smartPtrs.h:55:39,
inlined from 'void nimSmartPtr<T>::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<OptimControlNimbleList>::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<Lhs, LhsMode, false, Rhs, 0, true>::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Block<Eigen::Matrix<double, -1, 1>, -1, 1, false>; Lhs = Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>; int LhsMode = 17; Rhs = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, -1, 1> >, const Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1>, -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<Scalar, Index, (internal::traits<ActualLhsTypeCleaned>::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<Scalar, Index, StorageOrder, UpLo, ConjugateLhs, ConjugateRhs, Version>::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<Scalar,Index,StorageOrder,UpLo,ConjugateLhs,ConjugateRhs,Version>::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<Mode, 1>::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<const Eigen::Block<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose<Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1, 1, -1, -1>, 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 | <Index,Mode,
| ~~~~~~~~~~~~
329 | LhsScalar, LhsBlasTraits::NeedToConjugate,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
330 | RhsScalar, RhsBlasTraits::NeedToConjugate,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
331 | RowMajor>
| ~~~~~~~~~
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<Index, Mode, LhsScalar, ConjLhs, RhsScalar, ConjRhs, 1, Version>::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<Index,Mode,LhsScalar,ConjLhs,RhsScalar,ConjRhs,RowMajor,Version>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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)