Install log for 'tinyVAST'

* installing *source* package ‘tinyVAST’ ...
** this is package ‘tinyVAST’ version ‘1.2.0’
** package ‘tinyVAST’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/tinyVAST/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DTMBAD_FRAMEWORK -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/TMB/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 tinyVAST.cpp -o tinyVAST.o
In file included from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/util/ConfigureVectorization.h:346,
                 from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Core:22,
                 from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Dense:1,
                 from /data/gannet/ripley/R/test-dev/TMB/include/TMB.hpp:92,
                 from tinyVAST.cpp:2:
In function ‘__m128i _mm_load_si128(const __m128i*)’,
    inlined from ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<__vector(2) long long int, 0>]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:717:126,
    inlined from ‘Packet Eigen::internal::ploadt(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<__vector(2) long long int, 0>; int Alignment = 16]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:967:25,
    inlined from ‘PacketType Eigen::internal::evaluator<Eigen::PlainObjectBase<Derived> >::packet(Eigen::Index) const [with int LoadMode = 16; PacketType = Eigen::internal::eigen_packet_wrapper<__vector(2) long long int, 0>; Derived = Eigen::Array<int, -1, 1>]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:245:40,
    inlined from ‘PacketType Eigen::internal::binary_evaluator<Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>, Eigen::internal::IndexBased, Eigen::internal::IndexBased>::packet(Eigen::Index) const [with int LoadMode = 16; PacketType = Eigen::internal::eigen_packet_wrapper<__vector(2) long long int, 0>; BinaryOp = Eigen::internal::scalar_product_op<int, int>; Lhs = const Eigen::Array<int, -1, 1>; Rhs = const Eigen::Array<int, -1, 1>]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:790:80,
    inlined from ‘static Eigen::internal::redux_impl<Func, Evaluator, 3, 0>::Scalar Eigen::internal::redux_impl<Func, Evaluator, 3, 0>::run(const Evaluator&, const Func&, const XprType&) [with XprType = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<int, int>, const Eigen::Array<int, -1, 1>, const Eigen::Array<int, -1, 1> >; Func = Eigen::internal::scalar_sum_op<int, int>; Evaluator = Eigen::internal::redux_evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<int, int>, const Eigen::Array<int, -1, 1>, const Eigen::Array<int, -1, 1> > >]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/Redux.h:254:80,
    inlined from ‘typename Eigen::internal::traits<T>::Scalar Eigen::DenseBase<Derived>::redux(const Func&) const [with BinaryOp = Eigen::internal::scalar_sum_op<int, int>; Derived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<int, int>, const Eigen::Array<int, -1, 1>, const Eigen::Array<int, -1, 1> >]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/Redux.h:418:56,
    inlined from ‘typename Eigen::internal::traits<T>::Scalar Eigen::DenseBase<Derived>::sum() const [with Derived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<int, int>, const Eigen::Array<int, -1, 1>, const Eigen::Array<int, -1, 1> >]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/Redux.h:463:25,
    inlined from ‘typename Eigen::internal::traits<T>::Scalar Eigen::DenseBase<Derived>::sum() const [with Derived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<int, int>, const Eigen::Array<int, -1, 1>, const Eigen::Array<int, -1, 1> >]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/Redux.h:459:1,
    inlined from ‘int tmbutils::array<Type>::index(tmbutils::vector<int>) [with Type = TMBad::global::ad_aug]’ at /data/gannet/ripley/R/test-dev/TMB/include/tmbutils/array.hpp:248:26,
    inlined from ‘Type& tmbutils::array<Type>::operator()(int, int) [with Type = TMBad::global::ad_aug]’ at /data/gannet/ripley/R/test-dev/TMB/include/tmbutils/array.hpp:221:43:
/usr/lib/gcc/x86_64-redhat-linux/15/include/emmintrin.h:701:11: warning: ‘((const __m128i*)result)[1]’ may be used uninitialized [-Wmaybe-uninitialized]
  701 |   return *__P;
      |           ^~~
In file included from /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/Core:253:
In member function ‘Eigen::internal::scalar_product_op<LhsScalar, RhsScalar>::result_type Eigen::internal::scalar_product_op<LhsScalar, RhsScalar>::operator()(const LhsScalar&, const RhsScalar&) const [with LhsScalar = int; RhsScalar = int]’,
    inlined from ‘Eigen::internal::binary_evaluator<Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>, Eigen::internal::IndexBased, Eigen::internal::IndexBased>::CoeffReturnType Eigen::internal::binary_evaluator<Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>, Eigen::internal::IndexBased, Eigen::internal::IndexBased>::coeff(Eigen::Index) const [with BinaryOp = Eigen::internal::scalar_product_op<int, int>; Lhs = const Eigen::Array<int, -1, 1>; Rhs = const Eigen::Array<int, -1, 1>]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:775:22,
    inlined from ‘static Eigen::internal::redux_impl<Func, Evaluator, 3, 0>::Scalar Eigen::internal::redux_impl<Func, Evaluator, 3, 0>::run(const Evaluator&, const Func&, const XprType&) [with XprType = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<int, int>, const Eigen::Array<int, -1, 1>, const Eigen::Array<int, -1, 1> >; Func = Eigen::internal::scalar_sum_op<int, int>; Evaluator = Eigen::internal::redux_evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<int, int>, const Eigen::Array<int, -1, 1>, const Eigen::Array<int, -1, 1> > >]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/Redux.h:278:34,
    inlined from ‘typename Eigen::internal::traits<T>::Scalar Eigen::DenseBase<Derived>::redux(const Func&) const [with BinaryOp = Eigen::internal::scalar_sum_op<int, int>; Derived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<int, int>, const Eigen::Array<int, -1, 1>, const Eigen::Array<int, -1, 1> >]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/Redux.h:418:56,
    inlined from ‘typename Eigen::internal::traits<T>::Scalar Eigen::DenseBase<Derived>::sum() const [with Derived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<int, int>, const Eigen::Array<int, -1, 1>, const Eigen::Array<int, -1, 1> >]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/Redux.h:463:25,
    inlined from ‘typename Eigen::internal::traits<T>::Scalar Eigen::DenseBase<Derived>::sum() const [with Derived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<int, int>, const Eigen::Array<int, -1, 1>, const Eigen::Array<int, -1, 1> >]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/Redux.h:459:1,
    inlined from ‘int tmbutils::array<Type>::index(tmbutils::vector<int>) [with Type = TMBad::global::ad_aug]’ at /data/gannet/ripley/R/test-dev/TMB/include/tmbutils/array.hpp:248:26,
    inlined from ‘Type& tmbutils::array<Type>::operator()(int, int) [with Type = TMBad::global::ad_aug]’ at /data/gannet/ripley/R/test-dev/TMB/include/tmbutils/array.hpp:221:43:
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:80:122: warning: ‘((const int*)result)[2]’ may be used uninitialized [-Wmaybe-uninitialized]
   80 |   EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE result_type operator() (const LhsScalar& a, const RhsScalar& b) const { return a * b; }
      |                                                                                                                        ~~^~~
In function ‘__m128i _mm_load_si128(const __m128i*)’,
    inlined from ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<__vector(2) long long int, 0>]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:717:126,
    inlined from ‘Packet Eigen::internal::ploadt(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<__vector(2) long long int, 0>; int Alignment = 16]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:967:25,
    inlined from ‘PacketType Eigen::internal::evaluator<Eigen::PlainObjectBase<Derived> >::packet(Eigen::Index) const [with int LoadMode = 16; PacketType = Eigen::internal::eigen_packet_wrapper<__vector(2) long long int, 0>; Derived = Eigen::Array<int, -1, 1>]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:245:40,
    inlined from ‘PacketType Eigen::internal::binary_evaluator<Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>, Eigen::internal::IndexBased, Eigen::internal::IndexBased>::packet(Eigen::Index) const [with int LoadMode = 16; PacketType = Eigen::internal::eigen_packet_wrapper<__vector(2) long long int, 0>; BinaryOp = Eigen::internal::scalar_product_op<int, int>; Lhs = const Eigen::Array<int, -1, 1>; Rhs = const Eigen::Array<int, -1, 1>]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:790:80,
    inlined from ‘static Eigen::internal::redux_impl<Func, Evaluator, 3, 0>::Scalar Eigen::internal::redux_impl<Func, Evaluator, 3, 0>::run(const Evaluator&, const Func&, const XprType&) [with XprType = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<int, int>, const Eigen::Array<int, -1, 1>, const Eigen::Array<int, -1, 1> >; Func = Eigen::internal::scalar_sum_op<int, int>; Evaluator = Eigen::internal::redux_evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<int, int>, const Eigen::Array<int, -1, 1>, const Eigen::Array<int, -1, 1> > >]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/Redux.h:254:80,
    inlined from ‘typename Eigen::internal::traits<T>::Scalar Eigen::DenseBase<Derived>::redux(const Func&) const [with BinaryOp = Eigen::internal::scalar_sum_op<int, int>; Derived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<int, int>, const Eigen::Array<int, -1, 1>, const Eigen::Array<int, -1, 1> >]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/Redux.h:418:56,
    inlined from ‘typename Eigen::internal::traits<T>::Scalar Eigen::DenseBase<Derived>::sum() const [with Derived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<int, int>, const Eigen::Array<int, -1, 1>, const Eigen::Array<int, -1, 1> >]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/Redux.h:463:25,
    inlined from ‘typename Eigen::internal::traits<T>::Scalar Eigen::DenseBase<Derived>::sum() const [with Derived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<int, int>, const Eigen::Array<int, -1, 1>, const Eigen::Array<int, -1, 1> >]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/Redux.h:459:1,
    inlined from ‘int tmbutils::array<Type>::index(tmbutils::vector<int>) [with Type = double]’ at /data/gannet/ripley/R/test-dev/TMB/include/tmbutils/array.hpp:248:26,
    inlined from ‘Type& tmbutils::array<Type>::operator()(int, int) [with Type = double]’ at /data/gannet/ripley/R/test-dev/TMB/include/tmbutils/array.hpp:221:43:
/usr/lib/gcc/x86_64-redhat-linux/15/include/emmintrin.h:701:11: warning: ‘((const __m128i*)result)[1]’ may be used uninitialized [-Wmaybe-uninitialized]
  701 |   return *__P;
      |           ^~~
In member function ‘Eigen::internal::scalar_product_op<LhsScalar, RhsScalar>::result_type Eigen::internal::scalar_product_op<LhsScalar, RhsScalar>::operator()(const LhsScalar&, const RhsScalar&) const [with LhsScalar = int; RhsScalar = int]’,
    inlined from ‘Eigen::internal::binary_evaluator<Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>, Eigen::internal::IndexBased, Eigen::internal::IndexBased>::CoeffReturnType Eigen::internal::binary_evaluator<Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>, Eigen::internal::IndexBased, Eigen::internal::IndexBased>::coeff(Eigen::Index) const [with BinaryOp = Eigen::internal::scalar_product_op<int, int>; Lhs = const Eigen::Array<int, -1, 1>; Rhs = const Eigen::Array<int, -1, 1>]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:775:22,
    inlined from ‘static Eigen::internal::redux_impl<Func, Evaluator, 3, 0>::Scalar Eigen::internal::redux_impl<Func, Evaluator, 3, 0>::run(const Evaluator&, const Func&, const XprType&) [with XprType = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<int, int>, const Eigen::Array<int, -1, 1>, const Eigen::Array<int, -1, 1> >; Func = Eigen::internal::scalar_sum_op<int, int>; Evaluator = Eigen::internal::redux_evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<int, int>, const Eigen::Array<int, -1, 1>, const Eigen::Array<int, -1, 1> > >]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/Redux.h:278:34,
    inlined from ‘typename Eigen::internal::traits<T>::Scalar Eigen::DenseBase<Derived>::redux(const Func&) const [with BinaryOp = Eigen::internal::scalar_sum_op<int, int>; Derived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<int, int>, const Eigen::Array<int, -1, 1>, const Eigen::Array<int, -1, 1> >]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/Redux.h:418:56,
    inlined from ‘typename Eigen::internal::traits<T>::Scalar Eigen::DenseBase<Derived>::sum() const [with Derived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<int, int>, const Eigen::Array<int, -1, 1>, const Eigen::Array<int, -1, 1> >]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/Redux.h:463:25,
    inlined from ‘typename Eigen::internal::traits<T>::Scalar Eigen::DenseBase<Derived>::sum() const [with Derived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<int, int>, const Eigen::Array<int, -1, 1>, const Eigen::Array<int, -1, 1> >]’ at /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/Redux.h:459:1,
    inlined from ‘int tmbutils::array<Type>::index(tmbutils::vector<int>) [with Type = double]’ at /data/gannet/ripley/R/test-dev/TMB/include/tmbutils/array.hpp:248:26,
    inlined from ‘Type& tmbutils::array<Type>::operator()(int, int) [with Type = double]’ at /data/gannet/ripley/R/test-dev/TMB/include/tmbutils/array.hpp:221:43:
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/functors/BinaryFunctors.h:80:122: warning: ‘((const int*)result)[2]’ may be used uninitialized [-Wmaybe-uninitialized]
   80 |   EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE result_type operator() (const LhsScalar& a, const RhsScalar& b) const { return a * b; }
      |                                                                                                                        ~~^~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o tinyVAST.so tinyVAST.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/tinyVAST/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/tinyVAST/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/tinyVAST/src'
installing to /data/gannet/ripley/R/packages/tests-devel/tinyVAST.Rcheck/00LOCK-tinyVAST/00new/tinyVAST/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (tinyVAST)