* installing *source* package ‘sdmTMB’ ...
** this is package ‘sdmTMB’ version ‘1.1.0’
** package ‘sdmTMB’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)’
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/sdmTMB/src'
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DTMBAD_FRAMEWORK -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/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 sdmTMB.cpp -o sdmTMB.o
In file included from /data/localhost/ripley/R/test-dev/RcppEigen/include/Eigen/SparseLU:35,
from /data/localhost/ripley/R/test-dev/RcppEigen/include/Eigen/Sparse:29,
from /data/localhost/ripley/R/test-dev/TMB/include/TMB.hpp:96,
from sdmTMB.cpp:3:
/data/localhost/ripley/R/test-dev/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h: In instantiation of ‘void Eigen::internal::SparseLUImpl<Scalar, StorageIndex>::heap_relax_snode(Eigen::Index, IndexVector&, Eigen::Index, IndexVector&, IndexVector&) [with Scalar = TMBad::global::ad_aug; StorageIndex = int; Eigen::Index = long int; IndexVector = Eigen::Matrix<int, -1, 1>]’:
/data/localhost/ripley/R/test-dev/RcppEigen/include/Eigen/src/SparseLU/SparseLU.h:669:27: required from ‘void Eigen::SparseLU<_MatrixType, _OrderingType>::factorize(const MatrixType&) [with _MatrixType = Eigen::SparseMatrix<TMBad::global::ad_aug>; _OrderingType = Eigen::COLAMDOrdering<int>; MatrixType = Eigen::SparseMatrix<TMBad::global::ad_aug>]’
669 | Base::heap_relax_snode(n, m_etree, m_perfv.relax, marker, relax_end);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/localhost/ripley/R/test-dev/RcppEigen/include/Eigen/src/SparseLU/SparseLU.h:187:7: required from ‘void Eigen::SparseLU<_MatrixType, _OrderingType>::compute(const MatrixType&) [with _MatrixType = Eigen::SparseMatrix<TMBad::global::ad_aug>; _OrderingType = Eigen::COLAMDOrdering<int>; MatrixType = Eigen::SparseMatrix<TMBad::global::ad_aug>]’
187 | factorize(matrix);
| ^~~~~~~~~
covariate-diffusion.h:192:43: required from ‘void sdmTMB::add_covariate_diffusion_to_eta_fixed(tmbutils::array<Type>&, CovariateDiffusionContext<Type>&, tmbutils::matrix<Type>*) [with Type = TMBad::global::ad_aug]’
192 | lu_spatial_by_covariate[cov_i].compute(spatial_system);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
sdmTMB.cpp:868:49: required from ‘Type objective_function<Type>::operator()() [with Type = TMBad::global::ad_aug]’
868 | sdmTMB::add_covariate_diffusion_to_eta_fixed(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
869 | eta_fixed_i, nl_ctx, model_col == 0 ? &covariate_diffusion_values : nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/localhost/ripley/R/test-dev/TMB/include/tmb_core.hpp:1281:6: required from here
1281 | F(); // Run through user template (modifies reportvector)
| ~^~
/data/localhost/ripley/R/test-dev/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable ‘nsuper_et_post’ set but not used [-Wunused-but-set-variable=]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^~~~~~~~~~~~~~
/data/localhost/ripley/R/test-dev/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable ‘nsuper_et’ set but not used [-Wunused-but-set-variable=]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^~~~~~~~~
/data/localhost/ripley/R/test-dev/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h: In instantiation of ‘void Eigen::internal::SparseLUImpl<Scalar, StorageIndex>::heap_relax_snode(Eigen::Index, IndexVector&, Eigen::Index, IndexVector&, IndexVector&) [with Scalar = double; StorageIndex = int; Eigen::Index = long int; IndexVector = Eigen::Matrix<int, -1, 1>]’:
/data/localhost/ripley/R/test-dev/RcppEigen/include/Eigen/src/SparseLU/SparseLU.h:669:27: required from ‘void Eigen::SparseLU<_MatrixType, _OrderingType>::factorize(const MatrixType&) [with _MatrixType = Eigen::SparseMatrix<double>; _OrderingType = Eigen::COLAMDOrdering<int>; MatrixType = Eigen::SparseMatrix<double>]’
669 | Base::heap_relax_snode(n, m_etree, m_perfv.relax, marker, relax_end);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/localhost/ripley/R/test-dev/RcppEigen/include/Eigen/src/SparseLU/SparseLU.h:187:7: required from ‘void Eigen::SparseLU<_MatrixType, _OrderingType>::compute(const MatrixType&) [with _MatrixType = Eigen::SparseMatrix<double>; _OrderingType = Eigen::COLAMDOrdering<int>; MatrixType = Eigen::SparseMatrix<double>]’
187 | factorize(matrix);
| ^~~~~~~~~
covariate-diffusion.h:192:43: required from ‘void sdmTMB::add_covariate_diffusion_to_eta_fixed(tmbutils::array<Type>&, CovariateDiffusionContext<Type>&, tmbutils::matrix<Type>*) [with Type = double]’
192 | lu_spatial_by_covariate[cov_i].compute(spatial_system);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
sdmTMB.cpp:868:49: required from ‘Type objective_function<Type>::operator()() [with Type = double]’
868 | sdmTMB::add_covariate_diffusion_to_eta_fixed(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
869 | eta_fixed_i, nl_ctx, model_col == 0 ? &covariate_diffusion_values : nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/localhost/ripley/R/test-dev/TMB/include/tmb_core.hpp:2035:7: required from here
2035 | PROTECT( res = asSEXP( pf->operator()() ) );
| ~~~~~~~~~~~~~~^~
/data/localhost/ripley/R/test-dev/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable ‘nsuper_et_post’ set but not used [-Wunused-but-set-variable=]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^~~~~~~~~~~~~~
/data/localhost/ripley/R/test-dev/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable ‘nsuper_et’ set but not used [-Wunused-but-set-variable=]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^~~~~~~~~
In file included from /data/localhost/ripley/R/test-dev/TMB/include/TMB.hpp:235:
sdmTMB.cpp: In member function ‘Type objective_function<Type>::operator()() [with Type = double]’:
/data/localhost/ripley/R/test-dev/TMB/include/tmb_core.hpp:345:39: warning: ‘tweedie_p’ may be used uninitialized [-Wmaybe-uninitialized]
345 | TMB_OBJECTIVE_PTR -> reportvector.push(name, #name);
| ^
sdmTMB.cpp:1846:36: note: in expansion of macro ‘ADREPORT’
1846 | if (family(0) == tweedie_family) ADREPORT(tweedie_p); // #302
| ^~~~~~~~
sdmTMB.cpp:996:73: note: ‘tweedie_p’ was declared here
996 | Type s1, s2, s3, lognzprob, tmp_ll, ll_1, ll_2, p_extreme, mix_ratio, tweedie_p, s2_large;
| ^~~~~~~~~
g++ -std=gnu++20 -shared -L/usr/local/lib64 -o sdmTMB.so sdmTMB.o
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/sdmTMB/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/sdmTMB/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/sdmTMB/src'
installing to /data/localhost/ripley/R/packages/tests-devel/sdmTMB.Rcheck/00LOCK-sdmTMB/00new/sdmTMB/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 (sdmTMB)