Install log for 'samc'

* installing *source* package ‘samc’ ...
** this is package ‘samc’ version ‘4.2.1’
** package ‘samc’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++17
using C++ compiler: ‘g++ (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)’
using C++17
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/samc/src'
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/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 RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/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 cond_passage.cpp -o cond_passage.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/RcppEigen/include/RcppEigenForward.h:29,
                 from /data/localhost/ripley/R/test-dev/RcppEigen/include/RcppEigen.h:25,
                 from cond_passage.cpp:5:
/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, 0, int>; _OrderingType = Eigen::COLAMDOrdering<int>; MatrixType = Eigen::SparseMatrix<double, 0, int>]’
  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, 0, int>; _OrderingType = Eigen::COLAMDOrdering<int>; MatrixType = Eigen::SparseMatrix<double, 0, int>]’
  187 |       factorize(matrix);
      |       ^~~~~~~~~
cond_passage.cpp:13:17:   required from here
   13 |   solver.compute(IQ);
      |   ~~~~~~~~~~~~~~^~~~
/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
      |         ^~~~~~~~~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/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 convolution.cpp -o convolution.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/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 dispersal.cpp -o dispersal.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/RcppEigen/include/RcppEigenForward.h:29,
                 from /data/localhost/ripley/R/test-dev/RcppEigen/include/RcppEigen.h:25,
                 from dispersal.cpp:5:
/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, 0, int>; _OrderingType = Eigen::COLAMDOrdering<int>; MatrixType = Eigen::SparseMatrix<double, 0, int>]’
  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, 0, int>; _OrderingType = Eigen::COLAMDOrdering<int>; MatrixType = Eigen::SparseMatrix<double, 0, int>]’
  187 |       factorize(matrix);
      |       ^~~~~~~~~
dispersal.cpp:31:17:   required from here
   31 |   solver.compute(M2);
      |   ~~~~~~~~~~~~~~^~~~
/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
      |         ^~~~~~~~~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/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 distribution.cpp -o distribution.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/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 mortality.cpp -o mortality.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/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 solver-cache.cpp -o solver-cache.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/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 survival.cpp -o survival.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/RcppEigen/include/RcppEigenForward.h:29,
                 from /data/localhost/ripley/R/test-dev/RcppEigen/include/RcppEigen.h:25,
                 from solver-cache.cpp:5:
/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, 0, int>; _OrderingType = Eigen::COLAMDOrdering<int>; MatrixType = Eigen::SparseMatrix<double, 0, int>]’
  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, 0, int>; _OrderingType = Eigen::COLAMDOrdering<int>; MatrixType = Eigen::SparseMatrix<double, 0, int>]’
  187 |       factorize(matrix);
      |       ^~~~~~~~~
solver-cache.cpp:21:21:   required from here
   21 |     m_solver.compute(M);
      |     ~~~~~~~~~~~~~~~~^~~
/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
      |         ^~~~~~~~~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/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 visitation.cpp -o visitation.o
visitation.cpp: In function ‘Rcpp::NumericVector f_col(const Eigen::Map<Eigen::SparseMatrix<double, 0, int>, 0, Eigen::Stride<0, 0> >&, const Eigen::VectorXd&, Rcpp::XPtr<SolverCache>&)’:
visitation.cpp:113:7: warning: unused variable ‘sz’ [-Wunused-variable]
  113 |   int sz = M.rows();
      |       ^~
visitation.cpp: In function ‘Rcpp::NumericVector f_col_iter(const Eigen::Map<Eigen::SparseMatrix<double, 0, int>, 0, Eigen::Stride<0, 0> >&, const Eigen::VectorXd&)’:
visitation.cpp:129:7: warning: unused variable ‘sz’ [-Wunused-variable]
  129 |   int sz = M.rows();
      |       ^~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o samc.so RcppExports.o cond_passage.o convolution.o dispersal.o distribution.o mortality.o solver-cache.o survival.o visitation.o -latomic -lpthread
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/samc/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/samc/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/samc/src'
installing to /data/localhost/ripley/R/packages/tests-devel/samc.Rcheck/00LOCK-samc/00new/samc/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 (samc)