* installing *source* package ‘SuperpixelImageSegmentation’ ...
** this is package ‘SuperpixelImageSegmentation’ version ‘1.0.5’
** package ‘SuperpixelImageSegmentation’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
using C++11
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/SuperpixelImageSegmentation/src'
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/ClusterR/include' -I'/data/gannet/ripley/R/test-dev/OpenImageR/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -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
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/ClusterR/include' -I'/data/gannet/ripley/R/test-dev/OpenImageR/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c init.c -o init.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I../inst/include/ -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/ClusterR/include' -I'/data/gannet/ripley/R/test-dev/OpenImageR/include' -I/usr/local/include -fopenmp -DARMA_64BIT_WORD -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 superPx_AP_Kmeans_Segment.cpp -o superPx_AP_Kmeans_Segment.o
In file included from superPx_AP_Kmeans_Segment.cpp:2:
/data/gannet/ripley/R/test-dev/ClusterR/include/ClusterRHeader.h: In member function ‘arma::mat clustR::ClustHeader::KMEANS_arma(arma::mat&, int, int, bool, std::string, Rcpp::Nullable<Rcpp::Matrix<14> >, int)’:
/data/gannet/ripley/R/test-dev/ClusterR/include/ClusterRHeader.h:862:14: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
862 | bool status;
| ^~~~~~
/data/gannet/ripley/R/test-dev/ClusterR/include/ClusterRHeader.h: In instantiation of ‘T clustR::ClustHeader::GMM_arma_covariance_type(T, arma::mat&, int, std::string, std::string, int, int, bool, double, int) [with T = arma::gmm_priv::gmm_full<double>; arma::mat = arma::Mat<double>; std::string = std::__cxx11::basic_string<char>]’:
/data/gannet/ripley/R/test-dev/ClusterR/include/ClusterRHeader.h:1592:65: required from here
1592 | model_inner = GMM_arma_covariance_type<arma::gmm_full>(model_inner,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
1593 | data,
| ~~~~~
1594 | gaussian_comps,
| ~~~~~~~~~~~~~~~
1595 | dist_mode,
| ~~~~~~~~~~
1596 | seed_mode,
| ~~~~~~~~~~
1597 | km_iter,
| ~~~~~~~~
1598 | em_iter,
| ~~~~~~~~
1599 | verbose,
| ~~~~~~~~
1600 | var_floor,
| ~~~~~~~~~~
1601 | seed);
| ~~~~~
/data/gannet/ripley/R/test-dev/ClusterR/include/ClusterRHeader.h:1530:14: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
1530 | bool status;
| ^~~~~~
/data/gannet/ripley/R/test-dev/ClusterR/include/ClusterRHeader.h: In instantiation of ‘T clustR::ClustHeader::GMM_arma_covariance_type(T, arma::mat&, int, std::string, std::string, int, int, bool, double, int) [with T = arma::gmm_priv::gmm_diag<double>; arma::mat = arma::Mat<double>; std::string = std::__cxx11::basic_string<char>]’:
/data/gannet/ripley/R/test-dev/ClusterR/include/ClusterRHeader.h:1626:65: required from here
1626 | model_inner = GMM_arma_covariance_type<arma::gmm_diag>(model_inner,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
1627 | data,
| ~~~~~
1628 | gaussian_comps,
| ~~~~~~~~~~~~~~~
1629 | dist_mode,
| ~~~~~~~~~~
1630 | seed_mode,
| ~~~~~~~~~~
1631 | km_iter,
| ~~~~~~~~
1632 | em_iter,
| ~~~~~~~~
1633 | verbose,
| ~~~~~~~~
1634 | var_floor,
| ~~~~~~~~~~
1635 | seed);
| ~~~~~
/data/gannet/ripley/R/test-dev/ClusterR/include/ClusterRHeader.h:1530:14: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
1530 | bool status;
| ^~~~~~
In file included from /usr/include/c++/15/x86_64-redhat-linux/bits/c++allocator.h:33,
from /usr/include/c++/15/bits/allocator.h:46,
from /usr/include/c++/15/bits/alloc_traits.h:39,
from /usr/include/c++/15/ext/alloc_traits.h:36,
from /usr/include/c++/15/bits/hashtable_policy.h:39,
from /usr/include/c++/15/bits/hashtable.h:37,
from /usr/include/c++/15/bits/unordered_map.h:33,
from /usr/include/c++/15/unordered_map:43,
from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/platform/compiler.h:153,
from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/r/headers.h:66,
from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:30,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
from superPx_AP_Kmeans_Segment.cpp:1:
In member function ‘void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = double]’,
inlined from ‘static void std::allocator_traits<std::allocator<_Tp1> >::deallocate(allocator_type&, pointer, size_type) [with _Tp = double]’ at /usr/include/c++/15/bits/alloc_traits.h:649:23,
inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/15/bits/stl_vector.h:396:19,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/15/bits/stl_vector.h:375:15,
inlined from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/15/bits/stl_vector.h:805:7,
inlined from ‘static typename T1::elem_type arma::op_median::median_vec(const T1&, const typename arma::arma_not_cx<typename T1::elem_type>::result*) [with T1 = arma::Op<arma::subview_elem1<double, arma::Mat<long long unsigned int> >, arma::op_vectorise_col>]’ at /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/op_median_meat.hpp:212:3:
/usr/include/c++/15/bits/new_allocator.h:172:66: warning: ‘void operator delete(void*)’ called on pointer ‘<unknown>’ with nonzero offset [16, 9223372036854775800] [-Wfree-nonheap-object]
172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n));
| ^
In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = double]’,
inlined from ‘static _Tp* std::allocator_traits<std::allocator<_Tp1> >::allocate(allocator_type&, size_type) [with _Tp = double]’ at /usr/include/c++/15/bits/alloc_traits.h:614:28,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/15/bits/stl_vector.h:387:33,
inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/15/bits/stl_vector.h:405:44,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/15/bits/stl_vector.h:341:26,
inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/15/bits/stl_vector.h:587:47,
inlined from ‘static typename T1::elem_type arma::op_median::median_vec(const T1&, const typename arma::arma_not_cx<typename T1::elem_type>::result*) [with T1 = arma::Op<arma::subview_elem1<double, arma::Mat<long long unsigned int> >, arma::op_vectorise_col>]’ at /data/gannet/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/op_median_meat.hpp:207:19:
/usr/include/c++/15/bits/new_allocator.h:151:73: note: returned from ‘void* operator new(std::size_t)’
151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
| ^
g++ -std=gnu++11 -shared -L/usr/local/lib64 -o SuperpixelImageSegmentation.so RcppExports.o init.o superPx_AP_Kmeans_Segment.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -fopenmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/SuperpixelImageSegmentation/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/SuperpixelImageSegmentation/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/SuperpixelImageSegmentation/src'
installing to /data/gannet/ripley/R/packages/tests-devel/SuperpixelImageSegmentation.Rcheck/00LOCK-SuperpixelImageSegmentation/00new/SuperpixelImageSegmentation/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 (SuperpixelImageSegmentation)