* installing *source* package ‘colvR’ ...
** this is package ‘colvR’ version ‘0.2.1’
** package ‘colvR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++17
using C++ compiler: ‘g++ (GCC) 16.2.1 20261029 (Red Hat 16.2.1-3)’
using C++17
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/colvR/src'
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/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 -DSTRICT_R_HEADERS -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/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 nlopt_wrapper.cpp -o nlopt_wrapper.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/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 optim_rank_ZIP.cpp -o optim_rank_ZIP.o
In file included from optim_rank_ZIP.cpp:15:
Elbo_gradBB.h: In function ‘std::tuple<arma::Mat<double>, double, double, double, double, double, double, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<double> > Elbo_grad_LogS(const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, double)’:
Elbo_gradBB.h:107:9: warning: unused variable ‘n’ [-Wunused-variable]
107 | int n = Y.n_rows;
| ^
Elbo_gradBB.h:108:9: warning: unused variable ‘p’ [-Wunused-variable]
108 | int p = Y.n_cols;
| ^
Elbo_gradBB.h:109:9: warning: unused variable ‘q’ [-Wunused-variable]
109 | int q = M.n_cols;
| ^
optim_rank_ZIP.cpp: In lambda function:
optim_rank_ZIP.cpp:224:9: warning: unused variable ‘q’ [-Wunused-variable]
224 | int q = M.n_cols;
| ^
optim_rank_ZIP.cpp:225:9: warning: unused variable ‘d’ [-Wunused-variable]
225 | int d = X.n_cols;
| ^
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/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 optim_rank_ZIP_M.cpp -o optim_rank_ZIP_M.o
In file included from optim_rank_ZIP_M.cpp:15:
Elbo_gradBB.h: In function ‘std::tuple<arma::Mat<double>, double, double, double, double, double, double, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<double> > Elbo_grad_LogS(const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, double)’:
Elbo_gradBB.h:107:9: warning: unused variable ‘n’ [-Wunused-variable]
107 | int n = Y.n_rows;
| ^
Elbo_gradBB.h:108:9: warning: unused variable ‘p’ [-Wunused-variable]
108 | int p = Y.n_cols;
| ^
Elbo_gradBB.h:109:9: warning: unused variable ‘q’ [-Wunused-variable]
109 | int q = M.n_cols;
| ^
optim_rank_ZIP_M.cpp: In lambda function:
optim_rank_ZIP_M.cpp:123:9: warning: unused variable ‘d’ [-Wunused-variable]
123 | int d = X.n_cols;
| ^
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/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 optim_rank_ZIP_VE.cpp -o optim_rank_ZIP_VE.o
In file included from optim_rank_ZIP_VE.cpp:15:
Elbo_gradBB.h: In function ‘std::tuple<arma::Mat<double>, double, double, double, double, double, double, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<double> > Elbo_grad_LogS(const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, double)’:
Elbo_gradBB.h:107:9: warning: unused variable ‘n’ [-Wunused-variable]
107 | int n = Y.n_rows;
| ^
Elbo_gradBB.h:108:9: warning: unused variable ‘p’ [-Wunused-variable]
108 | int p = Y.n_cols;
| ^
Elbo_gradBB.h:109:9: warning: unused variable ‘q’ [-Wunused-variable]
109 | int q = M.n_cols;
| ^
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/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 optim_rank_ZIP_alternate.cpp -o optim_rank_ZIP_alternate.o
In file included from optim_rank_ZIP_alternate.cpp:15:
Elbo_gradBB.h: In function ‘std::tuple<arma::Mat<double>, double, double, double, double, double, double, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<double> > Elbo_grad_LogS(const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, double)’:
Elbo_gradBB.h:107:9: warning: unused variable ‘n’ [-Wunused-variable]
107 | int n = Y.n_rows;
| ^
Elbo_gradBB.h:108:9: warning: unused variable ‘p’ [-Wunused-variable]
108 | int p = Y.n_cols;
| ^
Elbo_gradBB.h:109:9: warning: unused variable ‘q’ [-Wunused-variable]
109 | int q = M.n_cols;
| ^
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/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 optim_rank_ZIP_q0.cpp -o optim_rank_ZIP_q0.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/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 optim_rank_cov.cpp -o optim_rank_cov.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/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 optim_rank_cov_inter.cpp -o optim_rank_cov_inter.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/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 optim_rank_zip_log.cpp -o optim_rank_zip_log.o
In file included from optim_rank_zip_log.cpp:15:
Elbo_gradBB.h: In function ‘std::tuple<arma::Mat<double>, double, double, double, double, double, double, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<double> > Elbo_grad_LogS(const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, double)’:
Elbo_gradBB.h:107:9: warning: unused variable ‘n’ [-Wunused-variable]
107 | int n = Y.n_rows;
| ^
Elbo_gradBB.h:108:9: warning: unused variable ‘p’ [-Wunused-variable]
108 | int p = Y.n_cols;
| ^
Elbo_gradBB.h:109:9: warning: unused variable ‘q’ [-Wunused-variable]
109 | int q = M.n_cols;
| ^
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/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 packing.cpp -o packing.o
In file included from /data/localhost/ripley/R/test-dev/RcppArmadillo/include/armadillo:439,
from /data/localhost/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:51,
from /data/localhost/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:29,
from packing.h:7,
from packing.cpp:1:
In static member function ‘static void arma::memory::release(eT*) [with eT = const double]’,
inlined from ‘arma::Mat<eT>::~Mat() [with eT = double]’ at /data/localhost/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:32:20,
inlined from ‘arma::Mat<eT>::~Mat() [with eT = double]’ at /data/localhost/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/Mat_meat.hpp:25:1,
inlined from ‘arma::Col<double>::~Col()’ at /data/localhost/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/Col_bones.hpp:25:7,
inlined from ‘bool cpp_test_packing()’ at packing.cpp:37:48:
/data/localhost/ripley/R/test-dev/RcppArmadillo/include/armadillo_bits/memory.hpp:125:14: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
125 | std::free( (void *)(mem) );
| ~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/16/x86_64-redhat-linux/bits/c++allocator.h:33,
from /usr/include/c++/16/bits/allocator.h:46,
from /usr/include/c++/16/bits/alloc_traits.h:39,
from /usr/include/c++/16/ext/alloc_traits.h:36,
from /usr/include/c++/16/bits/hashtable_policy.h:40,
from /usr/include/c++/16/bits/hashtable.h:37,
from /usr/include/c++/16/bits/unordered_map.h:33,
from /usr/include/c++/16/unordered_map:43,
from /data/localhost/ripley/R/test-dev/Rcpp/include/Rcpp/platform/compiler.h:39,
from /data/localhost/ripley/R/test-dev/Rcpp/include/Rcpp/r/headers.h:67,
from /data/localhost/ripley/R/test-dev/Rcpp/include/RcppCommon.h:30,
from /data/localhost/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:26:
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++/16/bits/alloc_traits.h:638:28,
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++/16/bits/stl_vector.h:389:33,
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++/16/bits/stl_vector.h:407:44,
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++/16/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++/16/bits/stl_vector.h:577:47,
inlined from ‘bool cpp_test_packing()’ at packing.cpp:27:59:
/usr/include/c++/16/bits/new_allocator.h:162:75: note: returned from ‘void* operator new(std::size_t)’
162 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
| ^
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppArmadillo/include' -I'/data/localhost/ripley/R/test-dev/nloptr/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 utilsBB.cpp -o utilsBB.o
utilsBB.cpp: In function ‘arma::mat GradB(const arma::vec&, const arma::mat&, const arma::vec&, const arma::vec&, const arma::vec&)’:
utilsBB.cpp:132:7: warning: unused variable ‘l’ [-Wunused-variable]
132 | int l = vecY.size();
| ^
utilsBB.cpp: In function ‘arma::mat GradC(const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&)’:
utilsBB.cpp:150:7: warning: unused variable ‘n’ [-Wunused-variable]
150 | int n = Y.n_rows;
| ^
utilsBB.cpp:151:7: warning: unused variable ‘p’ [-Wunused-variable]
151 | int p = Y.n_cols;
| ^
utilsBB.cpp: In function ‘arma::mat GradM(const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&)’:
utilsBB.cpp:175:7: warning: unused variable ‘n’ [-Wunused-variable]
175 | int n = Y.n_rows;
| ^
utilsBB.cpp:176:7: warning: unused variable ‘p’ [-Wunused-variable]
176 | int p = Y.n_cols;
| ^
utilsBB.cpp: In function ‘arma::mat GradS(const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&)’:
utilsBB.cpp:200:7: warning: unused variable ‘n’ [-Wunused-variable]
200 | int n = A.n_rows;
| ^
utilsBB.cpp:201:7: warning: unused variable ‘p’ [-Wunused-variable]
201 | int p = A.n_cols;
| ^
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o colvR.so RcppExports.o nlopt_wrapper.o optim_rank_ZIP.o optim_rank_ZIP_M.o optim_rank_ZIP_VE.o optim_rank_ZIP_alternate.o optim_rank_ZIP_q0.o optim_rank_cov.o optim_rank_cov_inter.o optim_rank_zip_log.o packing.o utilsBB.o -lnlopt -llapack -L/data/localhost/ripley/R/R-devel/lib -lRblas -lgfortran -lm -latomic_asneeded -lquadmath
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/colvR/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/colvR/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/colvR/src'
installing to /data/localhost/ripley/R/packages/tests-devel/colvR.Rcheck/00LOCK-colvR/00new/colvR/libs
** R
** data
** 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 (colvR)