* installing *source* package ‘scorematchingad’ ... ** this is package ‘scorematchingad’ version ‘0.1.1’ ** package ‘scorematchingad’ successfully unpacked and MD5 sums checked ** using staged installation checking for cmake... /usr/bin/cmake configure: Running CMake... -- The C compiler identification is GNU 14.2.1 -- The CXX compiler identification is GNU 14.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- cmake_install_datadir = share -- cmake_install_docdir = NOTFOUND -- cmake_install_includedirs = include -- cmake_install_libdirs = lib -- cmake_defined_ok = TRUE -- cppad_prefix = /usr/local -- cppad_postfix = NOTFOUND -- cppad_cxx_flags = -- cppad_profile_flag = NOTFOUND -- cppad_testvector = cppad -- cppad_max_num_threads = 48 -- cppad_tape_id_type = unsigned int -- cppad_tape_addr_type = unsigned int -- cppad_static_lib = FALSE -- cppad_debug_and_release = TRUE -- Performing Test minimal_cplusplus -- Performing Test minimal_cplusplus - Success -- minimal_cplusplus = 1 -- Performing Test use_cplusplus_2017_ok -- Performing Test use_cplusplus_2017_ok - Success -- use_cplusplus_2017_ok = 1 -- CMAKE_SYSTEM_NAME = Linux -- cppad_debug_which = debug_none -- CMAKE_BUILD_TYPE = minsizerel -- make check: avialable -- include_adolc = FALSE -- include_ipopt = FALSE -- CMAKE_CXX_FLAGS_RELEASE = -O3 -DNDEBUG -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") CMake Warning (dev) at CMakeLists.txt:418 (FIND_PACKAGE): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0") found components: thread -- boost_prefix = /usr -- Found /usr/include -- Found /usr/lib -- is_cppad_lib_dynamic = 1 -- cppad_c_compiler_cmd = gcc -- c_compiler_msvc_clang = 0 -- cppad_c_compiler_msvc_flags = 0 -- cppad_c_compiler_gnu_flags = 1 -- Performing Test compiler_has_conversion_warn -- Performing Test compiler_has_conversion_warn - Success -- compiler_has_conversion_warn = 1 -- cppad_boostvector = 0 -- cppad_cppadvector = 1 -- cppad_eigenvector = 0 -- cppad_stdvector = 0 -- Performing Test cppad_has_gettimeofday -- Performing Test cppad_has_gettimeofday - Success -- cppad_has_gettimeofday = 1 -- Performing Test cppad_tape_id_type_is_unsigned -- Performing Test cppad_tape_id_type_is_unsigned - Success -- cppad_tape_id_type_is_unsigned = 1 -- Performing Test cppad_tape_addr_type_is_unsigned -- Performing Test cppad_tape_addr_type_is_unsigned - Success -- cppad_tape_addr_type_is_unsigned = 1 -- Performing Test cppad_has_mkstemp -- Performing Test cppad_has_mkstemp - Success -- cppad_has_mkstemp = 1 -- Performing Test cppad_has_tmpnam_s -- Performing Test cppad_has_tmpnam_s - Failed -- cppad_has_tmpnam_s = 0 -- Performing Test cppad_is_same_unsigned_int_size_t -- Performing Test cppad_is_same_unsigned_int_size_t - Failed -- cppad_is_same_unsigned_int_size_t = 0 -- Performing Test cppad_is_same_tape_addr_type_size_t -- Performing Test cppad_is_same_tape_addr_type_size_t - Failed -- cppad_is_same_tape_addr_type_size_t = 0 -- Performing Test first_block_t_mod_double_zero -- Performing Test first_block_t_mod_double_zero - Success -- first_block_t_mod_double_zero = 1 -- Performing Test second_block_t_mod_double_zero -- Performing Test second_block_t_mod_double_zero - Success -- second_block_t_mod_double_zero = 1 -- soversion = 1828.5 -- Not Windows system so building shared cppad_lib -- make check_val_graph: available -- make check_example_abs_normal: available -- make check_example_atomic_four_lin_ode: available -- make check_example_atomic_four_mat_mul: available -- make check_example_atomic_four_vector: available -- make check_example_atomic_four: available -- make check_example_atomic_three: available -- make check_example_atomic_two: available -- make check_example_chkpoint_two: available -- make check_example_compare_change: available -- make check_example_general: available -- make check_example_get_started: available -- make check_example_graph: available -- make check_example_jit: available -- make check_example_json: available -- make check_example_multi_thread_openmp: available -- pthread library path = /usr/lib64/libpthread.a -- Looking for pthread_barrier_wait in pthread -- Looking for pthread_barrier_wait in pthread - found -- make check_example_multi_thread_pthread: available -- Performing Test boost_multi_thread_ok -- Performing Test boost_multi_thread_ok - Success -- boost_multi_thread_ok = 1 -- make check_example_multi_thread_bthread: available -- make check_example_multi_thread: available -- make check_example_optimize: available -- make check_example_print_for: available -- make check_example_sparse: available -- make check_example_utility: available -- make check_example: available -- make check_introduction: available -- make check_test_more_deprecated_atomic_two: available -- make check_test_more_deprecated_chkpoint_one: available -- make check_test_more_deprecated: available -- make check_test_more_compare_c_c: available -- make check_test_more_compare_c_cpp: available -- make check_test_more_compare_c: available -- make check_test_more_debug_rel: available -- make check_test_more_cppad_for_tmb: available -- make check_test_more_general: available -- make check_test_more: available -- make check_speed_cppad: available -- make check_speed_cppad_jit: available -- make check_speed_double: available -- make check_speed_example: available -- make check_speed_program: available -- make check_speed_xpackage: available -- make check_speed: available -- Configuring done (29.3s) -- Generating done (0.6s) -- Build files have been written to: /data/gannet/ripley/R/packages/tests-devel/scorematchingad/inst/cppad/build /data/gannet/ripley/R/packages/tests-devel/scorematchingad [1] TRUE [1] TRUE configure: creating ./config.status ** libs using C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/scorematchingad/src' g++ -std=gnu++17 -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/RcppEigen/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/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/RcppEigen/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 abort_recording.cpp -o abort_recording.o g++ -std=gnu++17 -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/RcppEigen/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 approx.cpp -o approx.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:130, from ../inst/include/scorematchingad_forward.h:6, from abort_recording.cpp:3: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/exceptions.h:60:21: warning: inline function ‘void Rcpp::exception::record_stack_trace()’ used but never defined 60 | inline void record_stack_trace(); | ^~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/exceptions.h:55:21: warning: inline function ‘void Rcpp::exception::copy_stack_trace_to_r() const’ used but never defined 55 | inline void copy_stack_trace_to_r() const; | ^~~~~~~~~~~~~~~~~~~~~ In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/protection/protection.h:23, from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:128: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/protection/Armor.h:38:23: warning: inline function ‘Rcpp::Armor<T>& Rcpp::Armor<T>::operator=(const U&) [with U = SEXPREC*; T = SEXPREC*]’ used but never defined 38 | inline Armor& operator=( const U& x ) ; | ^~~~~~~~ g++ -std=gnu++17 -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/RcppEigen/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 error_handler.cpp -o error_handler.o g++ -std=gnu++17 -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/RcppEigen/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 exposemanifold.cpp -o exposemanifold.o g++ -std=gnu++17 -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/RcppEigen/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 fixdynamic.cpp -o fixdynamic.o g++ -std=gnu++17 -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/RcppEigen/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 pADFun.cpp -o pADFun.o fixdynamic.cpp: In function ‘pADFun fixdynamic(pADFun&, veca1, Eigen::Matrix<int, -1, 1>)’: fixdynamic.cpp:8:25: warning: comparison of integer expressions of different signedness: ‘Eigen::EigenBase<Eigen::Matrix<int, -1, 1> >::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 8 | if (fixedtheta.size() != uld.size_dyn_ind()){ | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -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/RcppEigen/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 pADFun_retape.cpp -o pADFun_retape.o g++ -std=gnu++17 -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/RcppEigen/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 tapebdryweight.cpp -o tapebdryweight.o In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:130, from ../inst/include/scorematchingad_forward.h:6, from tapebdryweight.h:4, from tapebdryweight.cpp:1: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/exceptions.h:60:21: warning: inline function ‘void Rcpp::exception::record_stack_trace()’ used but never defined 60 | inline void record_stack_trace(); | ^~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/exceptions.h:55:21: warning: inline function ‘void Rcpp::exception::copy_stack_trace_to_r() const’ used but never defined 55 | inline void copy_stack_trace_to_r() const; | ^~~~~~~~~~~~~~~~~~~~~ In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/protection/protection.h:23, from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:128: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/protection/Armor.h:38:23: warning: inline function ‘Rcpp::Armor<T>& Rcpp::Armor<T>::operator=(const U&) [with U = SEXPREC*; T = SEXPREC*]’ used but never defined 38 | inline Armor& operator=( const U& x ) ; | ^~~~~~~~ g++ -std=gnu++17 -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/RcppEigen/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 tapell.cpp -o tapell.o g++ -std=gnu++17 -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/RcppEigen/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 tapesmd.cpp -o tapesmd.o In file included from tapell.h:9, from tapell.cpp:1: ../inst/include/utils/PrintFor.hpp: In instantiation of ‘void PrintForVec(const char*, const T&) [with T = Eigen::Matrix<CppAD::AD<double>, -1, 1>]’: tapell.cpp:52:16: required from here 52 | PrintForVec("\n thetavar is: ", thetavar); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/utils/PrintFor.hpp:11:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<CppAD::AD<double>, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] 11 | for(size_t i=1; i<printvec.size(); i++){ | ~^~~~~~~~~~~~~~~~ In file included from ../inst/include/likelihoods/likelihoods.hpp:6, from tapell.h:8: ../inst/include/likelihoods/ppi.hpp: In instantiation of ‘T ll::ll_ppi(const Eigen::Matrix<Type, -1, 1>&, const Eigen::Matrix<Type, -1, 1>&) [with T = CppAD::AD<double>]’: tapell.cpp:121:14: required from here 121 | ll = ll::ll_ppi; | ^~~~~~ ../inst/include/likelihoods/ppi.hpp:14:26: warning: comparison of integer expressions of different signedness: ‘Eigen::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 14 | if (theta.rows() != d + (d-1) + (d-2) * (d-1)/2 + (d-1)){ | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/likelihoods/likelihoods.hpp:7: ../inst/include/likelihoods/vMF.hpp: In instantiation of ‘T ll::ll_vMF(const Eigen::Matrix<Type, -1, 1>&, const Eigen::Matrix<Type, -1, 1>&) [with T = CppAD::AD<double>]’: tapell.cpp:124:14: required from here 124 | ll = ll::ll_vMF; | ^~~~~~ ../inst/include/likelihoods/vMF.hpp:14:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<CppAD::AD<double>, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] 14 | for(size_t i = 0; i < u.size(); i++) | ~~^~~~~~~~~~ In file included from tapesmd.h:8, from tapesmd.cpp:1: ../inst/include/manifoldtransforms/bdryweights.hpp: In instantiation of ‘Type bdryweight::minsq(const Eigen::Matrix<Type, -1, 1>&, const double&) [with Type = CppAD::AD<double>]’: tapesmd.cpp:17:25: required from here 17 | h2fun = bdryweight::minsq; | ^~~~~ ../inst/include/manifoldtransforms/bdryweights.hpp:30:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<CppAD::AD<double>, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] 30 | for(size_t i=0;i<x.size();i++){ | ~^~~~~~~~~ In file included from tapesmd.h:10: ../inst/include/utils/PrintFor.hpp: In instantiation of ‘void PrintForVec(const char*, const T&) [with T = Eigen::Matrix<CppAD::AD<double>, -1, 1>]’: tapesmd.cpp:52:18: required from here 52 | PrintForVec("\n\n(START) theta is: ", theta); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/utils/PrintFor.hpp:11:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<CppAD::AD<double>, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] 11 | for(size_t i=1; i<printvec.size(); i++){ | ~^~~~~~~~~~~~~~~~ ../inst/include/utils/PrintFor.hpp: In instantiation of ‘void PrintForMatrix(const char*, const Eigen::Matrix<Type, -1, -1>&) [with T = CppAD::AD<double>]’: tapesmd.cpp:60:32: required from here 60 | if (verbose){PrintForMatrix("\nThe value of Pmat is: \n", Pmat);} | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/utils/PrintFor.hpp:20:20: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 20 | for(size_t i=1; i<printmat.cols(); i++){ | ~^~~~~~~~~~~~~~~~ ../inst/include/utils/PrintFor.hpp:23:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 23 | for(size_t row=1; row<printmat.rows(); row++){ | ~~~^~~~~~~~~~~~~~~~ ../inst/include/utils/PrintFor.hpp:25:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 25 | for(size_t col=1; col<printmat.cols(); col++){ | ~~~^~~~~~~~~~~~~~~~ g++ -std=gnu++17 -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/RcppEigen/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 temp_file.cpp -o temp_file.o g++ -std=gnu++17 -shared -L/usr/local/lib64 -o scorematchingad.so RcppExports.o abort_recording.o approx.o error_handler.o exposemanifold.o fixdynamic.o pADFun.o pADFun_retape.o tapebdryweight.o tapell.o tapesmd.o temp_file.o make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/scorematchingad/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/scorematchingad/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/scorematchingad/src' installing to /data/gannet/ripley/R/packages/tests-devel/scorematchingad.Rcheck/00LOCK-scorematchingad/00new/scorematchingad/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading in method for ‘print’ with signature ‘"Rcpp_ADFun"’: no definition for class “Rcpp_ADFun” in method for ‘show’ with signature ‘"Rcpp_ADFun"’: no definition for class “Rcpp_ADFun” ** 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 (scorematchingad)