* 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... CMake Deprecation Warning at CMakeLists.txt:11 (CMAKE_MINIMUM_REQUIRED): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is GNU 15.1.1 -- The CXX compiler identification is GNU 15.1.1 -- 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 (28.4s) -- Generating done (0.8s) -- 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) 15.1.1 20250521 (Red Hat 15.1.1-2)’ 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 In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:133, from ../inst/include/scorematchingad_forward.h:6, from abort_recording.cpp:3: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/exceptions.h:61:21: warning: inline function ‘void Rcpp::exception::record_stack_trace()’ used but never defined 61 | inline void record_stack_trace(); | ^~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/exceptions.h:56:21: warning: inline function ‘void Rcpp::exception::copy_stack_trace_to_r() const’ used but never defined 56 | 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:131: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/protection/Armor.h:38:23: warning: inline function ‘Rcpp::Armor& Rcpp::Armor::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 approx.cpp -o approx.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 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)’: fixdynamic.cpp:8:25: warning: comparison of integer expressions of different signedness: ‘Eigen::EigenBase >::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 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 In file included from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:133, 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:61:21: warning: inline function ‘void Rcpp::exception::record_stack_trace()’ used but never defined 61 | inline void record_stack_trace(); | ^~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/exceptions.h:56:21: warning: inline function ‘void Rcpp::exception::copy_stack_trace_to_r() const’ used but never defined 56 | 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:131: /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/protection/Armor.h:38:23: warning: inline function ‘Rcpp::Armor& Rcpp::Armor::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 tapesmd.cpp -o tapesmd.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 temp_file.cpp -o temp_file.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, -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, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] 11 | for(size_t i=1; i&, const Eigen::Matrix&) [with T = CppAD::AD]’: 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&, const Eigen::Matrix&) [with T = CppAD::AD]’: 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, -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&, const double&) [with Type = CppAD::AD]’: 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, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] 30 | for(size_t i=0;i, -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, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] 11 | for(size_t i=1; i&) [with T = CppAD::AD]’: 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