* installing *source* package ‘PerMallows’ ... ** this is package ‘PerMallows’ version ‘1.14’ ** package ‘PerMallows’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’ 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/PerMallows/src' g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/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 Cayley.cpp -o Cayley.o In file included from Cayley.cpp:12: Ulam.h: In destructor ‘virtual Ulam::~Ulam()’: Ulam.h:115:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for ( int i = 0 ; i < shapes_of_n_->size() ; i++ ) delete shapes_of_n_->at(i); | ~~^~~~~~~~~~~~~~~~~~~~~~ Cayley.cpp: In member function ‘void Cayley::local_search_swap_mm(int, int**, int*, double*)’: Cayley.cpp:1012:35: warning: ‘index_i’ may be used uninitialized [-Wmaybe-uninitialized] 1012 | int aux = sigma_0_inv[index_i]; | ^~~~~~~ Cayley.cpp:980:9: note: ‘index_i’ was declared here 980 | int index_i,index_j, distance_variation = 0; | ^~~~~~~ Cayley.cpp:1013:48: warning: ‘index_j’ may be used uninitialized [-Wmaybe-uninitialized] 1013 | sigma_0_inv[index_i] = sigma_0_inv[index_j]; | ^~~~~~~ Cayley.cpp:980:17: note: ‘index_j’ was declared here 980 | int index_i,index_j, distance_variation = 0; | ^~~~~~~ Cayley.cpp: In member function ‘void Cayley::local_search_swap_gmm(int, int**, int*, double*)’: Cayley.cpp:1087:35: warning: ‘index_i’ may be used uninitialized [-Wmaybe-uninitialized] 1087 | int aux = sigma_0_inv[index_i]; | ^~~~~~~ Cayley.cpp:1040:9: note: ‘index_i’ was declared here 1040 | int index_i,index_j; | ^~~~~~~ Cayley.cpp:1088:48: warning: ‘index_j’ may be used uninitialized [-Wmaybe-uninitialized] 1088 | sigma_0_inv[index_i] = sigma_0_inv[index_j]; | ^~~~~~~ Cayley.cpp:1040:17: note: ‘index_j’ was declared here 1040 | int index_i,index_j; | ^~~~~~~ g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/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 Ferrers_diagram.cpp -o Ferrers_diagram.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/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 Generic.cpp -o Generic.o In file included from Generic.cpp:17: Ulam.h: In destructor ‘virtual Ulam::~Ulam()’: Ulam.h:115:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for ( int i = 0 ; i < shapes_of_n_->size() ; i++ ) delete shapes_of_n_->at(i); | ~~^~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/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 Hamming.cpp -o Hamming.o In file included from Hamming.cpp:11: Lap.h: In function ‘int Lap::lap(int, cost**, col*, row*, cost*, cost*)’: Lap.h:178:27: warning: ‘j2’ may be used uninitialized [-Wmaybe-uninitialized] 178 | rowsol[i] = j1; | ~~~~~~~~~~^~~~ Lap.h:73:21: note: ‘j2’ was declared here 73 | col j, j1, j2, endofpath, last, low, up, *collist, *matches; | ^~ Lap.h:257:23: warning: ‘min’ may be used uninitialized [-Wmaybe-uninitialized] 257 | h = assigncost[i][j1] - v[j1] - min; | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Lap.h:74:14: note: ‘min’ was declared here 74 | cost min, h, umin, usubmin, v2, *d; | ^~~ Lap.h:289:27: warning: ‘last’ may be used uninitialized [-Wmaybe-uninitialized] 289 | for (k = 0; k <= last; k++) | ~~^~~~~~~ Lap.h:73:36: note: ‘last’ was declared here 73 | col j, j1, j2, endofpath, last, low, up, *collist, *matches; | ^~~~ g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/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 Kendall.cpp -o Kendall.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/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 Newton_raphson.cpp -o Newton_raphson.o Newton_raphson.cpp: In member function ‘double Newton_raphson::dbrent(double, double, double, double (Newton_raphson::*)(double), double (Newton_raphson::*)(double), double, double*)’: Newton_raphson.cpp:667:33: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 667 | else | ^~~~ Newton_raphson.cpp:669:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 669 | if (fabs(d) <= fabs(0.5*olde)) { | ^~ g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/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 Ulam.cpp -o Ulam.o In file included from Ulam.cpp:9: Ulam.h: In destructor ‘virtual Ulam::~Ulam()’: Ulam.h:115:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for ( int i = 0 ; i < shapes_of_n_->size() ; i++ ) delete shapes_of_n_->at(i); | ~~^~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/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 Ulam_disk.cpp -o Ulam_disk.o In file included from Ulam_disk.h:25, from Ulam_disk.cpp:10: Ulam.h: In destructor ‘virtual Ulam::~Ulam()’: Ulam.h:115:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for ( int i = 0 ; i < shapes_of_n_->size() ; i++ ) delete shapes_of_n_->at(i); | ~~^~~~~~~~~~~~~~~~~~~~~~ Ulam_disk.cpp: In member function ‘virtual void Ulam_disk::distances_sampling(int, double, int**)’: Ulam_disk.cpp:196:9: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 196 | while(proba_acumul[ target_distance ] < rand_distance)//ekhine pone <= | ^~~~~ Ulam_disk.cpp:198:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 198 | m_target_distances[target_distance]++; | ^~~~~~~~~~~~~~~~~~ Ulam_disk.cpp: In member function ‘void Ulam_disk::read_mutiple_shapes_from_file_bin(int, double*, int, int**, int*)’: Ulam_disk.cpp:298:41: warning: ‘line_mid’ may be used uninitialized [-Wmaybe-uninitialized] 298 | while (line_mid[shape_len[i] + 3] != 0 && shape_len[i] < n_ ){ | ^ Ulam_disk.cpp:260:15: note: ‘line_mid’ was declared here 260 | int * line_mid, *line_pre, * line_last; | ^~~~~~~~ g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/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 Wrapper.cpp -o Wrapper.o In file included from Ulam_disk.h:25, from Wrapper.cpp:10: Ulam.h: In destructor ‘virtual Ulam::~Ulam()’: Ulam.h:115:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for ( int i = 0 ; i < shapes_of_n_->size() ; i++ ) delete shapes_of_n_->at(i); | ~~^~~~~~~~~~~~~~~~~~~~~~ Wrapper.cpp: In function ‘SEXPREC* get_log_likelihood(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: Wrapper.cpp:325:13: warning: variable ‘last_theta’ set but not used [-Wunused-but-set-variable] 325 | int last_theta = n; | ^~~~~~~~~~ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/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++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/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 main.cpp -o main.o In file included from main.cpp:16: Ulam.h: In destructor ‘virtual Ulam::~Ulam()’: Ulam.h:115:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for ( int i = 0 ; i < shapes_of_n_->size() ; i++ ) delete shapes_of_n_->at(i); | ~~^~~~~~~~~~~~~~~~~~~~~~ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/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 registerDynamicSymbol.c -o registerDynamicSymbol.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/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 test.cpp -o test.o In file included from Ulam_disk.h:25, from test.cpp:4: Ulam.h: In destructor ‘virtual Ulam::~Ulam()’: Ulam.h:115:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for ( int i = 0 ; i < shapes_of_n_->size() ; i++ ) delete shapes_of_n_->at(i); | ~~^~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -shared -L/usr/local/lib64 -o PerMallows.so Cayley.o Ferrers_diagram.o Generic.o Hamming.o Kendall.o Newton_raphson.o Ulam.o Ulam_disk.o Wrapper.o init.o main.o registerDynamicSymbol.o test.o make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/PerMallows/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/PerMallows/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/PerMallows/src' installing to /data/gannet/ripley/R/packages/tests-devel/PerMallows.Rcheck/00LOCK-PerMallows/00new/PerMallows/libs ** R ** data ** 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 (PerMallows)