* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’ * installing *source* package ‘PerMallows’ ... ** package ‘PerMallows’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-16) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-16) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpycPT0P/R.INSTALL2ee8ecb8df13c/PerMallows/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Ferrers_diagram.cpp -o Ferrers_diagram.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Kendall.cpp -o Kendall.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -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-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -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-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c registerDynamicSymbol.c -o registerDynamicSymbol.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -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++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -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 -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpycPT0P/R.INSTALL2ee8ecb8df13c/PerMallows/src' make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpycPT0P/R.INSTALL2ee8ecb8df13c/PerMallows/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpycPT0P/R.INSTALL2ee8ecb8df13c/PerMallows/src' installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-PerMallows/00new/PerMallows/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package ‘PerMallows’ finding HTML links ... done compose html count.perms html cycle2str html cycles2perm html data.apa html data.order html decomp2perm html dgmm html distance html dmm html dot-CAYLEY.DISTANCE html expectation.gmm html expectation.mm html freq.matrix html generate.aux.files html identity.permutation html insert html inverse.perm html inversion html is.permutation html lgmm html lgmm.theta html lmm html lmm.theta html marginal html maxi.dist html order.ratings html perm.sample.med html perm.sample.small html perm2cycles html perm2decomp html permutations.of html rdist.perm html read.perms html rgmm html rmm html runif.permutation html swap html ** 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)