* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* 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-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 '/tmp/RtmpBpwTe5/R.INSTALL3f79771d3f4f9e/PerMallows/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-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<Ferrers_diagram*>::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-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-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-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-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<Ferrers_diagram*>::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-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-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-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-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-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-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-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-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<Ferrers_diagram*>::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-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-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<Ferrers_diagram*>::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-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-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<Ferrers_diagram*>::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 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-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-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-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<Ferrers_diagram*>::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 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-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-devel-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-devel-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<Ferrers_diagram*>::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-devel-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-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpBpwTe5/R.INSTALL3f79771d3f4f9e/PerMallows/src'
make[1]: Entering directory '/tmp/RtmpBpwTe5/R.INSTALL3f79771d3f4f9e/PerMallows/src'
make[1]: Leaving directory '/tmp/RtmpBpwTe5/R.INSTALL3f79771d3f4f9e/PerMallows/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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)