* 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<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-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<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-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<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-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<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-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<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 -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<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 -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<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-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)