* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘fastkmedoids’ ...
** this is package ‘fastkmedoids’ version ‘1.7’
** package ‘fastkmedoids’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-16 (Debian 16.2.0-1) 16.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpMwZvkI/R.INSTALL1c94ab69dfdaa3/fastkmedoids/src'
g++-16 -std=gnu++20 -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 RcppExports.cpp -o RcppExports.o
g++-16 -std=gnu++20 -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 pam.cpp -o pam.o
In file included from pam.cpp:22:
pam.h: In member function ‘int Xoroshiro128Random::nextInt(int)’:
pam.h:58:55: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses]
58 | int r = (int)((n & -n) == n ? nextLong() & n - 1 // power of two
| ~~^~~
pam.h: In member function ‘std::vector<int> Xoroshiro128Random::randomSample(int, int)’:
pam.h:83:35: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<int, bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
83 | while (sample_dict.size() < samplesize) {
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
pam.h: At global scope:
pam.h:466:25: warning: ‘virtual Assignment& Assignment::operator=(const Assignment&)’ was hidden [-Woverloaded-virtual=]
466 | virtual Assignment& operator=(const Assignment& other);
| ^~~~~~~~
pam.h:534:7: note: by ‘FastAssignment& FastAssignment::operator=(const FastAssignment&)’
534 | class FastAssignment : public Assignment
| ^~~~~~~~~~~~~~
pam.cpp: In member function ‘double LAB::getMinDist(int, std::vector<int>&, std::vector<double>&)’:
pam.cpp:133:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
133 | for (int i=0; i<medids.size(); ++i) {
| ~^~~~~~~~~~~~~~
pam.cpp: In member function ‘virtual std::vector<int> LAB::run(const std::vector<int>&, int)’:
pam.cpp:167:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
167 | for (int j=0; j<tempd.size(); ++j) tempd[j] = DBL_MIN;
| ~^~~~~~~~~~~~~
pam.cpp:192:25: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
192 | while(medids.size() < k) {
| ~~~~~~~~~~~~~~^~~
pam.cpp:204:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
204 | for (int j=0; j<tempd.size(); ++j) tempd[j] = DBL_MIN;
| ~^~~~~~~~~~~~~
pam.cpp: In member function ‘virtual double PAM::assignToNearestCluster(std::vector<int>&)’:
pam.cpp:375:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
375 | for (int j=0; j<means.size(); ++j) {
| ~^~~~~~~~~~~~~
pam.cpp: In member function ‘virtual double FastPAM::run(std::vector<int>&, int)’:
pam.cpp:449:9: warning: variable ‘fastswaps’ set but not used [-Wunused-but-set-variable=]
449 | int fastswaps = 0; // For statistics
| ^~~~~~~~~
pam.cpp: In member function ‘void FastPAM::findBestSwaps(std::vector<int>&, std::vector<int>&, std::vector<double>&, std::vector<double>&)’:
pam.cpp:523:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
523 | for (int j=0; j<n_medoids; ++j) cost[j] = -nearest[h];
| ~^~~~~~~~~~
pam.cpp:528:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
528 | for(int i = 0; i < cost.size(); i++) {
| ~~^~~~~~~~~~~~~
pam.cpp: In member function ‘virtual void FastPAM::computeReassignmentCost(int, std::vector<double>&)’:
pam.cpp:567:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
567 | for(int pi = pj + 1; pi < cost.size(); pi++) {
| ~~~^~~~~~~~~~~~~
pam.cpp: In member function ‘virtual double FastPAM::assignToNearestCluster(std::vector<int>&)’:
pam.cpp:609:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
609 | for (int h=0; h< means.size(); ++h) {
| ~^~~~~~~~~~~~~~
pam.cpp: In member function ‘int FastPAM::argmin(const std::vector<double>&)’:
pam.cpp:643:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
643 | for(int i = 0; i < best.size(); i++) {
| ~~^~~~~~~~~~~~~
pam.cpp: In member function ‘int FastPAM::updateSecondNearest(int, std::vector<int>&, int, double, int)’:
pam.cpp:720:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
720 | for (int i=0; i<medoids.size(); ++i) {
| ~^~~~~~~~~~~~~~~
pam.cpp: In static member function ‘static std::vector<int> PAMUtils::randomSample(Xoroshiro128Random&, int, int, const std::vector<int>&)’:
pam.cpp:744:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
744 | for (int i=0; i<previous.size(); ++i) {
| ~^~~~~~~~~~~~~~~~
pam.cpp:752:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
752 | for (int i=0; i<rest_rnds.size(); ++i) {
| ~^~~~~~~~~~~~~~~~~
pam.cpp:760:28: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<int, bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
760 | if (sample_dict.size() < samplesize) {
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
pam.cpp:765:58: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<int, bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
765 | for (int i=0; i<samplesize && sample_dict.size() < samplesize; ++i) {
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
pam.cpp: In member function ‘virtual double CLARA::run()’:
pam.cpp:826:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
826 | for (int k=0; k<bestmedoids.size(); ++k ) {
| ~^~~~~~~~~~~~~~~~~~~
pam.cpp: In member function ‘double CLARA::assignRemainingToNearestCluster(std::vector<int>&, std::vector<int>&, std::vector<int>&, std::vector<int>&)’:
pam.cpp:848:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
848 | for (int j=0; j<r_assignment.size(); ++j) {
| ~^~~~~~~~~~~~~~~~~~~~
pam.cpp:860:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
860 | for (int i=0; i<means.size(); ++i) {
| ~^~~~~~~~~~~~~
pam.cpp: In member function ‘virtual double FastCLARA::run()’:
pam.cpp:920:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
920 | for (int k=0; k<bestmedoids.size(); ++k ) {
| ~^~~~~~~~~~~~~~~~~~~
pam.cpp: In member function ‘virtual double Assignment::recompute(int, int, double, int, double)’:
pam.cpp:1123:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1123 | for(int i = 0; i < medoids.size(); i++) {
| ~~^~~~~~~~~~~~~~~~
pam.cpp: In member function ‘virtual bool Assignment::hasMedoid(int)’:
pam.cpp:1161:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1161 | for (int i=0; i<medoids.size(); ++i) {
| ~^~~~~~~~~~~~~~~
pam.cpp: In member function ‘virtual double PAM::run(std::vector<int>&, int)’:
pam.cpp:345:30: warning: ‘bestid’ may be used uninitialized [-Wmaybe-uninitialized]
345 | medoids[bestcluster] = bestid;
pam.cpp:314:9: note: ‘bestid’ was declared here
314 | int bestid;
| ^~~~~~
In file included from /usr/include/c++/16/bits/stl_iterator.h:78,
from /usr/include/c++/16/bits/stl_algobase.h:66,
from /usr/include/c++/16/bits/stl_tree.h:65,
from /usr/include/c++/16/map:64,
from pam.cpp:14:
In function ‘constexpr _Tp* std::construct_at(_Tp*, _Args&& ...) [with _Tp = int; _Args = {const int&}]’,
inlined from ‘static constexpr void std::allocator_traits<std::allocator<_Up> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = int; _Args = {const int&}; _Tp = int]’ at /usr/include/c++/16/bits/alloc_traits.h:716:21,
inlined from ‘constexpr void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const int&}; _Tp = int; _Alloc = std::allocator<int>]’ at /usr/include/c++/16/bits/vector.tcc:594:26,
inlined from ‘constexpr void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = int; _Alloc = std::allocator<int>]’ at /usr/include/c++/16/bits/stl_vector.h:1417:21,
inlined from ‘virtual std::vector<int> BUILD::run(const std::vector<int>&, int)’ at pam.cpp:63:25:
/usr/include/c++/16/bits/stl_construct.h:110:16: warning: ‘bestid’ may be used uninitialized [-Wmaybe-uninitialized]
110 | return ::new(__loc) _Tp(std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pam.cpp: In member function ‘virtual std::vector<int> BUILD::run(const std::vector<int>&, int)’:
pam.cpp:43:9: note: ‘bestid’ was declared here
43 | int bestid;
| ^~~~~~
g++-16 -std=gnu++20 -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 rcpp_fastkmedoids.cpp -o rcpp_fastkmedoids.o
In file included from rcpp_fastkmedoids.cpp:19:
pam.h: In member function ‘int Xoroshiro128Random::nextInt(int)’:
pam.h:58:55: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses]
58 | int r = (int)((n & -n) == n ? nextLong() & n - 1 // power of two
| ~~^~~
pam.h: In member function ‘std::vector<int> Xoroshiro128Random::randomSample(int, int)’:
pam.h:83:35: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<int, bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
83 | while (sample_dict.size() < samplesize) {
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
pam.h: At global scope:
pam.h:466:25: warning: ‘virtual Assignment& Assignment::operator=(const Assignment&)’ was hidden [-Woverloaded-virtual=]
466 | virtual Assignment& operator=(const Assignment& other);
| ^~~~~~~~
pam.h:534:7: note: by ‘FastAssignment& FastAssignment::operator=(const FastAssignment&)’
534 | class FastAssignment : public Assignment
| ^~~~~~~~~~~~~~
g++-16 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o fastkmedoids.so RcppExports.o pam.o rcpp_fastkmedoids.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpMwZvkI/R.INSTALL1c94ab69dfdaa3/fastkmedoids/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpMwZvkI/R.INSTALL1c94ab69dfdaa3/fastkmedoids/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpMwZvkI/R.INSTALL1c94ab69dfdaa3/fastkmedoids/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-fastkmedoids/00new/fastkmedoids/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘fastkmedoids’
finding HTML links ... done
KmedoidsResult-class html
fastclara html
fastclarans html
fastkmedoids-package html
fastpam html
pam 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 (fastkmedoids)