* installing *source* package ‘fastkmedoids’ ...
** package ‘fastkmedoids’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
using C++11
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/fastkmedoids/src'
g++-13 -std=gnu++11 -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 RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++11 -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 pam.cpp -o pam.o
In file included from pam.cpp:21:
pam.h: In member function 'std::vector<int> Xoroshiro128Random::randomSample(int, int)':
pam.h:82:35: warning: comparison of integer expressions of different signedness: 'std::unordered_map<int, bool>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   82 |         while (sample_dict.size() < samplesize) {
      |                ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
pam.h: At global scope:
pam.h:465:25: warning: 'virtual Assignment& Assignment::operator=(const Assignment&)' was hidden [-Woverloaded-virtual=]
  465 |     virtual Assignment& operator=(const Assignment& other);
      |                         ^~~~~~~~
pam.h:533:7: note:   by 'FastAssignment& FastAssignment::operator=(const FastAssignment&)'
  533 | class FastAssignment : public Assignment
      |       ^~~~~~~~~~~~~~
pam.cpp: In member function 'double LAB::getMinDist(int, std::vector<int>&, std::vector<double>&)':
pam.cpp:132:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  132 |         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:166:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  166 |             for (int j=0; j<tempd.size(); ++j) tempd[j] = DBL_MIN;
      |                           ~^~~~~~~~~~~~~
pam.cpp:191:25: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  191 |     while(medids.size() < k) {
      |           ~~~~~~~~~~~~~~^~~
pam.cpp:203:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  203 |             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:374:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  374 |         for (int j=0; j<means.size(); ++j) {
      |                       ~^~~~~~~~~~~~~
pam.cpp: In member function 'void FastPAM::findBestSwaps(std::vector<int>&, std::vector<int>&, std::vector<double>&, std::vector<double>&)':
pam.cpp:522:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  522 |         for (int j=0; j<n_medoids; ++j) cost[j] = -nearest[h];
      |                       ~^~~~~~~~~~
pam.cpp:527:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  527 |         for(int i = 0; i < cost.size(); i++) {
      |                        ~~^~~~~~~~~~~~~
pam.cpp: In member function 'virtual void FastPAM::computeReassignmentCost(int, std::vector<double>&)':
pam.cpp:566:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  566 |             for(int pi = pj + 1; pi < cost.size(); pi++) {
      |                                  ~~~^~~~~~~~~~~~~
pam.cpp: In member function 'virtual double FastPAM::assignToNearestCluster(std::vector<int>&)':
pam.cpp:608:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  608 |         for (int h=0; h< means.size(); ++h) {
      |                       ~^~~~~~~~~~~~~~
pam.cpp: In member function 'int FastPAM::argmin(const std::vector<double>&)':
pam.cpp:639:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  639 |     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:716:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  716 |     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:740:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  740 |     for (int i=0; i<previous.size(); ++i) {
      |                   ~^~~~~~~~~~~~~~~~
pam.cpp:748:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  748 |     for (int i=0; i<rest_rnds.size(); ++i) {
      |                   ~^~~~~~~~~~~~~~~~~
pam.cpp:756:28: warning: comparison of integer expressions of different signedness: 'std::unordered_map<int, bool>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  756 |     if (sample_dict.size() < samplesize) {
      |         ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
pam.cpp:761:58: warning: comparison of integer expressions of different signedness: 'std::unordered_map<int, bool>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  761 |         for (int i=0; i<samplesize && sample_dict.size() < samplesize; ++i) {
      |                                       ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
pam.cpp: In member function 'virtual double CLARA::run()':
pam.cpp:822:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  822 |             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:844:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  844 |     for (int j=0; j<r_assignment.size(); ++j) {
      |                   ~^~~~~~~~~~~~~~~~~~~~
pam.cpp:856:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  856 |         for (int i=0; i<means.size(); ++i) {
      |                       ~^~~~~~~~~~~~~
pam.cpp: In member function 'virtual double FastCLARA::run()':
pam.cpp:916:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  916 |             for (int k=0; k<bestmedoids.size(); ++k ) {
      |                           ~^~~~~~~~~~~~~~~~~~~
pam.cpp: In member function 'virtual double Assignment::recompute(int, int, double, int, double)':
pam.cpp:1119:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1119 |     for(int i = 0; i < medoids.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~
pam.cpp: In member function 'virtual bool Assignment::hasMedoid(int)':
pam.cpp:1157:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1157 |         for (int i=0; i<medoids.size(); ++i) {
      |                       ~^~~~~~~~~~~~~~~
pam.cpp: In member function 'virtual double PAM::run(std::vector<int>&, int)':
pam.cpp:344:30: warning: 'bestid' may be used uninitialized [-Wmaybe-uninitialized]
  344 |         medoids[bestcluster] =  bestid;
pam.cpp:313:9: note: 'bestid' was declared here
  313 |     int bestid;
      |         ^~~~~~
g++-13 -std=gnu++11 -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 rcpp_fastkmedoids.cpp -o rcpp_fastkmedoids.o
In file included from rcpp_fastkmedoids.cpp:19:
pam.h: In member function 'std::vector<int> Xoroshiro128Random::randomSample(int, int)':
pam.h:82:35: warning: comparison of integer expressions of different signedness: 'std::unordered_map<int, bool>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   82 |         while (sample_dict.size() < samplesize) {
      |                ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
pam.h: At global scope:
pam.h:465:25: warning: 'virtual Assignment& Assignment::operator=(const Assignment&)' was hidden [-Woverloaded-virtual=]
  465 |     virtual Assignment& operator=(const Assignment& other);
      |                         ^~~~~~~~
pam.h:533:7: note:   by 'FastAssignment& FastAssignment::operator=(const FastAssignment&)'
  533 | class FastAssignment : public Assignment
      |       ^~~~~~~~~~~~~~
g++-13 -std=gnu++11 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o fastkmedoids.so RcppExports.o pam.o rcpp_fastkmedoids.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/fastkmedoids/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/fastkmedoids/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/fastkmedoids/src'
installing to /data/gannet/ripley/R/packages/tests-devel/fastkmedoids.Rcheck/00LOCK-fastkmedoids/00new/fastkmedoids/libs
** R
** 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 (fastkmedoids)