* installing *source* package ‘ProjectionBasedClustering’ ...
** this is package ‘ProjectionBasedClustering’ version ‘1.2.2’
** package ‘ProjectionBasedClustering’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/ProjectionBasedClustering/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 DijkstraSSSP.cpp -o DijkstraSSSP.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 NeRV.cpp -o NeRV.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 c_measure.cpp -o c_measure.o
DijkstraSSSP.cpp: In function ‘Rcpp::NumericVector DijkstraSSSP(Rcpp::NumericMatrix, Rcpp::NumericMatrix, int)’:
DijkstraSSSP.cpp:38:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
38 | for(int i=0;i<n;i++) //Building Graph
| ^~~
DijkstraSSSP.cpp:48:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
48 | for(int i=0;i<sz;i++) //Set initial distances to Infinity
| ^~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 calculatedistancematrix.cpp -o calculatedistancematrix.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 conjugategradientopt.cpp -o conjugategradientopt.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 conttrust.cpp -o conttrust.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 datamatrix.cpp -o datamatrix.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 dataset.cpp -o dataset.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 distancematrix.cpp -o distancematrix.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 dynamicdouble.cpp -o dynamicdouble.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 euclidean.cpp -o euclidean.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 euclideansquared.cpp -o euclideansquared.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 exception.cpp -o exception.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 goldensectionsearch.cpp -o goldensectionsearch.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 inputprobentropy.cpp -o inputprobentropy.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 klmeasure.cpp -o klmeasure.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 klrank.cpp -o klrank.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 nervcostfunction.cpp -o nervcostfunction.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 nervoptstrat.cpp -o nervoptstrat.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 nervprobability.cpp -o nervprobability.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 randomdatagenerator.cpp -o randomdatagenerator.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 rankmatrix.cpp -o rankmatrix.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 recorder.cpp -o recorder.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 splittree.cpp -o splittree.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -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 tsne.cpp -o tsne.o
In member function ‘void TSNE<treeT, dist_fn>::run(double*, int, int, double*, int, double, double, int, int, int, int, bool, int, double, double, double*, bool, double) [with treeT = SplitTree; double (* dist_fn)(const DataPoint&, const DataPoint&) = euclidean_distance]’,
inlined from ‘Rcpp::NumericMatrix opt_multicore_tnse_cpp(Rcpp::NumericMatrix, int, double, int, int, double, int, double, double, int, double, int)’ at tsne.cpp:653:23:
tsne.cpp:186:17: warning: ‘error_rc_prev’ may be used uninitialized [-Wmaybe-uninitialized]
186 | if (error_rc < error_rc_prev && iter > auto_iter_buffer_ee) {
| ^~
tsne.cpp: In function ‘Rcpp::NumericMatrix opt_multicore_tnse_cpp(Rcpp::NumericMatrix, int, double, int, int, double, int, double, double, int, double, int)’:
tsne.cpp:159:12: note: ‘error_rc_prev’ was declared here
159 | double error_rc_prev; // to store previous iteration's error rate of change in auto_iter mode
| ^~~~~~~~~~~~~
In member function ‘double TSNE<treeT, dist_fn>::computeGradient(int*, int*, double*, double*, int, int, double*, double, bool) [with treeT = SplitTree; double (* dist_fn)(const DataPoint&, const DataPoint&) = euclidean_distance]’,
inlined from ‘void TSNE<treeT, dist_fn>::run(double*, int, int, double*, int, double, double, int, int, int, int, bool, int, double, double, double*, bool, double) [with treeT = SplitTree; double (* dist_fn)(const DataPoint&, const DataPoint&) = euclidean_distance]’ at tsne.cpp:180:39,
inlined from ‘Rcpp::NumericMatrix opt_multicore_tnse_cpp(Rcpp::NumericMatrix, int, double, int, int, double, int, double, double, int, double, int)’ at tsne.cpp:653:23:
tsne.cpp:271:13: warning: ‘need_eval_error_algo’ may be used uninitialized [-Wmaybe-uninitialized]
271 | #pragma omp parallel for reduction(+:P_i_sum,C)
| ^~~
tsne.cpp: In function ‘Rcpp::NumericMatrix opt_multicore_tnse_cpp(Rcpp::NumericMatrix, int, double, int, int, double, int, double, double, int, double, int)’:
tsne.cpp:169:14: note: ‘need_eval_error_algo’ was declared here
169 | bool need_eval_error_algo, need_eval_error_verbose = false;
| ^~~~~~~~~~~~~~~~~~~~
In member function ‘void TSNE<treeT, dist_fn>::run(double*, int, int, double*, int, double, double, int, int, int, int, bool, int, double, double, double*, bool, double) [with treeT = SplitTree; double (* dist_fn)(const DataPoint&, const DataPoint&) = euclidean_distance_squared]’,
inlined from ‘Rcpp::NumericMatrix opt_multicore_tnse_cpp(Rcpp::NumericMatrix, int, double, int, int, double, int, double, double, int, double, int)’ at tsne.cpp:649:23:
tsne.cpp:186:17: warning: ‘error_rc_prev’ may be used uninitialized [-Wmaybe-uninitialized]
186 | if (error_rc < error_rc_prev && iter > auto_iter_buffer_ee) {
| ^~
tsne.cpp: In function ‘Rcpp::NumericMatrix opt_multicore_tnse_cpp(Rcpp::NumericMatrix, int, double, int, int, double, int, double, double, int, double, int)’:
tsne.cpp:159:12: note: ‘error_rc_prev’ was declared here
159 | double error_rc_prev; // to store previous iteration's error rate of change in auto_iter mode
| ^~~~~~~~~~~~~
In member function ‘double TSNE<treeT, dist_fn>::computeGradient(int*, int*, double*, double*, int, int, double*, double, bool) [with treeT = SplitTree; double (* dist_fn)(const DataPoint&, const DataPoint&) = euclidean_distance_squared]’,
inlined from ‘void TSNE<treeT, dist_fn>::run(double*, int, int, double*, int, double, double, int, int, int, int, bool, int, double, double, double*, bool, double) [with treeT = SplitTree; double (* dist_fn)(const DataPoint&, const DataPoint&) = euclidean_distance_squared]’ at tsne.cpp:180:39,
inlined from ‘Rcpp::NumericMatrix opt_multicore_tnse_cpp(Rcpp::NumericMatrix, int, double, int, int, double, int, double, double, int, double, int)’ at tsne.cpp:649:23:
tsne.cpp:271:13: warning: ‘need_eval_error_algo’ may be used uninitialized [-Wmaybe-uninitialized]
271 | #pragma omp parallel for reduction(+:P_i_sum,C)
| ^~~
tsne.cpp: In function ‘Rcpp::NumericMatrix opt_multicore_tnse_cpp(Rcpp::NumericMatrix, int, double, int, int, double, int, double, double, int, double, int)’:
tsne.cpp:169:14: note: ‘need_eval_error_algo’ was declared here
169 | bool need_eval_error_algo, need_eval_error_verbose = false;
| ^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o ProjectionBasedClustering.so DijkstraSSSP.o NeRV.o RcppExports.o c_measure.o calculatedistancematrix.o conjugategradientopt.o conttrust.o datamatrix.o dataset.o distancematrix.o dynamicdouble.o euclidean.o euclideansquared.o exception.o goldensectionsearch.o inputprobentropy.o klmeasure.o klrank.o nervcostfunction.o nervoptstrat.o nervprobability.o randomdatagenerator.o rankmatrix.o recorder.o splittree.o tsne.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -fopenmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/ProjectionBasedClustering/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/ProjectionBasedClustering/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/ProjectionBasedClustering/src'
installing to /data/gannet/ripley/R/packages/tests-devel/ProjectionBasedClustering.Rcheck/00LOCK-ProjectionBasedClustering/00new/ProjectionBasedClustering/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (ProjectionBasedClustering)