* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘geokmeans’ ...
** this is package ‘geokmeans’ version ‘0.1.0’
** package ‘geokmeans’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++17
using C++ compiler: ‘Debian clang version 22.1.8 (1)’
using C++17
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp3LKwzH/R.INSTALL363eac5ca4502/geokmeans/src'
clang++-22 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DGEOKM_R_BUILD -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:29:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Sparse:26:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/SparseCore:61:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from RcppExports.cpp:4:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:29:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Sparse:29:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/SparseLU:35:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
In file included from RcppExports.cpp:4:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:31:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
72 | Index replacements = 0;
| ^
In file included from RcppExports.cpp:4:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:37:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
246 | int count = 0;
| ^
5 warnings generated.
clang++-22 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DGEOKM_R_BUILD -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c kmeans_rcpp.cpp -o kmeans_rcpp.o
In file included from kmeans_rcpp.cpp:15:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:29:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Sparse:26:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/SparseCore:61:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
273 | Index count = 0;
| ^
In file included from kmeans_rcpp.cpp:15:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:29:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/Sparse:29:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/SparseLU:35:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree
| ^
In file included from kmeans_rcpp.cpp:15:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:31:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
72 | Index replacements = 0;
| ^
In file included from kmeans_rcpp.cpp:15:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigen.h:25:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/RcppEigenForward.h:37:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
246 | int count = 0;
| ^
In file included from kmeans_rcpp.cpp:44:
In file included from ./IOutils.h:9:
./misc_utils.h:143:5: warning: unused variable 'limit' [-Wunused-variable]
143 | int limit = 0;
| ^~~~~
In file included from kmeans_rcpp.cpp:44:
./IOutils.h:181:9: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation]
181 | numRows-=1;
| ^
./IOutils.h:179:5: note: previous statement is here
179 | if (head_present)
| ^
In file included from kmeans_rcpp.cpp:45:
./algo_utils.h:231:16: warning: unused variable 'j' [-Wunused-variable]
231 | int i = 0, j = 0, size = dataset.size();
| ^
./algo_utils.h:654:17: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
654 | diff += (temp_diff * temp_diff);
| ^
./algo_utils.h:652:13: note: previous statement is here
652 | for (j=0; j< new_centroids[i].size(); j++)
| ^
./algo_utils.h:706:43: warning: unused variable 'acc1' [-Wunused-variable]
706 | float temp = 0, temp1 = 0, temp2 = 0, acc1 = 0, acc2 = 0;
| ^~~~
./algo_utils.h:706:53: warning: unused variable 'acc2' [-Wunused-variable]
706 | float temp = 0, temp1 = 0, temp2 = 0, acc1 = 0, acc2 = 0;
| ^~~~
In file included from kmeans_rcpp.cpp:47:
./lloyd_kmeans.h:36:17: warning: unused variable 'pu' [-Wunused-variable]
36 | print_utils pu;
| ^~
./lloyd_kmeans.h:44:9: warning: unused variable 'tt' [-Wunused-variable]
44 | int tt = 1;
| ^~
In file included from kmeans_rcpp.cpp:48:
In file included from ./geokmeans.h:9:
./geokm_utils.h:191:11: warning: unused variable 'shortestDist2' [-Wunused-variable]
191 | float shortestDist2 = 0;
| ^~~~~~~~~~~~~
./geokm_utils.h:271:11: warning: unused variable 'shortestDist2' [-Wunused-variable]
271 | float shortestDist2 = 0;
| ^~~~~~~~~~~~~
./geokm_utils.h:360:50: warning: unused variable 'closest_neighbor' [-Wunused-variable]
360 | int curr_center = 0, ot_center = 0, cnt = 0, closest_neighbor = 0, temp_val = 0, closest_ind = 0;
| ^~~~~~~~~~~~~~~~
./geokm_utils.h:360:72: warning: unused variable 'temp_val' [-Wunused-variable]
360 | int curr_center = 0, ot_center = 0, cnt = 0, closest_neighbor = 0, temp_val = 0, closest_ind = 0;
| ^~~~~~~~
./geokm_utils.h:360:86: warning: unused variable 'closest_ind' [-Wunused-variable]
360 | int curr_center = 0, ot_center = 0, cnt = 0, closest_neighbor = 0, temp_val = 0, closest_ind = 0;
| ^~~~~~~~~~~
./geokm_utils.h:361:11: warning: unused variable 'shortestDist2' [-Wunused-variable]
361 | float shortestDist2 = 0;
| ^~~~~~~~~~~~~
./geokm_utils.h:441:41: warning: unused variable 'cnt' [-Wunused-variable]
441 | int curr_center = 0, ot_center = 0, cnt = 0;
| ^~~
In file included from kmeans_rcpp.cpp:49:
./elkan.h:61:9: warning: unused variable 'tt' [-Wunused-variable]
61 | int tt = 1;
| ^~
./elkan.h:67:16: warning: unused variable 'dc_utils' [-Wunused-variable]
67 | dckm_utils dc_utils;
| ^~~~~~~~
In file included from kmeans_rcpp.cpp:50:
./hamerly.h:42:9: warning: unused variable 'tt' [-Wunused-variable]
42 | int tt = 12;
| ^~
./hamerly.h:48:16: warning: unused variable 'dc_utils' [-Wunused-variable]
48 | dckm_utils dc_utils;
| ^~~~~~~~
In file included from kmeans_rcpp.cpp:51:
./annulus.h:97:9: warning: unused variable 'v' [-Wunused-variable]
97 | int v = 0;
| ^
In file included from kmeans_rcpp.cpp:52:
./exponion.h:72:19: warning: unused variable 'ann' [-Wunused-variable]
72 | annulus_utils ann;
| ^~~
./exponion.h:87:9: warning: unused variable 'tt' [-Wunused-variable]
87 | int tt = 1;
| ^~
./exponion.h:88:9: warning: unused variable 'my_point' [-Wunused-variable]
88 | int my_point = 424;
| ^~~~~~~~
In file included from kmeans_rcpp.cpp:53:
./ball_kmeans_xf.h:31:1: warning: typedef requires a name [-Wmissing-declarations]
31 | typedef struct Neighbor
| ^~~~~~~~~~~~~~~~~~~~~~~
./ball_kmeans_xf.h:99:17: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
99 | diff = diff + (temp_diff * temp_diff);
| ^
./ball_kmeans_xf.h:97:13: note: previous statement is here
97 | for (j=0; j<new_centroids.cols(); j++)
| ^
./ball_kmeans_xf.h:434:21: warning: unused variable 'lenth' [-Wunused-variable]
434 | int lenth = old_now_index.size();
| ^~~~~
./ball_kmeans_xf.h:553:18: warning: variable 'now_centers_rows' set but not used [-Wunused-but-set-variable]
553 | unsigned int now_centers_rows;
| ^
./ball_kmeans_xf.h:570:10: warning: unused variable 'start' [-Wunused-variable]
570 | auto start = std::chrono::high_resolution_clock::now();
| ^~~~~
In file included from kmeans_rcpp.cpp:49:
./elkan.h:56:40: warning: unused variable 'k' [-Wunused-variable]
56 | Tint my_cluster = 0, i = 0, j = 0, k = 0, l = 0, m = 0;
| ^
kmeans_rcpp.cpp:145:19: note: in instantiation of function template specialization 'elkan_kmeans<float, int>' requested here
145 | output_data r = elkan_kmeans(X, num_clusters, static_cast<float>(threshold),
| ^
In file included from kmeans_rcpp.cpp:49:
./elkan.h:56:47: warning: unused variable 'l' [-Wunused-variable]
56 | Tint my_cluster = 0, i = 0, j = 0, k = 0, l = 0, m = 0;
| ^
./elkan.h:56:54: warning: unused variable 'm' [-Wunused-variable]
56 | Tint my_cluster = 0, i = 0, j = 0, k = 0, l = 0, m = 0;
| ^
./elkan.h:57:37: warning: unused variable 'vec_sum' [-Wunused-variable]
57 | Tfloat temp_diff = 0, diff = 0, vec_sum = 0;
| ^~~~~~~
In file included from kmeans_rcpp.cpp:50:
./hamerly.h:38:40: warning: unused variable 'k' [-Wunused-variable]
38 | Tint my_cluster = 0, i = 0, j = 0, k = 0, l = 0, m = 0;
| ^
kmeans_rcpp.cpp:156:19: note: in instantiation of function template specialization 'hamerly_kmeans<float, int>' requested here
156 | output_data r = hamerly_kmeans(X, num_clusters, static_cast<float>(threshold),
| ^
In file included from kmeans_rcpp.cpp:50:
./hamerly.h:38:47: warning: unused variable 'l' [-Wunused-variable]
38 | Tint my_cluster = 0, i = 0, j = 0, k = 0, l = 0, m = 0;
| ^
./hamerly.h:38:54: warning: unused variable 'm' [-Wunused-variable]
38 | Tint my_cluster = 0, i = 0, j = 0, k = 0, l = 0, m = 0;
| ^
./hamerly.h:39:37: warning: unused variable 'vec_sum' [-Wunused-variable]
39 | Tfloat temp_diff = 0, diff = 0, vec_sum = 0, max123 = 0, dist =0;
| ^~~~~~~
In file included from kmeans_rcpp.cpp:51:
./annulus.h:88:24: warning: unused variable 'k' [-Wunused-variable]
88 | Tint i = 0, j = 0, k = 0, l = 0, m = 0;
| ^
kmeans_rcpp.cpp:167:19: note: in instantiation of function template specialization 'annulus<float, int>' requested here
167 | output_data r = annulus(X, num_clusters, static_cast<float>(threshold),
| ^
In file included from kmeans_rcpp.cpp:51:
./annulus.h:88:31: warning: unused variable 'l' [-Wunused-variable]
88 | Tint i = 0, j = 0, k = 0, l = 0, m = 0;
| ^
./annulus.h:88:38: warning: unused variable 'm' [-Wunused-variable]
88 | Tint i = 0, j = 0, k = 0, l = 0, m = 0;
| ^
./annulus.h:89:37: warning: unused variable 'vec_sum' [-Wunused-variable]
89 | Tfloat temp_diff = 0, diff = 0, vec_sum = 0, max = 0, dist2 =0;
| ^~~~~~~
./annulus.h:89:50: warning: unused variable 'max' [-Wunused-variable]
89 | Tfloat temp_diff = 0, diff = 0, vec_sum = 0, max = 0, dist2 =0;
| ^~~
In file included from kmeans_rcpp.cpp:52:
./exponion.h:68:24: warning: unused variable 'k' [-Wunused-variable]
68 | Tint i = 0, j = 0, k = 0, l = 0, m = 0;
| ^
kmeans_rcpp.cpp:178:19: note: in instantiation of function template specialization 'exponion<float, int>' requested here
178 | output_data r = exponion(X, num_clusters, static_cast<float>(threshold),
| ^
In file included from kmeans_rcpp.cpp:52:
./exponion.h:68:31: warning: unused variable 'l' [-Wunused-variable]
68 | Tint i = 0, j = 0, k = 0, l = 0, m = 0;
| ^
./exponion.h:68:38: warning: unused variable 'm' [-Wunused-variable]
68 | Tint i = 0, j = 0, k = 0, l = 0, m = 0;
| ^
./exponion.h:69:37: warning: unused variable 'vec_sum' [-Wunused-variable]
69 | Tfloat temp_diff = 0, diff = 0, vec_sum = 0, max = 0, dist2 =0;
| ^~~~~~~
./exponion.h:69:50: warning: unused variable 'max' [-Wunused-variable]
69 | Tfloat temp_diff = 0, diff = 0, vec_sum = 0, max = 0, dist2 =0;
| ^~~
In file included from kmeans_rcpp.cpp:48:
In file included from ./geokmeans.h:9:
./geokm_utils.h:437:8: warning: unused variable 'radius' [-Wunused-variable]
437 | TD radius = 0;
| ^~~~~~
./exponion.h:101:9: note: in instantiation of function template specialization 'find_exp_neighbors<float, int>' requested here
101 | find_exp_neighbors(centroids, center_dist_mat, closest_center_dist, center_center_dist, dist_counter);
| ^
kmeans_rcpp.cpp:178:19: note: in instantiation of function template specialization 'exponion<float, int>' requested here
178 | output_data r = exponion(X, num_clusters, static_cast<float>(threshold),
| ^
In file included from kmeans_rcpp.cpp:48:
./geokmeans.h:58:10: warning: unused variable 'my_cluster' [-Wunused-variable]
58 | Tint my_cluster = 0, i = 0, j = 0, k = 0, l = 0, m = 0;
| ^~~~~~~~~~
kmeans_rcpp.cpp:189:19: note: in instantiation of function template specialization 'geokmeans<float, int>' requested here
189 | output_data r = geokmeans(X, num_clusters, static_cast<float>(threshold),
| ^
In file included from kmeans_rcpp.cpp:48:
./geokmeans.h:58:40: warning: unused variable 'k' [-Wunused-variable]
58 | Tint my_cluster = 0, i = 0, j = 0, k = 0, l = 0, m = 0;
| ^
./geokmeans.h:58:47: warning: unused variable 'l' [-Wunused-variable]
58 | Tint my_cluster = 0, i = 0, j = 0, k = 0, l = 0, m = 0;
| ^
./geokmeans.h:58:54: warning: unused variable 'm' [-Wunused-variable]
58 | Tint my_cluster = 0, i = 0, j = 0, k = 0, l = 0, m = 0;
| ^
./geokmeans.h:59:37: warning: unused variable 'vec_sum' [-Wunused-variable]
59 | Tfloat temp_diff = 0, diff = 0, vec_sum = 0;
| ^~~~~~~
57 warnings generated.
clang++-22 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o geokmeans.so RcppExports.o kmeans_rcpp.o -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp3LKwzH/R.INSTALL363eac5ca4502/geokmeans/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp3LKwzH/R.INSTALL363eac5ca4502/geokmeans/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp3LKwzH/R.INSTALL363eac5ca4502/geokmeans/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-geokmeans/00new/geokmeans/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (geokmeans)