* installing *source* package ‘RPatternJoin’ ... ** this is package ‘RPatternJoin’ version ‘1.0.0’ ** package ‘RPatternJoin’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘clang version 23.1.0-rc2’ make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-clang-trunk/RPatternJoin/src' /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -DARMA_64BIT_WORD -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c RcppExports.cpp -o RcppExports.o /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -DARMA_64BIT_WORD -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c bounded_edit_distance.cpp -o bounded_edit_distance.o bounded_edit_distance.cpp:104:16: error: use of undeclared identifier 'abs' 104 | int dist = abs(a_size - b_size); | ^~~ 1 error generated. make[1]: *** [/data/localhost/ripley/R/R-clang-trunk/etc/Makeconf:197: bounded_edit_distance.o] Error 1 In file included from RcppExports.cpp:4: In file included from /data/localhost/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:51: In file included from /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo:436: /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:198:1: warning: unused function template 'arma_stop_runtime_error' [-Wunused-template] 198 | arma_stop_runtime_error(const T1& x) | ^~~~~~~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:241:1: warning: unused function template 'arma_print' [-Wunused-template] 241 | arma_print(const T1& x, const T2& y) | ^~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:253:1: warning: unused function template 'arma_print' [-Wunused-template] 253 | arma_print(const T1& x, const T2& y, const T3& z) | ^~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:335:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 335 | arma_plain_warn(const T1& arg1) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:346:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 346 | arma_plain_warn(const T1& arg1, const T2& arg2) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:357:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 357 | arma_plain_warn(const T1& arg1, const T2& arg2, const T3& arg3) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:368:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 368 | arma_plain_warn(const T1& arg1, const T2& arg2, const T3& arg3, const T4& arg4) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:545:1: warning: unused function template 'arma_incompat_size_string' [-Wunused-template] 545 | arma_incompat_size_string(const subview_cube& Q, const Mat& A, const char* x) | ^~~~~~~~~~~~~~~~~~~~~~~~~ 8 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -DARMA_64BIT_WORD -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c file_io.cpp -o file_io.o In file included from file_io.cpp:1: In file included from ./include/file_io.hpp:11: In file included from /data/localhost/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:51: In file included from /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo:436: /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:198:1: warning: unused function template 'arma_stop_runtime_error' [-Wunused-template] 198 | arma_stop_runtime_error(const T1& x) | ^~~~~~~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:241:1: warning: unused function template 'arma_print' [-Wunused-template] 241 | arma_print(const T1& x, const T2& y) | ^~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:253:1: warning: unused function template 'arma_print' [-Wunused-template] 253 | arma_print(const T1& x, const T2& y, const T3& z) | ^~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:335:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 335 | arma_plain_warn(const T1& arg1) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:346:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 346 | arma_plain_warn(const T1& arg1, const T2& arg2) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:357:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 357 | arma_plain_warn(const T1& arg1, const T2& arg2, const T3& arg3) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:368:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 368 | arma_plain_warn(const T1& arg1, const T2& arg2, const T3& arg3, const T4& arg4) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:545:1: warning: unused function template 'arma_incompat_size_string' [-Wunused-template] 545 | arma_incompat_size_string(const subview_cube& Q, const Mat& A, const char* x) | ^~~~~~~~~~~~~~~~~~~~~~~~~ 8 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -DARMA_64BIT_WORD -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c main.cpp -o main.o /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -DARMA_64BIT_WORD -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c patterns_generators.cpp -o patterns_generators.o /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -DARMA_64BIT_WORD -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c sim_search_part_patterns.cpp -o sim_search_part_patterns.o /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -DARMA_64BIT_WORD -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c sim_search_patterns.cpp -o sim_search_patterns.o In file included from main.cpp:5: In file included from ./include/duplicates_search.hpp:4: In file included from ./include/file_io.hpp:11: In file included from /data/localhost/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:51: In file included from /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo:436: /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:198:1: warning: unused function template 'arma_stop_runtime_error' [-Wunused-template] 198 | arma_stop_runtime_error(const T1& x) | ^~~~~~~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:241:1: warning: unused function template 'arma_print' [-Wunused-template] 241 | arma_print(const T1& x, const T2& y) | ^~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:253:1: warning: unused function template 'arma_print' [-Wunused-template] 253 | arma_print(const T1& x, const T2& y, const T3& z) | ^~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:335:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 335 | arma_plain_warn(const T1& arg1) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:346:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 346 | arma_plain_warn(const T1& arg1, const T2& arg2) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:357:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 357 | arma_plain_warn(const T1& arg1, const T2& arg2, const T3& arg3) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:368:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 368 | arma_plain_warn(const T1& arg1, const T2& arg2, const T3& arg3, const T4& arg4) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:545:1: warning: unused function template 'arma_incompat_size_string' [-Wunused-template] 545 | arma_incompat_size_string(const subview_cube& Q, const Mat& A, const char* x) | ^~~~~~~~~~~~~~~~~~~~~~~~~ 8 warnings generated. In file included from sim_search_patterns.cpp:1: In file included from ./include/sim_search_patterns.hpp:6: In file included from ./include/map_patterns.hpp:10: In file included from /data/localhost/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:51: In file included from /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo:436: /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:198:1: warning: unused function template 'arma_stop_runtime_error' [-Wunused-template] 198 | arma_stop_runtime_error(const T1& x) | ^~~~~~~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:241:1: warning: unused function template 'arma_print' [-Wunused-template] 241 | arma_print(const T1& x, const T2& y) | ^~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:253:1: warning: unused function template 'arma_print' [-Wunused-template] 253 | arma_print(const T1& x, const T2& y, const T3& z) | ^~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:335:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 335 | arma_plain_warn(const T1& arg1) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:346:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 346 | arma_plain_warn(const T1& arg1, const T2& arg2) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:357:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 357 | arma_plain_warn(const T1& arg1, const T2& arg2, const T3& arg3) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:368:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 368 | arma_plain_warn(const T1& arg1, const T2& arg2, const T3& arg3, const T4& arg4) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:545:1: warning: unused function template 'arma_incompat_size_string' [-Wunused-template] 545 | arma_incompat_size_string(const subview_cube& Q, const Mat& A, const char* x) | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from sim_search_part_patterns.cpp:1: In file included from ./include/sim_search_part_patterns.hpp:6: In file included from ./include/map_patterns.hpp:10: In file included from /data/localhost/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:51: In file included from /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo:436: /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:198:1: warning: unused function template 'arma_stop_runtime_error' [-Wunused-template] 198 | arma_stop_runtime_error(const T1& x) | ^~~~~~~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:241:1: warning: unused function template 'arma_print' [-Wunused-template] 241 | arma_print(const T1& x, const T2& y) | ^~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:253:1: warning: unused function template 'arma_print' [-Wunused-template] 253 | arma_print(const T1& x, const T2& y, const T3& z) | ^~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:335:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 335 | arma_plain_warn(const T1& arg1) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:346:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 346 | arma_plain_warn(const T1& arg1, const T2& arg2) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:357:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 357 | arma_plain_warn(const T1& arg1, const T2& arg2, const T3& arg3) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:368:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 368 | arma_plain_warn(const T1& arg1, const T2& arg2, const T3& arg3, const T4& arg4) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:545:1: warning: unused function template 'arma_incompat_size_string' [-Wunused-template] 545 | arma_incompat_size_string(const subview_cube& Q, const Mat& A, const char* x) | ^~~~~~~~~~~~~~~~~~~~~~~~~ 8 warnings generated. 8 warnings generated. /usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang-trunk/include" -DNDEBUG -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include -DARMA_64BIT_WORD -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c sim_search_semi_patterns.cpp -o sim_search_semi_patterns.o In file included from sim_search_semi_patterns.cpp:1: In file included from ./include/sim_search_semi_patterns.hpp:6: In file included from ./include/map_patterns.hpp:10: In file included from /data/localhost/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/localhost/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:51: In file included from /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo:436: /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:198:1: warning: unused function template 'arma_stop_runtime_error' [-Wunused-template] 198 | arma_stop_runtime_error(const T1& x) | ^~~~~~~~~~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:241:1: warning: unused function template 'arma_print' [-Wunused-template] 241 | arma_print(const T1& x, const T2& y) | ^~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:253:1: warning: unused function template 'arma_print' [-Wunused-template] 253 | arma_print(const T1& x, const T2& y, const T3& z) | ^~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:335:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 335 | arma_plain_warn(const T1& arg1) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:346:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 346 | arma_plain_warn(const T1& arg1, const T2& arg2) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:357:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 357 | arma_plain_warn(const T1& arg1, const T2& arg2, const T3& arg3) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:368:1: warning: unused function template 'arma_plain_warn' [-Wunused-template] 368 | arma_plain_warn(const T1& arg1, const T2& arg2, const T3& arg3, const T4& arg4) | ^~~~~~~~~~~~~~~ /data/localhost/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/debug.hpp:545:1: warning: unused function template 'arma_incompat_size_string' [-Wunused-template] 545 | arma_incompat_size_string(const subview_cube& Q, const Mat& A, const char* x) | ^~~~~~~~~~~~~~~~~~~~~~~~~ 8 warnings generated. make[1]: Target 'all' not remade because of errors. make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-clang-trunk/RPatternJoin/src' ERROR: compilation failed for package ‘RPatternJoin’ * removing ‘/data/localhost/ripley/R/packages/tests-clang-trunk/RPatternJoin.Rcheck/RPatternJoin’