* installing *source* package ‘fastTopics’ ... ** package ‘fastTopics’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘clang version 18.1.4’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/fastTopics/src' /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_DONT_PRINT_ERRORS -DARMA_NO_DEBUG -DARMA_USE_BLAS -DARMA_DONT_USE_OPENMP -DARMA_USE_TBB_ALLOC -DRCPP_PARALLEL_USE_TBB=1 -DARMA_WARN_LEVEL=1 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo:26: /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages] 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages] 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages] 329 | #pragma message ("INFO: see the documentation for details") | ^ /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_DONT_PRINT_ERRORS -DARMA_NO_DEBUG -DARMA_USE_BLAS -DARMA_DONT_USE_OPENMP -DARMA_USE_TBB_ALLOC -DRCPP_PARALLEL_USE_TBB=1 -DARMA_WARN_LEVEL=1 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c ccd.cpp -o ccd.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_DONT_PRINT_ERRORS -DARMA_NO_DEBUG -DARMA_USE_BLAS -DARMA_DONT_USE_OPENMP -DARMA_USE_TBB_ALLOC -DRCPP_PARALLEL_USE_TBB=1 -DARMA_WARN_LEVEL=1 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c cost.cpp -o cost.o In file included from cost.cpp:1: In file included from ./misc.h:4: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo:26: /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages] 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages] 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages] 329 | #pragma message ("INFO: see the documentation for details") | ^ In file included from ccd.cpp:2: In file included from ./misc.h:4: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo:26: /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages] 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages] 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages] 329 | #pragma message ("INFO: see the documentation for details") | ^ 3 warnings generated. 3 warnings generated. 3 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_DONT_PRINT_ERRORS -DARMA_NO_DEBUG -DARMA_USE_BLAS -DARMA_DONT_USE_OPENMP -DARMA_USE_TBB_ALLOC -DRCPP_PARALLEL_USE_TBB=1 -DARMA_WARN_LEVEL=1 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c misc.cpp -o misc.o In file included from misc.cpp:1: In file included from ./misc.h:4: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo:26: /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages] 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages] 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages] 329 | #pragma message ("INFO: see the documentation for details") | ^ /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_DONT_PRINT_ERRORS -DARMA_NO_DEBUG -DARMA_USE_BLAS -DARMA_DONT_USE_OPENMP -DARMA_USE_TBB_ALLOC -DRCPP_PARALLEL_USE_TBB=1 -DARMA_WARN_LEVEL=1 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c mixem.cpp -o mixem.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_DONT_PRINT_ERRORS -DARMA_NO_DEBUG -DARMA_USE_BLAS -DARMA_DONT_USE_OPENMP -DARMA_USE_TBB_ALLOC -DRCPP_PARALLEL_USE_TBB=1 -DARMA_WARN_LEVEL=1 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c pnmfem.cpp -o pnmfem.o In file included from mixem.cpp:1: In file included from ./mixem.h:4: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo:26: /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages] 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages] 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages] 329 | #pragma message ("INFO: see the documentation for details") | ^ /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_DONT_PRINT_ERRORS -DARMA_NO_DEBUG -DARMA_USE_BLAS -DARMA_DONT_USE_OPENMP -DARMA_USE_TBB_ALLOC -DRCPP_PARALLEL_USE_TBB=1 -DARMA_WARN_LEVEL=1 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c poismix.cpp -o poismix.o In file included from pnmfem.cpp:2: In file included from ./misc.h:4: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo:26: /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages] 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages] 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages] 329 | #pragma message ("INFO: see the documentation for details") | ^ /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_DONT_PRINT_ERRORS -DARMA_NO_DEBUG -DARMA_USE_BLAS -DARMA_DONT_USE_OPENMP -DARMA_USE_TBB_ALLOC -DRCPP_PARALLEL_USE_TBB=1 -DARMA_WARN_LEVEL=1 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c poisson.cpp -o poisson.o In file included from poismix.cpp:1: In file included from ./poismix.h:4: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo:26: /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages] 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages] 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages] 329 | #pragma message ("INFO: see the documentation for details") | ^ In file included from poisson.cpp:1: In file included from ./misc.h:4: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo:26: /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages] 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages] 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages] 329 | #pragma message ("INFO: see the documentation for details") | ^ 3 warnings generated. 3 warnings generated. 3 warnings generated. 3 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -DARMA_DONT_PRINT_ERRORS -DARMA_NO_DEBUG -DARMA_USE_BLAS -DARMA_DONT_USE_OPENMP -DARMA_USE_TBB_ALLOC -DRCPP_PARALLEL_USE_TBB=1 -DARMA_WARN_LEVEL=1 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c scd.cpp -o scd.o 3 warnings generated. In file included from scd.cpp:2: In file included from ./misc.h:4: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57: In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo:26: /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages] 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages] 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages] 329 | #pragma message ("INFO: see the documentation for details") | ^ 3 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o fastTopics.so RcppExports.o ccd.o cost.o misc.o mixem.o pnmfem.o poismix.o poisson.o scd.o -fopenmp -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortran_main -lFortranRuntime -lFortranDecimal -lm make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/fastTopics/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/fastTopics/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/fastTopics/src' installing to /data/gannet/ripley/R/packages/tests-clang/fastTopics.Rcheck/00LOCK-fastTopics/00new/fastTopics/libs ** R ** data *** moving datasets to lazyload DB ** 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 (fastTopics)