* installing *source* package ‘rncl’ ... ** package ‘rncl’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘clang version 19.1.0’ using C++ compiler: ‘clang version 19.1.0’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rncl/src' /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c GetNCL.cpp -o GetNCL.o /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c collapse_singles.cpp -o collapse_singles.o /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c nxsassumptionsblock.cpp -o nxsassumptionsblock.o /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c nxsblock.cpp -o nxsblock.o /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c nxscharactersblock.cpp -o nxscharactersblock.o /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c nxscxxdiscretematrix.cpp -o nxscxxdiscretematrix.o nxscharactersblock.cpp:1692:16: warning: variable 'colIndex' set but not used [-Wunused-but-set-variable] 1692 | for (unsigned colIndex = 0; rowIt != discreteMatrix.end(); ++colIndex, ++rowIt) | ^ nxscharactersblock.cpp:3355:34: warning: unused variable 'cit' [-Wunused-variable] 3355 | NxsStringVector::const_iterator cit; | ^~~ /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c nxsdatablock.cpp -o nxsdatablock.o /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c nxsdistancedatum.cpp -o nxsdistancedatum.o /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c nxsdistancesblock.cpp -o nxsdistancesblock.o /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c nxsemptyblock.cpp -o nxsemptyblock.o /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c nxsexception.cpp -o nxsexception.o /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c nxsmultiformat.cpp -o nxsmultiformat.o /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c nxspublicblocks.cpp -o nxspublicblocks.o 2 warnings generated. /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c nxsreader.cpp -o nxsreader.o /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c nxssetreader.cpp -o nxssetreader.o /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c nxsstring.cpp -o nxsstring.o /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c nxstaxaassociationblock.cpp -o nxstaxaassociationblock.o /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c nxstaxablock.cpp -o nxstaxablock.o /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c nxstoken.cpp -o nxstoken.o /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c nxstreesblock.cpp -o nxstreesblock.o /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c nxsunalignedblock.cpp -o nxsunalignedblock.o /usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -DHAVE_INTTYPES_H -DASSERTS_TO_EXCEPTIONS -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/progress/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c rncl_init.c -o rncl_init.o /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o rncl.so GetNCL.o RcppExports.o collapse_singles.o nxsassumptionsblock.o nxsblock.o nxscharactersblock.o nxscxxdiscretematrix.o nxsdatablock.o nxsdistancedatum.o nxsdistancesblock.o nxsemptyblock.o nxsexception.o nxsmultiformat.o nxspublicblocks.o nxsreader.o nxssetreader.o nxsstring.o nxstaxaassociationblock.o nxstaxablock.o nxstoken.o nxstreesblock.o nxsunalignedblock.o rncl_init.o make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rncl/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rncl/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rncl/src' installing to /data/gannet/ripley/R/packages/tests-clang/rncl.Rcheck/00LOCK-rncl/00new/rncl/libs ** R ** 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 (rncl)