Install log for 'rncl'

* installing *source* package ‘rncl’ ...
** package ‘rncl’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 18.1.2’
using C++ compiler: ‘clang version 18.1.2’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rncl/src'
/usr/local/clang18/bin/clang++ -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c GetNCL.cpp -o GetNCL.o
/usr/local/clang18/bin/clang++ -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c RcppExports.cpp -o RcppExports.o
/usr/local/clang18/bin/clang++ -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/clang18/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/clang18/bin/clang++ -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c nxsassumptionsblock.cpp -o nxsassumptionsblock.o
/usr/local/clang18/bin/clang++ -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c nxsblock.cpp -o nxsblock.o
/usr/local/clang18/bin/clang++ -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c nxscharactersblock.cpp -o nxscharactersblock.o
/usr/local/clang18/bin/clang++ -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/clang18/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/clang18/bin/clang++ -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c nxsdatablock.cpp -o nxsdatablock.o
/usr/local/clang18/bin/clang++ -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c nxsdistancedatum.cpp -o nxsdistancedatum.o
/usr/local/clang18/bin/clang++ -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c nxsdistancesblock.cpp -o nxsdistancesblock.o
/usr/local/clang18/bin/clang++ -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c nxsemptyblock.cpp -o nxsemptyblock.o
/usr/local/clang18/bin/clang++ -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c nxsexception.cpp -o nxsexception.o
/usr/local/clang18/bin/clang++ -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c nxsmultiformat.cpp -o nxsmultiformat.o
/usr/local/clang18/bin/clang++ -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c nxspublicblocks.cpp -o nxspublicblocks.o
/usr/local/clang18/bin/clang++ -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c nxsreader.cpp -o nxsreader.o
2 warnings generated.
/usr/local/clang18/bin/clang++ -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c nxssetreader.cpp -o nxssetreader.o
/usr/local/clang18/bin/clang++ -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c nxsstring.cpp -o nxsstring.o
/usr/local/clang18/bin/clang++ -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c nxstaxaassociationblock.cpp -o nxstaxaassociationblock.o
/usr/local/clang18/bin/clang++ -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c nxstaxablock.cpp -o nxstaxablock.o
/usr/local/clang18/bin/clang++ -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c nxstoken.cpp -o nxstoken.o
/usr/local/clang18/bin/clang++ -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c nxstreesblock.cpp -o nxstreesblock.o
/usr/local/clang18/bin/clang++ -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/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c nxsunalignedblock.cpp -o nxsunalignedblock.o
/usr/local/clang18/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/clang18/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/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 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)