Install log for 'kmeRtone'

* installing *source* package ‘kmeRtone’ ...
** package ‘kmeRtone’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 19.1.6’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/kmeRtone/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/stringi/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw  -DR_NO_REMAP -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 -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/stringi/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw  -DR_NO_REMAP -c countKmers.cpp -o countKmers.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/stringi/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw  -DR_NO_REMAP -c countMidPatternContext.cpp -o countMidPatternContext.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/stringi/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw  -DR_NO_REMAP -c countMidPatternContext2.cpp -o countMidPatternContext2.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/stringi/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw  -DR_NO_REMAP -c countMidPatternKmers.cpp -o countMidPatternKmers.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/stringi/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw  -DR_NO_REMAP -c countMidPatternRangedKmers.cpp -o countMidPatternRangedKmers.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/stringi/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw  -DR_NO_REMAP -c countPointContext.cpp -o countPointContext.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/stringi/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw  -DR_NO_REMAP -c countPointContext2.cpp -o countPointContext2.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/stringi/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw  -DR_NO_REMAP -c countRangedKmers.cpp -o countRangedKmers.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/stringi/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw  -DR_NO_REMAP -c countSlidingWindow.cpp -o countSlidingWindow.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/stringi/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw  -DR_NO_REMAP -c countSlidingWindow2.cpp -o countSlidingWindow2.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/stringi/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw  -DR_NO_REMAP -c count_substring_fixed.cpp -o count_substring_fixed.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/stringi/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw  -DR_NO_REMAP -c count_substring_regex.cpp -o count_substring_regex.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/stringi/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw  -DR_NO_REMAP -c import_stringi.cpp -o import_stringi.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/stringi/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw  -DR_NO_REMAP -c simulatePopulation.cpp -o simulatePopulation.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 kmeRtone.so RcppExports.o countKmers.o countMidPatternContext.o countMidPatternContext2.o countMidPatternKmers.o countMidPatternRangedKmers.o countPointContext.o countPointContext2.o countRangedKmers.o countSlidingWindow.o countSlidingWindow2.o count_substring_fixed.o count_substring_regex.o import_stringi.o simulatePopulation.o /data/gannet/ripley/R/test-clang/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -lz
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/kmeRtone/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/kmeRtone/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/kmeRtone/src'
installing to /data/gannet/ripley/R/packages/tests-clang/kmeRtone.Rcheck/00LOCK-kmeRtone/00new/kmeRtone/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (kmeRtone)