* installing *source* package ‘rchime’ ...
** this is package ‘rchime’ version ‘0.1.0’
** package ‘rchime’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 22.1.8 (https://github.com/llvm/llvm-project ca7933e47d3a3451d81e72ac174dcb5aa28b59d1)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rchime/src'
clang++-22 -stdlib=libc++ -std=gnu++20 -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/RcppXsimd/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c RcppExports.cpp -o RcppExports.o
clang++-22 -stdlib=libc++ -std=gnu++20 -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/RcppXsimd/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c align_simd.cc -o align_simd.o
clang++-22 -stdlib=libc++ -std=gnu++20 -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/RcppXsimd/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c bitmap.cc -o bitmap.o
clang++-22 -stdlib=libc++ -std=gnu++20 -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/RcppXsimd/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c chimera_vsearch.cpp -o chimera_vsearch.o
clang++-22 -stdlib=libc++ -std=gnu++20 -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/RcppXsimd/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c cigar.cpp -o cigar.o
clang++-22 -stdlib=libc++ -std=gnu++20 -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/RcppXsimd/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c cpu.cc -o cpu.o
clang++-22 -stdlib=libc++ -std=gnu++20 -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/RcppXsimd/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c db.cc -o db.o
clang++-22 -stdlib=libc++ -std=gnu++20 -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/RcppXsimd/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c dbindex.cc -o dbindex.o
clang++-22 -stdlib=libc++ -std=gnu++20 -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/RcppXsimd/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c linmemalign.cc -o linmemalign.o
clang++-22 -stdlib=libc++ -std=gnu++20 -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/RcppXsimd/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c maps.cpp -o maps.o
clang++-22 -stdlib=libc++ -std=gnu++20 -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/RcppXsimd/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c minheap.cc -o minheap.o
clang++-22 -stdlib=libc++ -std=gnu++20 -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/RcppXsimd/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c rcpp_rchime.cpp -o rcpp_rchime.o
clang++-22 -stdlib=libc++ -std=gnu++20 -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/RcppXsimd/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c searchcore.cc -o searchcore.o
clang++-22 -stdlib=libc++ -std=gnu++20 -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/RcppXsimd/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c seqcmp.cpp -o seqcmp.o
clang++-22 -stdlib=libc++ -std=gnu++20 -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/RcppXsimd/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c unique.cc -o unique.o
clang++-22 -stdlib=libc++ -std=gnu++20 -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/RcppXsimd/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c util.cc -o util.o
clang++-22 -stdlib=libc++ -std=gnu++20 -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/RcppThread/include' -I'/data/gannet/ripley/R/test-clang/RcppXsimd/include' -I'/data/gannet/ripley/R/test-clang/cli/include' -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c vsearch_main.cc -o vsearch_main.o
clang++-22 -stdlib=libc++ -std=gnu++20 -shared -L/usr/local/clang/lib64 -L/usr/local/clang22/lib -L/usr/local/clang22/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -o rchime.so RcppExports.o align_simd.o bitmap.o chimera_vsearch.o cigar.o cpu.o db.o dbindex.o linmemalign.o maps.o minheap.o rcpp_rchime.o searchcore.o seqcmp.o unique.o util.o vsearch_main.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rchime/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rchime/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rchime/src'
installing to /data/gannet/ripley/R/packages/tests-clang/rchime.Rcheck/00LOCK-rchime/00new/rchime/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (rchime)