Install log for 'rchime'

* installing *source* package ‘rchime’ ...
** this is package ‘rchime’ version ‘0.1.1’
** package ‘rchime’ successfully unpacked and MD5 sums checked
** using staged installation
Error in which(flags) : argument to 'which' is not logical
Calls: cat -> <Anonymous> -> .makeFlags -> which
Execution halted
** libs
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.3.19.1)’
using SDK: ‘MacOSX14.5.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppThread/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppXsimd/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/cli/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppThread/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppXsimd/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/cli/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c align_simd.cc -o align_simd.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppThread/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppXsimd/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/cli/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c bitmap.cc -o bitmap.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppThread/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppXsimd/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/cli/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c chimera_vsearch.cpp -o chimera_vsearch.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppThread/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppXsimd/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/cli/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c cigar.cpp -o cigar.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppThread/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppXsimd/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/cli/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c cpu.cc -o cpu.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppThread/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppXsimd/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/cli/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c db.cc -o db.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppThread/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppXsimd/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/cli/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c dbindex.cc -o dbindex.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppThread/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppXsimd/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/cli/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c linmemalign.cc -o linmemalign.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppThread/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppXsimd/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/cli/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c maps.cpp -o maps.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppThread/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppXsimd/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/cli/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c minheap.cc -o minheap.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppThread/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppXsimd/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/cli/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rcpp_rchime.cpp -o rcpp_rchime.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppThread/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppXsimd/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/cli/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c searchcore.cc -o searchcore.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppThread/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppXsimd/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/cli/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c seqcmp.cpp -o seqcmp.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppThread/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppXsimd/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/cli/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c unique.cc -o unique.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppThread/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppXsimd/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/cli/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c util.cc -o util.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppThread/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppXsimd/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/cli/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c vsearch_main.cc -o vsearch_main.o
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -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 -F/Library/Frameworks/R.framework/.. -framework R
installing to /Volumes/Builds/packages/sonoma-arm64/results/4.6/rchime.Rcheck/00LOCK-rchime/00new/rchime/libs
** generating debug symbols (dSYM)
** 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)