* installing *source* package ‘jackalope’ ... ** this is package ‘jackalope’ version ‘1.1.5’ ** package ‘jackalope’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/Rhtslib/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/Rhtslib/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c alter_reference.cpp -o alter_reference.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/Rhtslib/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c create_sequences.cpp -o create_sequences.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/Rhtslib/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c hap_classes.cpp -o hap_classes.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/Rhtslib/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c haps_ssites.cpp -o haps_ssites.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/Rhtslib/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c hts_illumina.cpp -o hts_illumina.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/Rhtslib/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c hts_pacbio.cpp -o hts_pacbio.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/Rhtslib/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c io_fasta.cpp -o io_fasta.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/Rhtslib/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c io_ms.cpp -o io_ms.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/Rhtslib/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c io_vcf.cpp -o io_vcf.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/Rhtslib/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c mutator.cpp -o mutator.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/Rhtslib/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c mutator_indels.cpp -o mutator_indels.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/Rhtslib/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c mutator_subs.cpp -o mutator_subs.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/Rhtslib/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c phylogenomics.cpp -o phylogenomics.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/Rhtslib/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ref_hap_access.cpp -o ref_hap_access.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/Rhtslib/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c sub_models.cpp -o sub_models.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/Rcpp/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppArmadillo/include' -I'/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.5/RcppProgress/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/Rhtslib/include' -I'/Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c util.cpp -o util.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o jackalope.so RcppExports.o alter_reference.o create_sequences.o hap_classes.o haps_ssites.o hts_illumina.o hts_pacbio.o io_fasta.o io_ms.o io_vcf.o mutator.o mutator_indels.o mutator_subs.o phylogenomics.o ref_hap_access.o sub_models.o util.o -lz -llzma -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath /Volumes/Builds/packages/big-sur-x86_64/extralib/4.5/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.5/jackalope.Rcheck/00LOCK-jackalope/00new/jackalope/libs ** generating debug symbols (dSYM) ** 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 ** 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 (jackalope)