* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘VCFArrow’ ...
** this is package ‘VCFArrow’ version ‘0.9.0’
** package ‘VCFArrow’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++17
using C++ compiler: ‘g++-16 (Debian 16.2.0-3) 16.2.0’
using C++17
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp1UdWX2/R.INSTALL2fb21963ecbb7e/VCFArrow/src'
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c assign_matrix.cpp -o assign_matrix.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c assign_vector.cpp -o assign_vector.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c read_vcf_arrow.cpp -o read_vcf_arrow.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c sample_counts.cpp -o sample_counts.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c theta_counts.cpp -o theta_counts.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c vcf_wide.cpp -o vcf_wide.o
g++-16 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c write_vcf_arrow.cpp -o write_vcf_arrow.o
g++-16 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o VCFArrow.so RcppExports.o assign_matrix.o assign_vector.o read_vcf_arrow.o sample_counts.o theta_counts.o vcf_wide.o write_vcf_arrow.o -lz -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp1UdWX2/R.INSTALL2fb21963ecbb7e/VCFArrow/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp1UdWX2/R.INSTALL2fb21963ecbb7e/VCFArrow/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp1UdWX2/R.INSTALL2fb21963ecbb7e/VCFArrow/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-VCFArrow/00new/VCFArrow/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘VCFArrow’
finding HTML links ... done
VCFArrow-class html
VCFArrow-package html
assess_vcf_coverage html
assess_vcf_missing_data html
read_vcf html
set_vcf_groups html
show-VCFArrow-method html
sub-VCFArrow-method html
vcf2admixture html
vcf2apparent html
vcf2arlequin html
vcf2bayesass html
vcf2bayescan html
vcf2eigenstrat html
vcf2fasta html
vcf2fineradstructure html
vcf2genepop html
vcf2genlight html
vcf2gt_long html
vcf2migrate html
vcf2nexus html
vcf2plink_bed html
vcf2plink_ped html
vcf2related html
vcf2smartsnp html
vcf2snapp html
vcf2snmf html
vcf2structure html
vcf2treemix html
vcf_bind html
vcf_bind_sparse html
vcf_copy html
vcf_extract_groups html
vcf_extract_samples html
vcf_filter_adr html
vcf_filter_biallelic html
vcf_filter_coverage html
vcf_filter_hets html
vcf_filter_indels html
vcf_filter_invariant html
vcf_filter_maf html
vcf_filter_missing html
vcf_filter_missingness html
vcf_filter_multiSNV html
vcf_filter_oneSNV html
vcf_filter_paralogs html
vcf_filter_pass html
vcf_filter_quality html
vcf_filter_rank html
vcf_filter_rpt html
vcf_gc html
vcf_memory_estimate html
vcf_set_workers html
vcf_stats html
vcf_sub_SNVs html
vcf_sub_SNVs_stratified html
vcf_suggest_chunk_size html
vcf_theta html
write_vcf html
*** 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 (VCFArrow)