* installing *source* package ‘jackalope’ ...
** using staged installation
** libs
using C++ compiler: ‘Debian clang version 16.0.6 (15)’
using C++11
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c RcppExports.cpp -o RcppExports.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c alter_reference.cpp -o alter_reference.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c create_sequences.cpp -o create_sequences.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c hap_classes.cpp -o hap_classes.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c haps_ssites.cpp -o haps_ssites.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c hts_illumina.cpp -o hts_illumina.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c hts_pacbio.cpp -o hts_pacbio.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c io_fasta.cpp -o io_fasta.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c io_ms.cpp -o io_ms.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c io_vcf.cpp -o io_vcf.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c mutator.cpp -o mutator.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c mutator_indels.cpp -o mutator_indels.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c mutator_subs.cpp -o mutator_subs.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c phylogenomics.cpp -o phylogenomics.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c ref_hap_access.cpp -o ref_hap_access.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c sub_models.cpp -o sub_models.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R-d-clang-16/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rhtslib/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/zlibbioc/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c util.cpp -o util.o
clang++-16 -std=gnu++11 -shared -L/home/hornik/tmp/R-d-clang-16/lib -Wl,-O1 -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 -llapack -L/home/hornik/tmp/R-d-clang-16/lib -lRblas -lgfortran -lm -lquadmath /home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rhtslib/usrlib/libhts.a -lcurl -L/home/hornik/tmp/R-d-clang-16/lib -lR
installing to /srv/hornik/tmp/CRAN/jackalope.Rcheck/00LOCK-jackalope/00new/jackalope/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
** 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)