* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’ * installing *source* package ‘jackalope’ ... ** package ‘jackalope’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/tmp/RtmpHyvsTR/R.INSTALL36d139529d8482/jackalope/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c alter_reference.cpp -o alter_reference.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c create_sequences.cpp -o create_sequences.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c hap_classes.cpp -o hap_classes.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c haps_ssites.cpp -o haps_ssites.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c hts_illumina.cpp -o hts_illumina.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c hts_pacbio.cpp -o hts_pacbio.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c io_fasta.cpp -o io_fasta.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c io_ms.cpp -o io_ms.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c io_vcf.cpp -o io_vcf.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mutator.cpp -o mutator.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mutator_indels.cpp -o mutator_indels.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mutator_subs.cpp -o mutator_subs.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c phylogenomics.cpp -o phylogenomics.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ref_hap_access.cpp -o ref_hap_access.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c sub_models.cpp -o sub_models.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppProgress/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rhtslib/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/zlibbioc/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c util.cpp -o util.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/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.check/r-devel-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR make[1]: Leaving directory '/tmp/RtmpHyvsTR/R.INSTALL36d139529d8482/jackalope/src' make[1]: Entering directory '/tmp/RtmpHyvsTR/R.INSTALL36d139529d8482/jackalope/src' make[1]: Leaving directory '/tmp/RtmpHyvsTR/R.INSTALL36d139529d8482/jackalope/src' installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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)