* installing *source* package 'jackalope' ...
** package 'jackalope' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++.exe (GCC) 13.2.0'
make[1]: Entering directory '/d/temp/RtmpGMIVO2/R.INSTALL1bde47bd72405/jackalope/src'
g++ -std=gnu++17  -I"D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include" -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include" -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c alter_reference.cpp -o alter_reference.o
g++ -std=gnu++17  -I"D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include" -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c create_sequences.cpp -o create_sequences.o
g++ -std=gnu++17  -I"D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include" -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hap_classes.cpp -o hap_classes.o
g++ -std=gnu++17  -I"D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include" -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c haps_ssites.cpp -o haps_ssites.o
g++ -std=gnu++17  -I"D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include" -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hts_illumina.cpp -o hts_illumina.o
g++ -std=gnu++17  -I"D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include" -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hts_pacbio.cpp -o hts_pacbio.o
g++ -std=gnu++17  -I"D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include" -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c io_fasta.cpp -o io_fasta.o
g++ -std=gnu++17  -I"D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include" -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c io_ms.cpp -o io_ms.o
g++ -std=gnu++17  -I"D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include" -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c io_vcf.cpp -o io_vcf.o
g++ -std=gnu++17  -I"D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include" -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c mutator.cpp -o mutator.o
g++ -std=gnu++17  -I"D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include" -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c mutator_indels.cpp -o mutator_indels.o
g++ -std=gnu++17  -I"D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include" -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c mutator_subs.cpp -o mutator_subs.o
g++ -std=gnu++17  -I"D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include" -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c phylogenomics.cpp -o phylogenomics.o
g++ -std=gnu++17  -I"D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include" -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ref_hap_access.cpp -o ref_hap_access.o
g++ -std=gnu++17  -I"D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include" -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sub_models.cpp -o sub_models.o
g++ -std=gnu++17  -I"D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include" -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.4/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include'   -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c util.cpp -o util.o
g++ -std=gnu++17 -shared -s -static-libgcc -o jackalope.dll tmp.def 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 -lws2_32 -LD:/RCompile/recent/R-4.4.0/bin/x64 -lRlapack -LD:/RCompile/recent/R-4.4.0/bin/x64 -lRblas -lgfortran -lm -lquadmath D:/RCompile/CRANpkg/lib/4.4/Rhtslib/usrlib/x64/libhts.a -lm -lbz2 -llzma -lcurl -lpsl -lbrotlidec -lbrotlicommon -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lz -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -L/lib/x64 -LD:/RCompile/CRANpkg/lib/4.4/zlibbioc/libs/x64 -lzlib1bioc -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.4.0/bin/x64 -lR
make[1]: Leaving directory '/d/temp/RtmpGMIVO2/R.INSTALL1bde47bd72405/jackalope/src'
make[1]: Entering directory '/d/temp/RtmpGMIVO2/R.INSTALL1bde47bd72405/jackalope/src'
make[1]: Leaving directory '/d/temp/RtmpGMIVO2/R.INSTALL1bde47bd72405/jackalope/src'
installing to d:/Rcompile/CRANpkg/lib/4.4/00LOCK-jackalope/00new/jackalope/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'jackalope' as jackalope_1.1.5.zip
* DONE (jackalope)