* installing *source* package 'jackalope' ... ** package 'jackalope' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: 'g++.exe (GCC) 12.3.0' make[1]: Entering directory '/d/temp/RtmpGen39s/R.INSTALL82644dc45961/jackalope/src' g++ -std=gnu++17 -I"D:/RCompile/CRANpkg/lib/4.3/zlibbioc/include" -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.3/zlibbioc/include' -I"d:/rtools43/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/4.3/zlibbioc/include" -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.3/zlibbioc/include' -I"d:/rtools43/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/4.3/zlibbioc/include" -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.3/zlibbioc/include' -I"d:/rtools43/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/4.3/zlibbioc/include" -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.3/zlibbioc/include' -I"d:/rtools43/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/4.3/zlibbioc/include" -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.3/zlibbioc/include' -I"d:/rtools43/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/4.3/zlibbioc/include" -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.3/zlibbioc/include' -I"d:/rtools43/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/4.3/zlibbioc/include" -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.3/zlibbioc/include' -I"d:/rtools43/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/4.3/zlibbioc/include" -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.3/zlibbioc/include' -I"d:/rtools43/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/4.3/zlibbioc/include" -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.3/zlibbioc/include' -I"d:/rtools43/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/4.3/zlibbioc/include" -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.3/zlibbioc/include' -I"d:/rtools43/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/4.3/zlibbioc/include" -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.3/zlibbioc/include' -I"d:/rtools43/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/4.3/zlibbioc/include" -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.3/zlibbioc/include' -I"d:/rtools43/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/4.3/zlibbioc/include" -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.3/zlibbioc/include' -I"d:/rtools43/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/4.3/zlibbioc/include" -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.3/zlibbioc/include' -I"d:/rtools43/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/4.3/zlibbioc/include" -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.3/zlibbioc/include' -I"d:/rtools43/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/4.3/zlibbioc/include" -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.3/zlibbioc/include' -I"d:/rtools43/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/4.3/zlibbioc/include" -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.3/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.3/zlibbioc/include' -I"d:/rtools43/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-4.3.3/bin/x64 -lRlapack -LD:/RCompile/recent/R-4.3.3/bin/x64 -lRblas -lgfortran -lm -lquadmath D:/RCompile/CRANpkg/lib/4.3/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -L/lib/x64 -LD:/RCompile/CRANpkg/lib/4.3/zlibbioc/libs/x64 -lzlib1bioc -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.3.3/bin/x64 -lR make[1]: Leaving directory '/d/temp/RtmpGen39s/R.INSTALL82644dc45961/jackalope/src' make[1]: Entering directory '/d/temp/RtmpGen39s/R.INSTALL82644dc45961/jackalope/src' make[1]: Leaving directory '/d/temp/RtmpGen39s/R.INSTALL82644dc45961/jackalope/src' installing to d:/Rcompile/CRANpkg/lib/4.3/00LOCK-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)