* using log directory 'd:/Rcompile/CRANpkg/local/4.4/jackalope.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'jackalope/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'jackalope' version '1.1.5'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'jackalope' can be installed ... ERROR
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.4/jackalope.Rcheck/00install.out' for details.
* DONE
The installation logfile:
* 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/Rtmp2Z0Ow3/R.INSTALL273e0139f63c7/jackalope/src'
g++ -std=gnu++17  -I"D:/RCompile/CRANpkg/lib/4.4/zlibbioc/include" -I"D:/RCompile/recent/R/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/bin/x64 -lRlapack -LD:/RCompile/recent/R/bin/x64 -lRblas -lgfortran -lm -lquadmath D:/RCompile/CRANpkg/lib/4.4/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:/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/bin/x64 -lR
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: d:/rtools44/x86_64-w64-mingw32.static.posix/lib/libcurl.a(libcurl_la-psl.o):psl.c:(.text+0x31): undefined reference to `psl_free'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: d:/rtools44/x86_64-w64-mingw32.static.posix/lib/libcurl.a(libcurl_la-psl.o):psl.c:(.text+0xcd): undefined reference to `psl_latest'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: d:/rtools44/x86_64-w64-mingw32.static.posix/lib/libcurl.a(libcurl_la-psl.o):psl.c:(.text+0x107): undefined reference to `psl_free'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: d:/rtools44/x86_64-w64-mingw32.static.posix/lib/libcurl.a(libcurl_la-psl.o):psl.c:(.text+0x177): undefined reference to `psl_builtin'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: d:/rtools44/x86_64-w64-mingw32.static.posix/lib/libcurl.a(libcurl_la-version.o):version.c:(.text+0x122): undefined reference to `BrotliDecoderVersion'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: d:/rtools44/x86_64-w64-mingw32.static.posix/lib/libcurl.a(libcurl_la-version.o):version.c:(.text+0x209): undefined reference to `psl_check_version_number'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: d:/rtools44/x86_64-w64-mingw32.static.posix/lib/libcurl.a(libcurl_la-version.o):version.c:(.text+0x357): undefined reference to `BrotliDecoderVersion'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: d:/rtools44/x86_64-w64-mingw32.static.posix/lib/libcurl.a(libcurl_la-version.o):version.c:(.text+0x362): undefined reference to `BrotliDecoderVersion'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: d:/rtools44/x86_64-w64-mingw32.static.posix/lib/libcurl.a(libcurl_la-content_encoding.o):content_encodi:(.text+0x222): undefined reference to `BrotliDecoderDestroyInstance'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: d:/rtools44/x86_64-w64-mingw32.static.posix/lib/libcurl.a(libcurl_la-content_encoding.o):content_encodi:(.text+0x2dc): undefined reference to `BrotliDecoderDecompressStream'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: d:/rtools44/x86_64-w64-mingw32.static.posix/lib/libcurl.a(libcurl_la-content_encoding.o):content_encodi:(.text+0x339): undefined reference to `BrotliDecoderDestroyInstance'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: d:/rtools44/x86_64-w64-mingw32.static.posix/lib/libcurl.a(libcurl_la-content_encoding.o):content_encodi:(.text+0x385): undefined reference to `BrotliDecoderGetErrorCode'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: d:/rtools44/x86_64-w64-mingw32.static.posix/lib/libcurl.a(libcurl_la-content_encoding.o):content_encodi:(.text+0x410): undefined reference to `BrotliDecoderCreateInstance'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: d:/rtools44/x86_64-w64-mingw32.static.posix/lib/libcurl.a(libcurl_la-cookie.o):cookie.c:(.text+0x1166): undefined reference to `psl_is_cookie_domain_acceptable'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: d:/rtools44/x86_64-w64-mingw32.static.posix/lib/libcrypto.a(libcrypto-lib-c_zlib.obj):c_zlib.c:(.text+0xabc): undefined reference to `uncompress'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: d:/rtools44/x86_64-w64-mingw32.static.posix/lib/libcrypto.a(libcrypto-lib-c_zlib.obj):c_zlib.c:(.text+0xb0c): undefined reference to `compress'
collect2.exe: error: ld returned 1 exit status
make[1]: Leaving directory '/d/temp/Rtmp2Z0Ow3/R.INSTALL273e0139f63c7/jackalope/src'
make[1]: Entering directory '/d/temp/Rtmp2Z0Ow3/R.INSTALL273e0139f63c7/jackalope/src'
make[1]: Leaving directory '/d/temp/Rtmp2Z0Ow3/R.INSTALL273e0139f63c7/jackalope/src'
no DLL was created
ERROR: compilation failed for package 'jackalope'
* removing 'd:/Rcompile/CRANpkg/lib/4.4/jackalope'
* restoring previous 'd:/Rcompile/CRANpkg/lib/4.4/jackalope'