* installing *source* package 'jackalope' ...
** this is package 'jackalope' version '1.1.5'
** package 'jackalope' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++.exe (GCC) 14.2.0'
make[1]: Entering directory '/d/temp/2025_09_02_09_03_13_2588/Rtmpk1m8JD/R.INSTALL2b700387a47c2/jackalope/src'
g++ -std=gnu++17 -I"D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include" -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.5/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from jackalope_types.h:15,
from RcppExports.cpp:4:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include" -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.5/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c alter_reference.cpp -o alter_reference.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from alter_reference.cpp:8:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include" -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.5/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c create_sequences.cpp -o create_sequences.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from create_sequences.cpp:13:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include" -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.5/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hap_classes.cpp -o hap_classes.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from hap_classes.cpp:13:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include" -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.5/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c haps_ssites.cpp -o haps_ssites.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from haps_ssites.cpp:4:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include" -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.5/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hts_illumina.cpp -o hts_illumina.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from hts_illumina.cpp:4:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include" -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.5/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hts_pacbio.cpp -o hts_pacbio.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from hts_pacbio.cpp:4:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include" -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.5/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c io_fasta.cpp -o io_fasta.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from io_fasta.cpp:8:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include" -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.5/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c io_ms.cpp -o io_ms.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from io_ms.cpp:7:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include" -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.5/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c io_vcf.cpp -o io_vcf.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from io_vcf.cpp:7:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include" -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.5/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mutator.cpp -o mutator.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from mutator.cpp:9:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include" -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.5/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mutator_indels.cpp -o mutator_indels.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from mutator_indels.cpp:10:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include" -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.5/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mutator_subs.cpp -o mutator_subs.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from mutator_subs.cpp:5:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include" -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.5/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c phylogenomics.cpp -o phylogenomics.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from phylogenomics.cpp:13:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include" -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.5/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ref_hap_access.cpp -o ref_hap_access.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from ref_hap_access.cpp:14:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include" -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.5/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sub_models.cpp -o sub_models.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from sub_models.cpp:16:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++17 -I"D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include" -I"D:/RCompile/recent/R-4.5.1/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppProgress/include' -I'D:/RCompile/CRANpkg/lib/4.5/Rhtslib/include' -I'D:/RCompile/CRANpkg/lib/4.5/zlibbioc/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c util.cpp -o util.o
In file included from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:29,
from util.cpp:3:
D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: '#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.'
71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.")
| ^
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-4.5.1/bin/x64 -lRlapack -LD:/RCompile/recent/R-4.5.1/bin/x64 -lRblas -lgfortran -lquadmath D:/RCompile/CRANpkg/lib/4.5/Rhtslib/usrlib/x64/libhts.a -lm -lbz2 -llzma -lcurl -lnghttp2 -lpsl -lbrotlidec -lbrotlicommon -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lz -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -L/lib/x64 -LD:/RCompile/CRANpkg/lib/4.5/zlibbioc/libs/x64 -lzlib1bioc -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.5.1/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2025_09_02_09_03_13_2588/Rtmpk1m8JD/R.INSTALL2b700387a47c2/jackalope/src'
make[1]: Entering directory '/d/temp/2025_09_02_09_03_13_2588/Rtmpk1m8JD/R.INSTALL2b700387a47c2/jackalope/src'
make[1]: Leaving directory '/d/temp/2025_09_02_09_03_13_2588/Rtmpk1m8JD/R.INSTALL2b700387a47c2/jackalope/src'
installing to d:/Rcompile/CRANpkg/lib/4.5/00LOCK-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)