* installing *source* package 'rchime' ...
** this is package 'rchime' version '0.1.0'
** package 'rchime' successfully unpacked and MD5 sums checked
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
using C++ compiler: 'g++.exe (GCC) 14.3.0'
make[1]: Entering directory '/d/temp/2026_07_24_01_50_00_28611/RtmpeMaZQI/R.INSTALL4e8048a935f0/rchime/src'
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppThread/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppXsimd/include' -I'D:/RCompile/CRANpkg/lib/4.7/cli/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -D_HAS_STD_BYTE=0 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppThread/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppXsimd/include' -I'D:/RCompile/CRANpkg/lib/4.7/cli/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -D_HAS_STD_BYTE=0 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c align_simd.cc -o align_simd.o
align_simd.cc:200:30: warning: ignoring attributes on template argument 'VECTOR_SHORT' {aka '__m128i'} [-Wignored-attributes]
200 | std::array<VECTOR_SHORT, 32> matrix {{}};
| ^
align_simd.cc: In member function 'void Vsearch_AlignSimd::search16(s16info_s*, unsigned int, unsigned int*, CELL*, short unsigned int*, short unsigned int*, short unsigned int*, short unsigned int*, char**, Vsearch_Database*)':
align_simd.cc:1199:29: warning: ignoring attributes on template argument 'VECTOR_SHORT' {aka '__m128i'} [-Wignored-attributes]
1199 | std::array<VECTOR_SHORT, 4> QR_target {{}};
| ^
align_simd.cc:1200:29: warning: ignoring attributes on template argument 'VECTOR_SHORT' {aka '__m128i'} [-Wignored-attributes]
1200 | std::array<VECTOR_SHORT, 4> R_target {{}};
| ^
align_simd.cc:1213:34: warning: ignoring attributes on template argument 'VECTOR_SHORT' {aka '__m128i'} [-Wignored-attributes]
1213 | std::array<VECTOR_SHORT, CDEPTH> dseqalloc {{}};
| ^
align_simd.cc:1214:29: warning: ignoring attributes on template argument 'VECTOR_SHORT' {aka '__m128i'} [-Wignored-attributes]
1214 | std::array<VECTOR_SHORT, 4> S {{}};
| ^
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppThread/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppXsimd/include' -I'D:/RCompile/CRANpkg/lib/4.7/cli/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -D_HAS_STD_BYTE=0 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bitmap.cc -o bitmap.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppThread/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppXsimd/include' -I'D:/RCompile/CRANpkg/lib/4.7/cli/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -D_HAS_STD_BYTE=0 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chimera_vsearch.cpp -o chimera_vsearch.o
chimera_vsearch.cpp: In member function 'void ChimeraVsearch::sortDescending(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<float>&)':
chimera_vsearch.cpp:72:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
72 | for (auto i = 0; i < (abunds).size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
chimera_vsearch.cpp:81:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
81 | for (auto i = 0; i < (abunds).size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
chimera_vsearch.cpp: In member function 'Rcpp::List ChimeraVsearch::removeChimeras()':
chimera_vsearch.cpp:132:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
132 | for (int k = 0; k < pNames->size(); k++) {
| ~~^~~~~~~~~~~~~~~~
chimera_vsearch.cpp:151:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
151 | for (int j = 0; j < pNames->at(k).size(); j++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~
chimera_vsearch.cpp:201:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<ChimeHit2> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
201 | for (auto i = 0; i < vsearchOut.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~
chimera_vsearch.cpp:203:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ChimeHit2>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
203 | for (int j = 0; j < vsearchOut[i].size(); j++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~
chimera_vsearch.cpp: In member function 'Rcpp::List ChimeraVsearch::removeChimeras(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&)':
chimera_vsearch.cpp:306:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<RcppThread::Thread*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
306 | for (auto i = 0; i < workerThreads.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~
chimera_vsearch.cpp: In member function 'Rcpp::List ChimeraVsearch::createVsearchResults(std::vector<ChimeHit2>)':
chimera_vsearch.cpp:342:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ChimeHit2>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
342 | for (auto i = 0; i < hits.size(); i++) {
| ~~^~~~~~~~~~~~~
In file included from chimera_vsearch.h:5,
from chimera_vsearch.cpp:2:
chime.h: In instantiation of 'void applyOrder(T&, const std::vector<unsigned int>&) [with T = std::vector<std::__cxx11::basic_string<char> >]':
chimera_vsearch.cpp:87:15: required from here
87 | applyOrder(sequences, order);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~
chime.h:164:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<unsigned int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
164 | for (auto i = 0; i < order.size(); i++) {
| ~~^~~~~~~~~~~~~~
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppThread/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppXsimd/include' -I'D:/RCompile/CRANpkg/lib/4.7/cli/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -D_HAS_STD_BYTE=0 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cigar.cpp -o cigar.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppThread/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppXsimd/include' -I'D:/RCompile/CRANpkg/lib/4.7/cli/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -D_HAS_STD_BYTE=0 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cpu.cc -o cpu.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppThread/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppXsimd/include' -I'D:/RCompile/CRANpkg/lib/4.7/cli/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -D_HAS_STD_BYTE=0 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c db.cc -o db.o
db.cc: In member function 'void Vsearch_Database::read(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<long long int>&)':
db.cc:165:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
165 | for (auto i = 0; i < seqs.size(); i++) {
| ~~^~~~~~~~~~~~~
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppThread/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppXsimd/include' -I'D:/RCompile/CRANpkg/lib/4.7/cli/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -D_HAS_STD_BYTE=0 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dbindex.cc -o dbindex.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppThread/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppXsimd/include' -I'D:/RCompile/CRANpkg/lib/4.7/cli/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -D_HAS_STD_BYTE=0 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c linmemalign.cc -o linmemalign.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppThread/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppXsimd/include' -I'D:/RCompile/CRANpkg/lib/4.7/cli/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -D_HAS_STD_BYTE=0 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c maps.cpp -o maps.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppThread/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppXsimd/include' -I'D:/RCompile/CRANpkg/lib/4.7/cli/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -D_HAS_STD_BYTE=0 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c minheap.cc -o minheap.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppThread/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppXsimd/include' -I'D:/RCompile/CRANpkg/lib/4.7/cli/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -D_HAS_STD_BYTE=0 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_rchime.cpp -o rcpp_rchime.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppThread/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppXsimd/include' -I'D:/RCompile/CRANpkg/lib/4.7/cli/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -D_HAS_STD_BYTE=0 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c searchcore.cc -o searchcore.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppThread/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppXsimd/include' -I'D:/RCompile/CRANpkg/lib/4.7/cli/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -D_HAS_STD_BYTE=0 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c seqcmp.cpp -o seqcmp.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppThread/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppXsimd/include' -I'D:/RCompile/CRANpkg/lib/4.7/cli/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -D_HAS_STD_BYTE=0 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c unique.cc -o unique.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppThread/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppXsimd/include' -I'D:/RCompile/CRANpkg/lib/4.7/cli/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -D_HAS_STD_BYTE=0 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c util.cc -o util.o
g++ -std=gnu++20 -I"D:/RCompile/recent/R/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.7/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppThread/include' -I'D:/RCompile/CRANpkg/lib/4.7/RcppXsimd/include' -I'D:/RCompile/CRANpkg/lib/4.7/cli/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -D_HAS_STD_BYTE=0 -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vsearch_main.cc -o vsearch_main.o
vsearch_main.cc: In member function 'void Vsearch_Main::dust_all(uint64_t)':
vsearch_main.cc:1416:24: warning: comparison of integer expressions of different signedness: 'int' and 'uint64_t' {aka 'long long unsigned int'} [-Wsign-compare]
1416 | for (auto i = 0; i < seqcount; i++) {
| ~~^~~~~~~~~~
g++ -std=gnu++20 -shared -s -static-libgcc -o rchime.dll tmp.def RcppExports.o align_simd.o bitmap.o chimera_vsearch.o cigar.o cpu.o db.o dbindex.o linmemalign.o maps.o minheap.o rcpp_rchime.o searchcore.o seqcmp.o unique.o util.o vsearch_main.o -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2026_07_24_01_50_00_28611/RtmpeMaZQI/R.INSTALL4e8048a935f0/rchime/src'
make[1]: Entering directory '/d/temp/2026_07_24_01_50_00_28611/RtmpeMaZQI/R.INSTALL4e8048a935f0/rchime/src'
make[1]: Leaving directory '/d/temp/2026_07_24_01_50_00_28611/RtmpeMaZQI/R.INSTALL4e8048a935f0/rchime/src'
installing to d:/Rcompile/CRANpkg/lib/4.7/00LOCK-rchime/00new/rchime/libs/x64
** R
** 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 'rchime' as rchime_0.1.0.zip
* DONE (rchime)