* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘rchime’ ...
** this is package ‘rchime’ version ‘0.1.2’
** package ‘rchime’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-16 (Debian 16.2.0-1) 16.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpj9dwNY/R.INSTALL6a92971bf1689/rchime/src'
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppThread/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppXsimd/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cli/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppThread/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppXsimd/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cli/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c align_simd.cc -o align_simd.o
align_simd.cc:199:30: warning: ignoring attributes on template argument ‘VECTOR_SHORT’ {aka ‘__m128i’} [-Wignored-attributes]
  199 |   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:1198:29: warning: ignoring attributes on template argument ‘VECTOR_SHORT’ {aka ‘__m128i’} [-Wignored-attributes]
 1198 |   std::array<VECTOR_SHORT, 4> QR_target {{}};
      |                             ^
align_simd.cc:1199:29: warning: ignoring attributes on template argument ‘VECTOR_SHORT’ {aka ‘__m128i’} [-Wignored-attributes]
 1199 |   std::array<VECTOR_SHORT, 4> R_target {{}};
      |                             ^
align_simd.cc:1212:34: warning: ignoring attributes on template argument ‘VECTOR_SHORT’ {aka ‘__m128i’} [-Wignored-attributes]
 1212 |   std::array<VECTOR_SHORT, CDEPTH> dseqalloc {{}};
      |                                  ^
align_simd.cc:1213:29: warning: ignoring attributes on template argument ‘VECTOR_SHORT’ {aka ‘__m128i’} [-Wignored-attributes]
 1213 |   std::array<VECTOR_SHORT, 4> S {{}};
      |                             ^
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppThread/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppXsimd/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cli/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c bitmap.cc -o bitmap.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppThread/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppXsimd/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cli/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -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 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 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 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 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 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 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 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 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 unsigned int’} [-Wsign-compare]
  164 |     for (auto i = 0; i < order.size(); i++) {
      |                      ~~^~~~~~~~~~~~~~
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppThread/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppXsimd/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cli/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c cigar.cpp -o cigar.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppThread/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppXsimd/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cli/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c cpu.cc -o cpu.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppThread/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppXsimd/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cli/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -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 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 unsigned int’} [-Wsign-compare]
  165 |     for (auto i = 0; i < seqs.size(); i++) {
      |                      ~~^~~~~~~~~~~~~
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppThread/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppXsimd/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cli/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c dbindex.cc -o dbindex.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppThread/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppXsimd/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cli/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c linmemalign.cc -o linmemalign.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppThread/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppXsimd/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cli/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c maps.cpp -o maps.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppThread/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppXsimd/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cli/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c minheap.cc -o minheap.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppThread/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppXsimd/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cli/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c rcpp_rchime.cpp -o rcpp_rchime.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppThread/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppXsimd/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cli/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c searchcore.cc -o searchcore.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppThread/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppXsimd/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cli/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c seqcmp.cpp -o seqcmp.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppThread/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppXsimd/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cli/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c unique.cc -o unique.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppThread/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppXsimd/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cli/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c util.cc -o util.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppThread/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppXsimd/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cli/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -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 unsigned int’} [-Wsign-compare]
 1416 |     for (auto i = 0; i < seqcount; i++) {
      |                      ~~^~~~~~~~~~
g++-16 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o rchime.so 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 -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpj9dwNY/R.INSTALL6a92971bf1689/rchime/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpj9dwNY/R.INSTALL6a92971bf1689/rchime/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpj9dwNY/R.INSTALL6a92971bf1689/rchime/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-rchime/00new/rchime/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘rchime’
    finding HTML links ... done
    rchime-package                          html  
    rchime                                  html  
    rchime_example                          html  
    rchime_options                          html  
    silva_gold                              html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rchime)