Install log for 'rchime'

* installing *source* package ‘rchime’ ...
** this is package ‘rchime’ version ‘0.1.0’
** package ‘rchime’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)’
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/rchime/src'
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/RcppXsimd/include' -I'/data/localhost/ripley/R/test-dev/cli/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/RcppXsimd/include' -I'/data/localhost/ripley/R/test-dev/cli/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c align_simd.cc -o align_simd.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/RcppXsimd/include' -I'/data/localhost/ripley/R/test-dev/cli/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c bitmap.cc -o bitmap.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/RcppXsimd/include' -I'/data/localhost/ripley/R/test-dev/cli/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c chimera_vsearch.cpp -o chimera_vsearch.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/RcppXsimd/include' -I'/data/localhost/ripley/R/test-dev/cli/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c cigar.cpp -o cigar.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/RcppXsimd/include' -I'/data/localhost/ripley/R/test-dev/cli/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c cpu.cc -o cpu.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/RcppXsimd/include' -I'/data/localhost/ripley/R/test-dev/cli/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c db.cc -o db.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/RcppXsimd/include' -I'/data/localhost/ripley/R/test-dev/cli/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c dbindex.cc -o dbindex.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/RcppXsimd/include' -I'/data/localhost/ripley/R/test-dev/cli/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c linmemalign.cc -o linmemalign.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++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/RcppXsimd/include' -I'/data/localhost/ripley/R/test-dev/cli/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c maps.cpp -o maps.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/RcppXsimd/include' -I'/data/localhost/ripley/R/test-dev/cli/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c minheap.cc -o minheap.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/RcppXsimd/include' -I'/data/localhost/ripley/R/test-dev/cli/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c rcpp_rchime.cpp -o rcpp_rchime.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++) {
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/RcppXsimd/include' -I'/data/localhost/ripley/R/test-dev/cli/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c searchcore.cc -o searchcore.o
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++) {
      |                      ~~^~~~~~~~~~~~~
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/RcppXsimd/include' -I'/data/localhost/ripley/R/test-dev/cli/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c seqcmp.cpp -o seqcmp.o
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++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/RcppXsimd/include' -I'/data/localhost/ripley/R/test-dev/cli/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c unique.cc -o unique.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/RcppXsimd/include' -I'/data/localhost/ripley/R/test-dev/cli/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c util.cc -o util.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppThread/include' -I'/data/localhost/ripley/R/test-dev/RcppXsimd/include' -I'/data/localhost/ripley/R/test-dev/cli/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -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++ -std=gnu++20 -shared -L/usr/local/lib64 -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
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/rchime/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/rchime/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/rchime/src'
installing to /data/localhost/ripley/R/packages/tests-devel/rchime.Rcheck/00LOCK-rchime/00new/rchime/libs
** 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
** 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)