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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/dada2_1.22.0.tar.gz && rm -rf dada2.buildbin-libdir && mkdir dada2.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dada2.buildbin-libdir dada2_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL dada2_1.22.0.zip && rm dada2_1.22.0.tar.gz dada2_1.22.0.zip
###
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install for i386

* installing *source* package 'dada2' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/dada2.h:7,
                 from RcppExports.cpp:4:
../inst/include/dada2_RcppExports.h:14:14: warning: 'void dada2::{anonymous}::validateSignature(const char*)' defined but not used [-Wunused-function]
         void validateSignature(const char* sig) {
              ^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Rmain.cpp -o Rmain.o
Rmain.cpp: In function 'Rcpp::List dada_uniques(std::vector<std::__cxx11::basic_string<char> >, std::vector<int>, std::vector<bool>, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, int, int, bool, double, int, double, double, double, bool, int, double, int, int, bool, bool, bool, int, bool, bool, int, bool, bool)':
Rmain.cpp:69:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
     if(quals.nrow() != maxlen) {
        ~~~~~~~~~~~~~^~~~~~~~~
Rmain.cpp:82:8: warning: variable 'HW_SSE3' set but not used [-Wunused-but-set-variable]
   bool HW_SSE3 = false;
        ^~~~~~~
Rmain.cpp: In function 'B* run_dada(Raw**, int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, double, double, bool, int, double, int, int, bool, bool, bool, bool, bool, int, bool, bool)':
Rmain.cpp:313:22: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
   while( (bb->nclust < max_clust) && (newi = b_bud(bb, min_fold, min_hamming, min_abund, verbose)) ) {
           ~~~~~~~~~~~^~~~~~~~~~~
Rmain.cpp: In function 'Rcpp::List dada_uniques(std::vector<std::__cxx11::basic_string<char> >, std::vector<int>, std::vector<bool>, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, int, int, bool, double, int, double, double, double, bool, int, double, int, int, bool, bool, bool, int, bool, bool, int, bool, bool)':
Rmain.cpp:287:9: warning: 'kord' may be used uninitialized in this function [-Wmaybe-uninitialized]
     free(kord);
     ~~~~^~~~~~
Rmain.cpp:286:9: warning: 'k16' may be used uninitialized in this function [-Wmaybe-uninitialized]
     free(k16);
     ~~~~^~~~~
Rmain.cpp:285:9: warning: 'k8' may be used uninitialized in this function [-Wmaybe-uninitialized]
     free(k8);
     ~~~~^~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c chimera.cpp -o chimera.o
chimera.cpp: In function 'bool C_is_bimera(std::__cxx11::string, std::vector<std::__cxx11::basic_string<char> >, bool, int, int, int, int, int)':
chimera.cpp:25:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(i=0;i<pars.size() && rval==false;i++) {
           ~^~~~~~~~~~~~
chimera.cpp:29:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     if((left+right) >= sq.size()) { // Toss id/pure-shift/internal-indel "parents"
        ~~~~~~~~~~~~~^~~~~~~~~~~~
chimera.cpp:44:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     if((max_right+max_left)>=sq.size()) {
        ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
chimera.cpp:48:39: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       if((oo_max_left+oo_max_right_oo)>=sq.size() || (oo_max_left_oo+oo_max_right)>=sq.size()) {
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
chimera.cpp:48:83: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       if((oo_max_left+oo_max_right_oo)>=sq.size() || (oo_max_left_oo+oo_max_right)>=sq.size()) {
                                                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
chimera.cpp: In function 'void get_lr(char**, int&, int&, int&, int&, bool, int)':
chimera.cpp:231:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   while(al[0][pos] == '-' && pos<len) {
                              ~~~^~~~
chimera.cpp:237:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   while(pos<len && al[0][pos] == al[1][pos]) {
         ~~~^~~~
chimera.cpp:244:11: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
     if(pos<len && al[0][pos] != '-') { left_oo++; }
        ~~~^~~~
chimera.cpp:245:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
     while(pos<len && al[0][pos] == al[1][pos]) {
           ~~~^~~~
chimera.cpp:254:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   while(al[1][pos] == '-' && pos>+(len-max_shift)) {
                              ~~~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cluster.cpp -o cluster.o
cluster.cpp: In function 'void b_compare(B*, unsigned int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, bool, int, bool, bool, bool)':
cluster.cpp:17:23: warning: variable 'cind' set but not used [-Wunused-but-set-variable]
   unsigned int index, cind, center_reads;
                       ^~~~
cluster.cpp: In function 'void b_compare_parallel(B*, unsigned int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, bool, int, bool, bool, bool)':
cluster.cpp:166:16: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
   for(row=0;row<errMat.nrow();row++) {
             ~~~^~~~~~~~~~~~~~
cluster.cpp:167:18: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
     for(col=0;col<errMat.ncol();col++) {
               ~~~^~~~~~~~~~~~~~
cluster.cpp:156:23: warning: variable 'cind' set but not used [-Wunused-but-set-variable]
   unsigned int index, cind, row, col, ncol;
                       ^~~~
cluster.cpp: In function 'int b_bud(B*, double, int, int, bool)':
cluster.cpp:284:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   for(i=0;i<b->nclust;i++) {
           ~^~~~~~~~~~
cluster.cpp:285:15: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
     for(r=1; r<b->bi[i]->nraw; r++) { // r=0 is the center
              ~^~~~~~~~~~~~~~~
cluster.cpp:288:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
       if(raw->reads < min_abund) { continue; }
          ~~~~~~~~~~~^~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c containers.cpp -o containers.o
containers.cpp: In function 'void b_free(B*)':
containers.cpp:141:16: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   for(int i=0;i<b->nclust;i++) { bi_free(b->bi[i]); }
               ~^~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c error.cpp -o error.o
error.cpp: In function 'Rcpp::DataFrame b_make_positional_substitution_df(B*, Sub**, unsigned int, Rcpp::NumericMatrix, bool)':
error.cpp:178:51: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
   unsigned int i, pos, pos1, qind, j, r, s, nti0, ncol;
                                                   ^~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c evaluate.cpp -o evaluate.o
evaluate.cpp: In function 'Rcpp::IntegerVector C_eval_pair(std::__cxx11::string, std::__cxx11::string)':
evaluate.cpp:88:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   } while((s1gap || s2gap) && start<s1.size());
                               ~~~~~^~~~~~~~~~
evaluate.cpp: In function 'Rcpp::CharacterVector C_pair_consensus(std::__cxx11::string, std::__cxx11::string, int, bool)':
evaluate.cpp:133:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(i=0;i<s1.size();i++) {
           ~^~~~~~~~~~
evaluate.cpp:152:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(i=0;i<s1.size();i++) {
             ~^~~~~~~~~~
evaluate.cpp:163:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(i=0;i<s1.size();i++) {
           ~^~~~~~~~~~
evaluate.cpp: In function 'Rcpp::NumericVector kmer_dist(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)':
evaluate.cpp:219:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0;i<nseqs;i++) {
               ~^~~~~~
evaluate.cpp: In function 'Rcpp::NumericVector kord_dist(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int, int)':
evaluate.cpp:243:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0;i<nseqs;i++) {
               ~^~~~~~
evaluate.cpp:255:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0;i<nseqs;i++) {
               ~^~~~~~
evaluate.cpp: In function 'Rcpp::IntegerVector kmer_matches(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)':
evaluate.cpp:286:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0;i<nseqs;i++) {
               ~^~~~~~
evaluate.cpp:298:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(i=0;i<nseqs;i++) {
           ~^~~~~~
evaluate.cpp:310:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
     for(j=0;j<klen_min;j++) {
             ~^~~~~~~~~
evaluate.cpp: In function 'Rcpp::IntegerVector kdist_matches(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)':
evaluate.cpp:339:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(i=0;i<nseqs;i++) {
           ~^~~~~~
evaluate.cpp:348:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
     for(j=0;j<n_kmers;j++) {
             ~^~~~~~~~
evaluate.cpp:327:10: warning: variable 'len1' set but not used [-Wunused-but-set-variable]
   size_t len1 = 0, len2 = 0;
          ^~~~
evaluate.cpp:327:20: warning: variable 'len2' set but not used [-Wunused-but-set-variable]
   size_t len1 = 0, len2 = 0;
                    ^~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c filter.cpp -o filter.o
filter.cpp: In function 'Rcpp::IntegerVector C_matchRef(std::vector<std::__cxx11::basic_string<char> >, std::__cxx11::string, unsigned int, bool)':
filter.cpp:16:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   for(i=0;i<len;i++) {
           ~^~~~
filter.cpp:20:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(i=0;i<seqs.size();i++) {
           ~^~~~~~~~~~~~
filter.cpp:24:14: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
     for(j=0;j<=(len-word_size);j++) {
             ~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c kmers.cpp -o kmers.o
kmers.cpp: In function 'double kmer_dist_SSEi_8(uint8_t*, int, uint8_t*, int, int)':
kmers.cpp:81:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(i=0;i<STEP;i++) {
           ~^~~~~
kmers.cpp: In function 'double kord_dist(uint16_t*, int, uint16_t*, int, int)':
kmers.cpp:101:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(i=0;i<klen;i++) {
           ~^~~~~
kmers.cpp: In function 'double kord_dist_SSEi(uint16_t*, int, uint16_t*, int, int)':
kmers.cpp:131:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(i=0;i<STEP;i++) {
           ~^~~~~
kmers.cpp:134:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(i=n_vec;i<klen;i++,kord1++,kord2++) { // kord starts pointing to where it was left
               ~^~~~~
kmers.cpp: In function 'void assign_kmer8(uint8_t*, const char*, int)':
kmers.cpp:146:8: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   if(k >= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
      ~~^~~~~~
kmers.cpp:158:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(i=0; i<klen; i++) {
            ~^~~~~
kmers.cpp: In function 'void assign_kmer(uint16_t*, const char*, int)':
kmers.cpp:195:8: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   if(k >= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
      ~~^~~~~~
kmers.cpp:205:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(i=0; i<klen; i++) {
            ~^~~~~
kmers.cpp: In function 'void assign_kmer_order(uint16_t*, char*, int)':
kmers.cpp:234:8: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   if(k >= len || k < 1 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
      ~~^~~~~~
kmers.cpp:239:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(i=0;i<klen;i++) { kord[i] = 0; }
           ~^~~~~
kmers.cpp:241:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(i=0; i<klen; i++) {
            ~^~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c misc.cpp -o misc.o
misc.cpp: In function 'void align_print(char**)':
misc.cpp:24:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0;i<strlen(al0);i++) {
               ~^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nwalign_endsfree.cpp -o nwalign_endsfree.o
nwalign_endsfree.cpp: In function 'char** nwalign_endsfree(const char*, size_t, const char*, size_t, int (*)[4], int, int)':
nwalign_endsfree.cpp:89:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for (i = 0; i <= len1; i++) {
               ~~^~~~~~~
nwalign_endsfree.cpp:95:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for (j = 0; j <= len2; j++) {
               ~~^~~~~~~
nwalign_endsfree.cpp:114:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                  ~~~~^~~~~
nwalign_endsfree.cpp:114:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                               ~~~~^~~~~
nwalign_endsfree.cpp:115:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
     for(i=0;i<=len1;i++) {
             ~^~~~~~
nwalign_endsfree.cpp:117:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
       if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
          ~~~~~~~~~~^~~~~~~
nwalign_endsfree.cpp:122:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
               ~~^~~~~~~
nwalign_endsfree.cpp:125:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
       r = i+rband; if(r>len2) { r = len2; }
                       ~^~~~~
nwalign_endsfree.cpp:130:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
       if (i == len1) {
           ~~^~~~~~~
nwalign_endsfree.cpp:137:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
       if (j == len2) {
           ~~^~~~~~~
nwalign_endsfree.cpp:201:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for (i=0;i<len_al;i++) {
            ~^~~~~~~
nwalign_endsfree.cpp: In function 'char** nwalign_endsfree_homo(const char*, size_t, const char*, size_t, int (*)[4], int, int, int)':
nwalign_endsfree.cpp:230:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for (i=0,j=0;j<len1;j++) {
                ~^~~~~
nwalign_endsfree.cpp:231:10: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
     if (j==len1-1 || s1[j]!=s1[j+1]) {
         ~^~~~~~~~
nwalign_endsfree.cpp:244:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for (i=0,j=0;j<len2;j++) {
                ~^~~~~
nwalign_endsfree.cpp:245:10: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
     if (j==len2-1 || s2[j]!=s2[j+1]) {
         ~^~~~~~~~
nwalign_endsfree.cpp:264:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for (i = 0; i <= len1; i++) {
               ~~^~~~~~~
nwalign_endsfree.cpp:270:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for (j = 0; j <= len2; j++) {
               ~~^~~~~~~
nwalign_endsfree.cpp:289:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                  ~~~~^~~~~
nwalign_endsfree.cpp:289:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                               ~~~~^~~~~
nwalign_endsfree.cpp:290:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
     for(i=0;i<=len1;i++) {
             ~^~~~~~
nwalign_endsfree.cpp:292:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
       if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
          ~~~~~~~~~~^~~~~~~
nwalign_endsfree.cpp:297:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
               ~~^~~~~~~
nwalign_endsfree.cpp:300:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
       r = i+rband; if(r>len2) { r = len2; }
                       ~^~~~~
nwalign_endsfree.cpp:305:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
       if (i == len1) {
           ~~^~~~~~~
nwalign_endsfree.cpp:314:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
       if (j == len2) {
           ~~^~~~~~~
nwalign_endsfree.cpp:379:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for (i=0;i<len_al;i++) {
            ~^~~~~~~
nwalign_endsfree.cpp: In function 'char** nwalign(const char*, size_t, const char*, size_t, int (*)[4], int, int)':
nwalign_endsfree.cpp:419:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
               ~~^~~~~~~
nwalign_endsfree.cpp:425:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for (j = 1; j <= len2; j++) {
               ~~^~~~~~~
nwalign_endsfree.cpp:444:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                  ~~~~^~~~~
nwalign_endsfree.cpp:444:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                               ~~~~^~~~~
nwalign_endsfree.cpp:445:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
     for(i=0;i<=len1;i++) {
             ~^~~~~~
nwalign_endsfree.cpp:447:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
       if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
          ~~~~~~~~~~^~~~~~~
nwalign_endsfree.cpp:452:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
               ~~^~~~~~~
nwalign_endsfree.cpp:455:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
       r = i+rband; if(r>len2) { r = len2; }
                       ~^~~~~
nwalign_endsfree.cpp:522:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for (i=0;i<len_al;i++) {
            ~^~~~~~~
nwalign_endsfree.cpp: In function 'char** nwalign_gapless(const char*, size_t, const char*, size_t)':
nwalign_endsfree.cpp:548:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for (int i=0;i<len_al;i++) {
                ~^~~~~~~
nwalign_endsfree.cpp:549:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
     al[0][i] = i < len1 ? s1[i] : '-';
                ~~^~~~~~
nwalign_endsfree.cpp:550:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
     al[1][i] = i < len2 ? s2[i] : '-';
                ~~^~~~~~
nwalign_endsfree.cpp: In function 'Sub* sub_new(Raw*, Raw*, int, int, int, int, bool, double, int, bool, int, bool)':
nwalign_endsfree.cpp:658:16: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
       for(s=0;s<sub->nsubs;s++) {
               ~^~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nwalign_vectorized.cpp -o nwalign_vectorized.o
nwalign_vectorized.cpp: In function 'char** nwalign_vectorized2(const char*, size_t, const char*, size_t, int16_t, int16_t, int16_t, int16_t, int)':
nwalign_vectorized.cpp:96:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   start_col = 1 + (1+(band<len1 ? band : len1))/2;
                       ~~~~^~~~~
nwalign_vectorized.cpp:125:26: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   while(row < (1 + (band < len1 ? band : len1))) {
                     ~~~~~^~~~~~
nwalign_vectorized.cpp:178:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
     if(row==(band<len1 ? band : len1)) {
              ~~~~^~~~~
nwalign_vectorized.cpp:218:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
     if(row < band && row < len1) { // upper tri for seq1
        ~~~~^~~~~~
nwalign_vectorized.cpp:75:21: warning: variable 'end_col' set but not used [-Wunused-but-set-variable]
   size_t start_col, end_col;
                     ^~~~~~~
nwalign_vectorized.cpp: In function 'Rcpp::CharacterVector C_nwvec(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int16_t, int16_t, int16_t, int, bool)':
nwalign_vectorized.cpp:330:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(i=0;i<s1.size();i++) {
           ~^~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pval.cpp -o pval.o
pval.cpp: In function 'double compute_lambda(Raw*, Sub*, Rcpp::NumericMatrix, bool, unsigned int)':
pval.cpp:121:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   for(s=0;s<sub->nsubs;s++) {
           ~^~~~~~~~~~~
pval.cpp:123:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
     if(pos0 < 0 || pos0 >= sub->len0) { Rcpp::stop("CL: Bad pos0: %i (len0=%i).", pos0, sub->len0); }
                    ~~~~~^~~~~~~~~~~~
pval.cpp: In function 'double compute_lambda_ts(Raw*, Sub*, unsigned int, double*, bool)':
pval.cpp:177:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   for(s=0;s<sub->nsubs;s++) {
           ~^~~~~~~~~~~
pval.cpp:179:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
     if(pos0 < 0 || pos0 >= sub->len0) { Rcpp::stop("CL: Bad pos0: %i (len0=%i).", pos0, sub->len0); }
                    ~~~~~^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c taxonomy.cpp -o taxonomy.o
taxonomy.cpp: In function 'void tax_kvec(const char*, unsigned int, unsigned char*)':
taxonomy.cpp:48:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
     if(kmer>=0 && kmer<n_kmers) {
                   ~~~~^~~~~~~~
taxonomy.cpp: In function 'int get_best_genus(int*, float*, unsigned int, unsigned int, unsigned int, float*)':
taxonomy.cpp:84:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   for(g=0;g<ngenus;g++) {
           ~^~~~~~~
taxonomy.cpp: In member function 'virtual void AssignParallel::operator()(std::size_t, std::size_t)':
taxonomy.cpp:145:31: warning: variable 'boot_match' set but not used [-Wunused-but-set-variable]
     unsigned int boot, booti, boot_match, arraylen, arraylen_rc;
                               ^~~~~~~~~~
taxonomy.cpp: In function 'Rcpp::List C_assign_taxonomy2(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<int>, Rcpp::IntegerMatrix, bool, bool)':
taxonomy.cpp:222:45: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type' {aka 'int'} and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
     if(ref_to_genus[i]<0 || ref_to_genus[i] >= ngenus) {
taxonomy.cpp:252:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
     for(kmer=0;kmer<n_kmers;kmer++) {
                ~~~~^~~~~~~~
taxonomy.cpp:261:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(kmer=0;kmer<n_kmers;kmer++) {
              ~~~~^~~~~~~~
taxonomy.cpp:268:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
     for(kmer=0;kmer<n_kmers;kmer++) {
                ~~~~^~~~~~~~
taxonomy.cpp:287:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
   for(i=0;i<unifs.size();i++) { C_unifs[i] = unifs(i); }
           ~^~~~~~~~~~~~~
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o dada2.dll tmp.def RcppExports.o Rmain.o chimera.o cluster.o containers.o error.o evaluate.o filter.o kmers.o misc.o nwalign_endsfree.o nwalign_vectorized.o pval.o taxonomy.o -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/dada2.buildbin-libdir/00LOCK-dada2/00new/dada2/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'dada2'
    finding HTML links ... done
    PacBioErrfun                            html  
    addSpecies                              html  
    finding level-2 HTML links ... done

    assignSpecies                           html  
    assignTaxonomy                          html  
    c-dada-method                           html  
    c-derep-method                          html  
    collapseNoMismatch                      html  
    dada-class                              html  
    dada                                    html  
    dada2-package                           html  
    derep-class                             html  
    derepFasta                              html  
    derepFastq                              html  
    errBalancedF                            html  
    errBalancedR                            html  
    fastqFilter                             html  
    fastqPairedFilter                       html  
    filterAndTrim                           html  
    getDadaOpt                              html  
    getErrors                               html  
    getSequences                            html  
    getUniques                              html  
    inflateErr                              html  
    isBimera                                html  
    isBimeraDenovo                          html  
    isBimeraDenovoTable                     html  
    isPhiX                                  html  
    isShiftDenovo                           html  
    learnErrors                             html  
    loessErrfun                             html  
    makeSequenceTable                       html  
    makeSpeciesFasta_RDP                    html  
    makeSpeciesFasta_Silva                  html  
    makeTaxonomyFasta_RDP                   html  
    makeTaxonomyFasta_Silva                 html  
    makeTaxonomyFasta_SilvaNR               html  
    mergePairs                              html  
    mergeSequenceTables                     html  
    names-set-dada-ANY-method               html  
    names-set-derep-ANY-method              html  
    noqualErrfun                            html  
    nwalign                                 html  
    nwhamming                               html  
    plotComplexity                          html  
    plotErrors                              html  
    plotQualityProfile                      html  
    qtables2                                html  
    rc                                      html  
    removeBimeraDenovo                      html  
    removePrimers                           html  
    seqComplexity                           html  
    setDadaOpt                              html  
    show-methods                            html  
    tperr1                                  html  
    uniques-vector                          html  
    uniquesToFasta                          html  
    writeFasta                              html  
** 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

install for x64

* installing *source* package 'dada2' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/dada2.h:7,
                 from RcppExports.cpp:4:
../inst/include/dada2_RcppExports.h:14:14: warning: 'void dada2::{anonymous}::validateSignature(const char*)' defined but not used [-Wunused-function]
         void validateSignature(const char* sig) {
              ^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Rmain.cpp -o Rmain.o
Rmain.cpp: In function 'Rcpp::List dada_uniques(std::vector<std::__cxx11::basic_string<char> >, std::vector<int>, std::vector<bool>, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, int, int, bool, double, int, double, double, double, bool, int, double, int, int, bool, bool, bool, int, bool, bool, int, bool, bool)':
Rmain.cpp:69:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
     if(quals.nrow() != maxlen) {
        ~~~~~~~~~~~~~^~~~~~~~~
Rmain.cpp:82:8: warning: variable 'HW_SSE3' set but not used [-Wunused-but-set-variable]
   bool HW_SSE3 = false;
        ^~~~~~~
Rmain.cpp: In function 'B* run_dada(Raw**, int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, double, double, bool, int, double, int, int, bool, bool, bool, bool, bool, int, bool, bool)':
Rmain.cpp:313:22: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
   while( (bb->nclust < max_clust) && (newi = b_bud(bb, min_fold, min_hamming, min_abund, verbose)) ) {
           ~~~~~~~~~~~^~~~~~~~~~~
Rmain.cpp: In function 'Rcpp::List dada_uniques(std::vector<std::__cxx11::basic_string<char> >, std::vector<int>, std::vector<bool>, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, int, int, bool, double, int, double, double, double, bool, int, double, int, int, bool, bool, bool, int, bool, bool, int, bool, bool)':
Rmain.cpp:287:9: warning: 'kord' may be used uninitialized in this function [-Wmaybe-uninitialized]
     free(kord);
     ~~~~^~~~~~
Rmain.cpp:286:9: warning: 'k16' may be used uninitialized in this function [-Wmaybe-uninitialized]
     free(k16);
     ~~~~^~~~~
Rmain.cpp:285:9: warning: 'k8' may be used uninitialized in this function [-Wmaybe-uninitialized]
     free(k8);
     ~~~~^~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c chimera.cpp -o chimera.o
chimera.cpp: In function 'bool C_is_bimera(std::__cxx11::string, std::vector<std::__cxx11::basic_string<char> >, bool, int, int, int, int, int)':
chimera.cpp:25:12: 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]
   for(i=0;i<pars.size() && rval==false;i++) {
           ~^~~~~~~~~~~~
chimera.cpp:29:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     if((left+right) >= sq.size()) { // Toss id/pure-shift/internal-indel "parents"
        ~~~~~~~~~~~~~^~~~~~~~~~~~
chimera.cpp:44:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     if((max_right+max_left)>=sq.size()) {
        ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
chimera.cpp:48:39: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
       if((oo_max_left+oo_max_right_oo)>=sq.size() || (oo_max_left_oo+oo_max_right)>=sq.size()) {
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
chimera.cpp:48:83: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
       if((oo_max_left+oo_max_right_oo)>=sq.size() || (oo_max_left_oo+oo_max_right)>=sq.size()) {
                                                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
chimera.cpp: In function 'void get_lr(char**, int&, int&, int&, int&, bool, int)':
chimera.cpp:231:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   while(al[0][pos] == '-' && pos<len) {
                              ~~~^~~~
chimera.cpp:237:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   while(pos<len && al[0][pos] == al[1][pos]) {
         ~~~^~~~
chimera.cpp:244:11: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     if(pos<len && al[0][pos] != '-') { left_oo++; }
        ~~~^~~~
chimera.cpp:245:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     while(pos<len && al[0][pos] == al[1][pos]) {
           ~~~^~~~
chimera.cpp:254:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   while(al[1][pos] == '-' && pos>+(len-max_shift)) {
                              ~~~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cluster.cpp -o cluster.o
cluster.cpp: In function 'void b_compare(B*, unsigned int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, bool, int, bool, bool, bool)':
cluster.cpp:17:23: warning: variable 'cind' set but not used [-Wunused-but-set-variable]
   unsigned int index, cind, center_reads;
                       ^~~~
cluster.cpp: In function 'void b_compare_parallel(B*, unsigned int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, bool, int, bool, bool, bool)':
cluster.cpp:166:16: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
   for(row=0;row<errMat.nrow();row++) {
             ~~~^~~~~~~~~~~~~~
cluster.cpp:167:18: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
     for(col=0;col<errMat.ncol();col++) {
               ~~~^~~~~~~~~~~~~~
cluster.cpp:156:23: warning: variable 'cind' set but not used [-Wunused-but-set-variable]
   unsigned int index, cind, row, col, ncol;
                       ^~~~
cluster.cpp: In function 'int b_bud(B*, double, int, int, bool)':
cluster.cpp:284:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   for(i=0;i<b->nclust;i++) {
           ~^~~~~~~~~~
cluster.cpp:285:15: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
     for(r=1; r<b->bi[i]->nraw; r++) { // r=0 is the center
              ~^~~~~~~~~~~~~~~
cluster.cpp:288:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
       if(raw->reads < min_abund) { continue; }
          ~~~~~~~~~~~^~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c containers.cpp -o containers.o
containers.cpp: In function 'void b_free(B*)':
containers.cpp:141:16: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   for(int i=0;i<b->nclust;i++) { bi_free(b->bi[i]); }
               ~^~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c error.cpp -o error.o
error.cpp: In function 'Rcpp::DataFrame b_make_positional_substitution_df(B*, Sub**, unsigned int, Rcpp::NumericMatrix, bool)':
error.cpp:178:51: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
   unsigned int i, pos, pos1, qind, j, r, s, nti0, ncol;
                                                   ^~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c evaluate.cpp -o evaluate.o
evaluate.cpp: In function 'Rcpp::IntegerVector C_eval_pair(std::__cxx11::string, std::__cxx11::string)':
evaluate.cpp:88:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   } while((s1gap || s2gap) && start<s1.size());
                               ~~~~~^~~~~~~~~~
evaluate.cpp: In function 'Rcpp::CharacterVector C_pair_consensus(std::__cxx11::string, std::__cxx11::string, int, bool)':
evaluate.cpp:133:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for(i=0;i<s1.size();i++) {
           ~^~~~~~~~~~
evaluate.cpp:152:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(i=0;i<s1.size();i++) {
             ~^~~~~~~~~~
evaluate.cpp:163:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for(i=0;i<s1.size();i++) {
           ~^~~~~~~~~~
evaluate.cpp: In function 'Rcpp::NumericVector kmer_dist(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)':
evaluate.cpp:219:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(int i=0;i<nseqs;i++) {
               ~^~~~~~
evaluate.cpp: In function 'Rcpp::NumericVector kord_dist(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int, int)':
evaluate.cpp:243:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(int i=0;i<nseqs;i++) {
               ~^~~~~~
evaluate.cpp:255:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(int i=0;i<nseqs;i++) {
               ~^~~~~~
evaluate.cpp: In function 'Rcpp::IntegerVector kmer_matches(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)':
evaluate.cpp:286:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(int i=0;i<nseqs;i++) {
               ~^~~~~~
evaluate.cpp:298:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(i=0;i<nseqs;i++) {
           ~^~~~~~
evaluate.cpp:310:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     for(j=0;j<klen_min;j++) {
             ~^~~~~~~~~
evaluate.cpp: In function 'Rcpp::IntegerVector kdist_matches(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)':
evaluate.cpp:339:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(i=0;i<nseqs;i++) {
           ~^~~~~~
evaluate.cpp:348:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     for(j=0;j<n_kmers;j++) {
             ~^~~~~~~~
evaluate.cpp:327:10: warning: variable 'len1' set but not used [-Wunused-but-set-variable]
   size_t len1 = 0, len2 = 0;
          ^~~~
evaluate.cpp:327:20: warning: variable 'len2' set but not used [-Wunused-but-set-variable]
   size_t len1 = 0, len2 = 0;
                    ^~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c filter.cpp -o filter.o
filter.cpp: In function 'Rcpp::IntegerVector C_matchRef(std::vector<std::__cxx11::basic_string<char> >, std::__cxx11::string, unsigned int, bool)':
filter.cpp:16:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   for(i=0;i<len;i++) {
           ~^~~~
filter.cpp:20:12: 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]
   for(i=0;i<seqs.size();i++) {
           ~^~~~~~~~~~~~
filter.cpp:24:14: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
     for(j=0;j<=(len-word_size);j++) {
             ~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c kmers.cpp -o kmers.o
kmers.cpp: In function 'double kmer_dist_SSEi_8(uint8_t*, int, uint8_t*, int, int)':
kmers.cpp:81:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(i=0;i<STEP;i++) {
           ~^~~~~
kmers.cpp: In function 'double kord_dist(uint16_t*, int, uint16_t*, int, int)':
kmers.cpp:101:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(i=0;i<klen;i++) {
           ~^~~~~
kmers.cpp: In function 'double kord_dist_SSEi(uint16_t*, int, uint16_t*, int, int)':
kmers.cpp:131:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(i=0;i<STEP;i++) {
           ~^~~~~
kmers.cpp:134:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(i=n_vec;i<klen;i++,kord1++,kord2++) { // kord starts pointing to where it was left
               ~^~~~~
kmers.cpp: In function 'void assign_kmer8(uint8_t*, const char*, int)':
kmers.cpp:146:8: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   if(k >= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
      ~~^~~~~~
kmers.cpp:158:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(i=0; i<klen; i++) {
            ~^~~~~
kmers.cpp: In function 'void assign_kmer(uint16_t*, const char*, int)':
kmers.cpp:195:8: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   if(k >= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
      ~~^~~~~~
kmers.cpp:205:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(i=0; i<klen; i++) {
            ~^~~~~
kmers.cpp: In function 'void assign_kmer_order(uint16_t*, char*, int)':
kmers.cpp:234:8: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   if(k >= len || k < 1 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
      ~~^~~~~~
kmers.cpp:239:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(i=0;i<klen;i++) { kord[i] = 0; }
           ~^~~~~
kmers.cpp:241:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(i=0; i<klen; i++) {
            ~^~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c misc.cpp -o misc.o
misc.cpp: In function 'void align_print(char**)':
misc.cpp:24:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(int i=0;i<strlen(al0);i++) {
               ~^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nwalign_endsfree.cpp -o nwalign_endsfree.o
nwalign_endsfree.cpp: In function 'char** nwalign_endsfree(const char*, size_t, const char*, size_t, int (*)[4], int, int)':
nwalign_endsfree.cpp:89:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for (i = 0; i <= len1; i++) {
               ~~^~~~~~~
nwalign_endsfree.cpp:95:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for (j = 0; j <= len2; j++) {
               ~~^~~~~~~
nwalign_endsfree.cpp:114:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                  ~~~~^~~~~
nwalign_endsfree.cpp:114:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                               ~~~~^~~~~
nwalign_endsfree.cpp:115:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     for(i=0;i<=len1;i++) {
             ~^~~~~~
nwalign_endsfree.cpp:117:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
       if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
          ~~~~~~~~~~^~~~~~~
nwalign_endsfree.cpp:122:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
               ~~^~~~~~~
nwalign_endsfree.cpp:125:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
       r = i+rband; if(r>len2) { r = len2; }
                       ~^~~~~
nwalign_endsfree.cpp:130:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
       if (i == len1) {
           ~~^~~~~~~
nwalign_endsfree.cpp:137:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
       if (j == len2) {
           ~~^~~~~~~
nwalign_endsfree.cpp:201:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for (i=0;i<len_al;i++) {
            ~^~~~~~~
nwalign_endsfree.cpp: In function 'char** nwalign_endsfree_homo(const char*, size_t, const char*, size_t, int (*)[4], int, int, int)':
nwalign_endsfree.cpp:230:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for (i=0,j=0;j<len1;j++) {
                ~^~~~~
nwalign_endsfree.cpp:231:10: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     if (j==len1-1 || s1[j]!=s1[j+1]) {
         ~^~~~~~~~
nwalign_endsfree.cpp:244:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for (i=0,j=0;j<len2;j++) {
                ~^~~~~
nwalign_endsfree.cpp:245:10: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     if (j==len2-1 || s2[j]!=s2[j+1]) {
         ~^~~~~~~~
nwalign_endsfree.cpp:264:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for (i = 0; i <= len1; i++) {
               ~~^~~~~~~
nwalign_endsfree.cpp:270:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for (j = 0; j <= len2; j++) {
               ~~^~~~~~~
nwalign_endsfree.cpp:289:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                  ~~~~^~~~~
nwalign_endsfree.cpp:289:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                               ~~~~^~~~~
nwalign_endsfree.cpp:290:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     for(i=0;i<=len1;i++) {
             ~^~~~~~
nwalign_endsfree.cpp:292:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
       if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
          ~~~~~~~~~~^~~~~~~
nwalign_endsfree.cpp:297:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
               ~~^~~~~~~
nwalign_endsfree.cpp:300:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
       r = i+rband; if(r>len2) { r = len2; }
                       ~^~~~~
nwalign_endsfree.cpp:305:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
       if (i == len1) {
           ~~^~~~~~~
nwalign_endsfree.cpp:314:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
       if (j == len2) {
           ~~^~~~~~~
nwalign_endsfree.cpp:379:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for (i=0;i<len_al;i++) {
            ~^~~~~~~
nwalign_endsfree.cpp: In function 'char** nwalign(const char*, size_t, const char*, size_t, int (*)[4], int, int)':
nwalign_endsfree.cpp:419:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
               ~~^~~~~~~
nwalign_endsfree.cpp:425:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for (j = 1; j <= len2; j++) {
               ~~^~~~~~~
nwalign_endsfree.cpp:444:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                  ~~~~^~~~~
nwalign_endsfree.cpp:444:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                               ~~~~^~~~~
nwalign_endsfree.cpp:445:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     for(i=0;i<=len1;i++) {
             ~^~~~~~
nwalign_endsfree.cpp:447:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
       if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
          ~~~~~~~~~~^~~~~~~
nwalign_endsfree.cpp:452:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
               ~~^~~~~~~
nwalign_endsfree.cpp:455:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
       r = i+rband; if(r>len2) { r = len2; }
                       ~^~~~~
nwalign_endsfree.cpp:522:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for (i=0;i<len_al;i++) {
            ~^~~~~~~
nwalign_endsfree.cpp: In function 'char** nwalign_gapless(const char*, size_t, const char*, size_t)':
nwalign_endsfree.cpp:548:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for (int i=0;i<len_al;i++) {
                ~^~~~~~~
nwalign_endsfree.cpp:549:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     al[0][i] = i < len1 ? s1[i] : '-';
                ~~^~~~~~
nwalign_endsfree.cpp:550:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     al[1][i] = i < len2 ? s2[i] : '-';
                ~~^~~~~~
nwalign_endsfree.cpp: In function 'Sub* sub_new(Raw*, Raw*, int, int, int, int, bool, double, int, bool, int, bool)':
nwalign_endsfree.cpp:658:16: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
       for(s=0;s<sub->nsubs;s++) {
               ~^~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nwalign_vectorized.cpp -o nwalign_vectorized.o
nwalign_vectorized.cpp: In function 'char** nwalign_vectorized2(const char*, size_t, const char*, size_t, int16_t, int16_t, int16_t, int16_t, int)':
nwalign_vectorized.cpp:96:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   start_col = 1 + (1+(band<len1 ? band : len1))/2;
                       ~~~~^~~~~
nwalign_vectorized.cpp:125:26: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   while(row < (1 + (band < len1 ? band : len1))) {
                     ~~~~~^~~~~~
nwalign_vectorized.cpp:178:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     if(row==(band<len1 ? band : len1)) {
              ~~~~^~~~~
nwalign_vectorized.cpp:218:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
     if(row < band && row < len1) { // upper tri for seq1
        ~~~~^~~~~~
nwalign_vectorized.cpp:75:21: warning: variable 'end_col' set but not used [-Wunused-but-set-variable]
   size_t start_col, end_col;
                     ^~~~~~~
nwalign_vectorized.cpp: In function 'Rcpp::CharacterVector C_nwvec(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int16_t, int16_t, int16_t, int, bool)':
nwalign_vectorized.cpp:330:12: 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]
   for(i=0;i<s1.size();i++) {
           ~^~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pval.cpp -o pval.o
pval.cpp: In function 'double compute_lambda(Raw*, Sub*, Rcpp::NumericMatrix, bool, unsigned int)':
pval.cpp:121:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   for(s=0;s<sub->nsubs;s++) {
           ~^~~~~~~~~~~
pval.cpp:123:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
     if(pos0 < 0 || pos0 >= sub->len0) { Rcpp::stop("CL: Bad pos0: %i (len0=%i).", pos0, sub->len0); }
                    ~~~~~^~~~~~~~~~~~
pval.cpp: In function 'double compute_lambda_ts(Raw*, Sub*, unsigned int, double*, bool)':
pval.cpp:177:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   for(s=0;s<sub->nsubs;s++) {
           ~^~~~~~~~~~~
pval.cpp:179:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
     if(pos0 < 0 || pos0 >= sub->len0) { Rcpp::stop("CL: Bad pos0: %i (len0=%i).", pos0, sub->len0); }
                    ~~~~~^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -msse2 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c taxonomy.cpp -o taxonomy.o
taxonomy.cpp: In function 'void tax_kvec(const char*, unsigned int, unsigned char*)':
taxonomy.cpp:48:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     if(kmer>=0 && kmer<n_kmers) {
                   ~~~~^~~~~~~~
taxonomy.cpp: In function 'int get_best_genus(int*, float*, unsigned int, unsigned int, unsigned int, float*)':
taxonomy.cpp:84:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   for(g=0;g<ngenus;g++) {
           ~^~~~~~~
taxonomy.cpp: In member function 'virtual void AssignParallel::operator()(std::size_t, std::size_t)':
taxonomy.cpp:145:31: warning: variable 'boot_match' set but not used [-Wunused-but-set-variable]
     unsigned int boot, booti, boot_match, arraylen, arraylen_rc;
                               ^~~~~~~~~~
taxonomy.cpp: In function 'Rcpp::List C_assign_taxonomy2(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<int>, Rcpp::IntegerMatrix, bool, bool)':
taxonomy.cpp:222:45: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type' {aka 'int'} and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     if(ref_to_genus[i]<0 || ref_to_genus[i] >= ngenus) {
taxonomy.cpp:252:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     for(kmer=0;kmer<n_kmers;kmer++) {
                ~~~~^~~~~~~~
taxonomy.cpp:261:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(kmer=0;kmer<n_kmers;kmer++) {
              ~~~~^~~~~~~~
taxonomy.cpp:268:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
     for(kmer=0;kmer<n_kmers;kmer++) {
                ~~~~^~~~~~~~
taxonomy.cpp:287:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
   for(i=0;i<unifs.size();i++) { C_unifs[i] = unifs(i); }
           ~^~~~~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o dada2.dll tmp.def RcppExports.o Rmain.o chimera.o cluster.o containers.o error.o evaluate.o filter.o kmers.o misc.o nwalign_endsfree.o nwalign_vectorized.o pval.o taxonomy.o -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/dada2.buildbin-libdir/dada2/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dada2' as dada2_1.22.0.zip
* DONE (dada2)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'dada2' successfully unpacked and MD5 sums checked