Back to Multiple platform build/check report for BioC 3.9
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

INSTALL report for dada2 on malbec2

This page was generated on 2019-04-09 11:44:57 -0400 (Tue, 09 Apr 2019).

Package 378/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dada2 1.11.3
Benjamin Callahan
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/dada2
Branch: master
Last Commit: 57f82f4
Last Changed Date: 2019-03-25 16:31:01 -0400 (Mon, 25 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64 [ OK ] OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: dada2
Version: 1.11.3
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL dada2
StartedAt: 2019-04-08 18:40:17 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 18:42:56 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 159.1 seconds
RetCode: 0
Status:  OK 

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL dada2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘dada2’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/dada2.h:7:0,
                 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) {
              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -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, int, double, int, int, bool, bool, bool, int, bool, bool, int, bool, bool)’:
Rmain.cpp:68:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(quals.nrow() != maxlen) {
        ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
Rmain.cpp:81:8: 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, int, double, int, int, bool, bool, bool, bool, bool, int, bool, bool)’:
Rmain.cpp:307:22: warning: comparison between signed and unsigned integer expressions [-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, int, double, int, int, bool, bool, bool, int, bool, bool, int, bool, bool)’:
Rmain.cpp:282:9: warning: ‘kord’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     free(kord);
     ˜˜˜˜^˜˜˜˜˜
Rmain.cpp:281:9: warning: ‘k16’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     free(k16);
     ˜˜˜˜^˜˜˜˜
Rmain.cpp:280:9: warning: ‘k8’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     free(k8);
     ˜˜˜˜^˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -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 between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<pars.size() && rval==false;i++) {
           ˜^˜˜˜˜˜˜˜˜˜˜˜
chimera.cpp:29:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if((left+right) >= sq.size()) { // Toss id/pure-shift/internal-indel "parents"
        ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
chimera.cpp:44:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if((max_right+max_left)>=sq.size()) {
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
chimera.cpp:48:39: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
   while(al[0][pos] == '-' && pos<len) {
                              ˜˜˜^˜˜˜
chimera.cpp:237:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(pos<len && al[0][pos] == al[1][pos]) {
         ˜˜˜^˜˜˜
chimera.cpp:244:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(pos<len && al[0][pos] != '-') { left_oo++; }
        ˜˜˜^˜˜˜
chimera.cpp:245:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     while(pos<len && al[0][pos] == al[1][pos]) {
           ˜˜˜^˜˜˜
chimera.cpp:254:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(al[1][pos] == '-' && pos>+(len-max_shift)) {
                              ˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -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 between signed and unsigned integer expressions [-Wsign-compare]
   for(row=0;row<errMat.nrow();row++) {
             ˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
cluster.cpp:167:18: warning: comparison between signed and unsigned integer expressions [-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:317:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<b->nclust;i++) {
           ˜^˜˜˜˜˜˜˜˜˜
cluster.cpp:318:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(r=1; r<b->bi[i]->nraw; r++) { // r=0 is the center
              ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
cluster.cpp:321:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(raw->reads < min_abund) { continue; }
          ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c containers.cpp -o containers.o
containers.cpp: In function ‘void b_free(B*)’:
containers.cpp:140:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<b->nclust;i++) { bi_free(b->bi[i]); }
               ˜^˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -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:170:51: warning: variable ‘ncol’ set but not used [-Wunused-but-set-variable]
   unsigned int i, pos, pos1, qind, j, r, s, nti0, ncol;
                                                   ^˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -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 between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<s1.size();i++) {
           ˜^˜˜˜˜˜˜˜˜˜
evaluate.cpp:152:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(i=0;i<s1.size();i++) {
             ˜^˜˜˜˜˜˜˜˜˜
evaluate.cpp:163:12: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<nseqs;i++) {
               ˜^˜˜˜˜˜
evaluate.cpp:255:16: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<nseqs;i++) {
               ˜^˜˜˜˜˜
evaluate.cpp:298:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<nseqs;i++) {
           ˜^˜˜˜˜˜
evaluate.cpp:310:14: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<nseqs;i++) {
           ˜^˜˜˜˜˜
evaluate.cpp:348:14: warning: comparison between signed and unsigned integer expressions [-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;
                    ^˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -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 between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<len;i++) {
           ˜^˜˜˜
filter.cpp:20:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<seqs.size();i++) {
           ˜^˜˜˜˜˜˜˜˜˜˜˜
filter.cpp:24:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(j=0;j<=(len-word_size);j++) {
             ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -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 between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<STEP;i++) {
           ˜^˜˜˜˜
kmers.cpp:134:16: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
   if(k >= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
      ˜˜^˜˜˜˜˜
kmers.cpp:158:13: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
   if(k >= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
      ˜˜^˜˜˜˜˜
kmers.cpp:205:13: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
   if(k >= len || k < 1 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
      ˜˜^˜˜˜˜˜
kmers.cpp:239:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<klen;i++) { kord[i] = 0; }
           ˜^˜˜˜˜
kmers.cpp:241:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0; i<klen; i++) {
            ˜^˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c misc.cpp -o misc.o
misc.cpp: In function ‘void align_print(char**)’:
misc.cpp:24:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<strlen(al0);i++) {
               ˜^˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -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 between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i <= len1; i++) {
               ˜˜^˜˜˜˜˜˜
nwalign_endsfree.cpp:95:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (j = 0; j <= len2; j++) {
               ˜˜^˜˜˜˜˜˜
nwalign_endsfree.cpp:114:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                  ˜˜˜˜^˜˜˜˜
nwalign_endsfree.cpp:114:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                               ˜˜˜˜^˜˜˜˜
nwalign_endsfree.cpp:115:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(i=0;i<=len1;i++) {
             ˜^˜˜˜˜˜
nwalign_endsfree.cpp:117:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
          ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
nwalign_endsfree.cpp:122:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
               ˜˜^˜˜˜˜˜˜
nwalign_endsfree.cpp:125:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       r = i+rband; if(r>len2) { r = len2; }
                       ˜^˜˜˜˜
nwalign_endsfree.cpp:130:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (i == len1) {
           ˜˜^˜˜˜˜˜˜
nwalign_endsfree.cpp:137:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (j == len2) {
           ˜˜^˜˜˜˜˜˜
nwalign_endsfree.cpp:201:13: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0,j=0;j<len1;j++) {
                ˜^˜˜˜˜
nwalign_endsfree.cpp:231:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (j==len1-1 || s1[j]!=s1[j+1]) {
         ˜^˜˜˜˜˜˜˜
nwalign_endsfree.cpp:244:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0,j=0;j<len2;j++) {
                ˜^˜˜˜˜
nwalign_endsfree.cpp:245:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (j==len2-1 || s2[j]!=s2[j+1]) {
         ˜^˜˜˜˜˜˜˜
nwalign_endsfree.cpp:264:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i <= len1; i++) {
               ˜˜^˜˜˜˜˜˜
nwalign_endsfree.cpp:270:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (j = 0; j <= len2; j++) {
               ˜˜^˜˜˜˜˜˜
nwalign_endsfree.cpp:289:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                  ˜˜˜˜^˜˜˜˜
nwalign_endsfree.cpp:289:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                               ˜˜˜˜^˜˜˜˜
nwalign_endsfree.cpp:290:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(i=0;i<=len1;i++) {
             ˜^˜˜˜˜˜
nwalign_endsfree.cpp:292:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
          ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
nwalign_endsfree.cpp:297:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
               ˜˜^˜˜˜˜˜˜
nwalign_endsfree.cpp:300:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       r = i+rband; if(r>len2) { r = len2; }
                       ˜^˜˜˜˜
nwalign_endsfree.cpp:305:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (i == len1) {
           ˜˜^˜˜˜˜˜˜
nwalign_endsfree.cpp:314:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (j == len2) {
           ˜˜^˜˜˜˜˜˜
nwalign_endsfree.cpp:379:13: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
               ˜˜^˜˜˜˜˜˜
nwalign_endsfree.cpp:425:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (j = 1; j <= len2; j++) {
               ˜˜^˜˜˜˜˜˜
nwalign_endsfree.cpp:444:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                  ˜˜˜˜^˜˜˜˜
nwalign_endsfree.cpp:444:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                               ˜˜˜˜^˜˜˜˜
nwalign_endsfree.cpp:445:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(i=0;i<=len1;i++) {
             ˜^˜˜˜˜˜
nwalign_endsfree.cpp:447:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
          ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
nwalign_endsfree.cpp:452:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
               ˜˜^˜˜˜˜˜˜
nwalign_endsfree.cpp:455:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       r = i+rband; if(r>len2) { r = len2; }
                       ˜^˜˜˜˜
nwalign_endsfree.cpp:522:13: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0;i<len_al;i++) {
                ˜^˜˜˜˜˜˜
nwalign_endsfree.cpp:549:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     al[0][i] = i < len1 ? s1[i] : '-';
                ˜˜^˜˜˜˜˜
nwalign_endsfree.cpp:550:18: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
       for(s=0;s<sub->nsubs;s++) {
               ˜^˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -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 between signed and unsigned integer expressions [-Wsign-compare]
   start_col = 1 + (1+(band<len1 ? band : len1))/2;
                       ˜˜˜˜^˜˜˜˜
nwalign_vectorized.cpp:125:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(row < (1 + (band < len1 ? band : len1))) {
                     ˜˜˜˜˜^˜˜˜˜˜
nwalign_vectorized.cpp:178:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(row==(band<len1 ? band : len1)) {
              ˜˜˜˜^˜˜˜˜
nwalign_vectorized.cpp:218:12: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<s1.size();i++) {
           ˜^˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -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 between signed and unsigned integer expressions [-Wsign-compare]
   for(s=0;s<sub->nsubs;s++) {
           ˜^˜˜˜˜˜˜˜˜˜˜
pval.cpp:123:25: warning: comparison between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-Wsign-compare]
   for(s=0;s<sub->nsubs;s++) {
           ˜^˜˜˜˜˜˜˜˜˜˜
pval.cpp:179:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(pos0 < 0 || pos0 >= sub->len0) { Rcpp::stop("CL: Bad pos0: %i (len0=%i).", pos0, sub->len0); }
                    ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c taxonomy.cpp -o taxonomy.o
taxonomy.cpp: In function ‘void tax_kvec(const char*, unsigned int, unsigned char*)’:
taxonomy.cpp:42:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(kmer>=0 && kmer<n_kmers) {
                   ˜˜˜˜^˜˜˜˜˜˜˜
taxonomy.cpp: In function ‘int get_best_genus(int*, double*, unsigned int, unsigned int, unsigned int*, unsigned int, double*, double*)’:
taxonomy.cpp:72:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(g=0;g<ngenus;g++) {
           ˜^˜˜˜˜˜˜
taxonomy.cpp: In function ‘Rcpp::List C_assign_taxonomy(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:120:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(ref_to_genus[i]<0 || ref_to_genus[i] >= ngenus) {
taxonomy.cpp:149:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(kmer=0;kmer<n_kmers;kmer++) {
                ˜˜˜˜^˜˜˜˜˜˜˜
taxonomy.cpp:158:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(kmer=0;kmer<n_kmers;kmer++) {
              ˜˜˜˜^˜˜˜˜˜˜˜
taxonomy.cpp:223:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(i=0;i<(genusmat.ncol());i++) {
               ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
taxonomy.cpp: In member function ‘virtual void AssignParallel::operator()(std::size_t, std::size_t)’:
taxonomy.cpp:277:15: warning: variable ‘seqlen’ set but not used [-Wunused-but-set-variable]
     size_t i, seqlen;
               ^˜˜˜˜˜
taxonomy.cpp:278:31: 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:345:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(ref_to_genus[i]<0 || ref_to_genus[i] >= ngenus) {
taxonomy.cpp:374:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(kmer=0;kmer<n_kmers;kmer++) {
                ˜˜˜˜^˜˜˜˜˜˜˜
taxonomy.cpp:383:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(kmer=0;kmer<n_kmers;kmer++) {
              ˜˜˜˜^˜˜˜˜˜˜˜
taxonomy.cpp:407:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<unifs.size();i++) { C_unifs[i] = unifs(i); }
           ˜^˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o dada2.so 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 -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-dada2/00new/dada2/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (dada2)