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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:dada2.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings dada2_1.37.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/dada2.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘dada2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dada2’ version ‘1.37.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘dada2’ can be installed ... WARNING
Found the following significant warnings:
  nwalign_vectorized.cpp:279:27: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  nwalign_vectorized.cpp:279:31: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  nwalign_vectorized.cpp:279:47: warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  nwalign_vectorized.cpp:279:50: warning: format ‘%i’ expects argument of type ‘int’, but argument 5 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  nwalign_vectorized.cpp:279:59: warning: format ‘%i’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  nwalign_vectorized.cpp:279:62: warning: format ‘%i’ expects argument of type ‘int’, but argument 7 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  nwalign_vectorized.cpp:279:71: warning: format ‘%i’ expects argument of type ‘int’, but argument 8 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  nwalign_vectorized.cpp:279:74: warning: format ‘%i’ expects argument of type ‘int’, but argument 9 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
See ‘/home/biocbuild/bbs-3.22-bioc/meat/dada2.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
  installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      6.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘ShortRead:::.set_omp_threads’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘C_isACGT’ ‘matchGenera’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call(ShortRead:::.set_omp_threads, ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
tax.check: warning in assignTaxonomy(sq.test, fn.tax, multi = TRUE):
  partial argument match of 'multi' to 'multithread'
plotComplexity: no visible binding for global variable ‘complexity’
plotErrors: no visible binding for global variable ‘Qual’
plotErrors: no visible binding for global variable ‘Observed’
plotErrors: no visible binding for global variable ‘count’
plotErrors: no visible binding for global variable ‘Input’
plotErrors: no visible binding for global variable ‘Estimated’
plotErrors: no visible binding for global variable ‘Nominal’
plotQualityProfile: no visible binding for global variable ‘Cycle’
plotQualityProfile: no visible binding for global variable ‘Score’
plotQualityProfile: no visible binding for global variable ‘Count’
plotQualityProfile: no visible binding for global variable ‘Mean’
plotQualityProfile: no visible binding for global variable ‘Q25’
plotQualityProfile: no visible binding for global variable ‘Q50’
plotQualityProfile: no visible binding for global variable ‘Q75’
plotQualityProfile: no visible binding for global variable ‘Cum’
Undefined global functions or variables:
  Count Cum Cycle Estimated Input Mean Nominal Observed Q25 Q50 Q75
  Qual Score complexity count
* checking Rd files ... NOTE
checkRd: (-1) dada-class.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dada-class.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dada-class.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dada-class.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dada-class.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dada-class.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dada-class.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dada-class.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dada-class.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dada-class.Rd:20: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addSpecies.Rd: FastqStreamer
  assignTaxonomy.Rd: setThreadOptions
  dada.Rd: setThreadOptions
  learnErrors.Rd: setThreadOptions
  plotComplexity.Rd: geom_histogram, ggplot, ggsave
  plotErrors.Rd: ggplot, ggsave
  plotQualityProfile.Rd: ggplot, ggsave
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... NOTE
   PKG_CFLAGS set in ‘src/Makevars.win’ without any corresponding files
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
PacBioErrfun        10.552  0.073  15.679
learnErrors          8.170  0.296   8.574
dada                 5.344  0.099   5.488
plotQualityProfile   4.488  0.645   5.364
mergePairs           4.731  0.133   9.668
isBimeraDenovoTable  4.440  0.019   5.403
addSpecies           3.216  0.173   5.426
isBimeraDenovo       2.988  0.183   6.843
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 10 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/dada2.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL dada2
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘dada2’ ...
** this is package ‘dada2’ version ‘1.37.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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]
   14 |         void validateSignature(const char* sig) {
      |              ^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:71:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   71 |     if(quals.nrow() != maxlen) {
      |        ~~~~~~~~~~~~~^~~~~~~~~
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:316:22: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  316 |   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:288:9: warning: ‘k8’ may be used uninitialized [-Wmaybe-uninitialized]
  288 |     free(k8);
      |     ~~~~^~~~
Rmain.cpp:122:12: note: ‘k8’ was declared here
  122 |   uint8_t *k8;
      |            ^~
Rmain.cpp:289:9: warning: ‘k16’ may be used uninitialized [-Wmaybe-uninitialized]
  289 |     free(k16);
      |     ~~~~^~~~~
Rmain.cpp:123:13: note: ‘k16’ was declared here
  123 |   uint16_t *k16;
      |             ^~~
Rmain.cpp:290:9: warning: ‘kord’ may be used uninitialized [-Wmaybe-uninitialized]
  290 |     free(kord);
      |     ~~~~^~~~~~
Rmain.cpp:124:13: note: ‘kord’ was declared here
  124 |   uint16_t *kord;
      |             ^~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c chimera.cpp -o chimera.o
chimera.cpp: In function ‘bool C_is_bimera(std::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 unsigned int’} [-Wsign-compare]
   25 |   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 unsigned int’} [-Wsign-compare]
   29 |     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 unsigned int’} [-Wsign-compare]
   44 |     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 unsigned int’} [-Wsign-compare]
   48 |       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 unsigned int’} [-Wsign-compare]
   48 |       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 unsigned int’} [-Wsign-compare]
  231 |   while(al[0][pos] == '-' && pos<len) {
      |                              ~~~^~~~
chimera.cpp:237:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  237 |   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 unsigned int’} [-Wsign-compare]
  244 |     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 unsigned int’} [-Wsign-compare]
  245 |     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 unsigned int’} [-Wsign-compare]
  254 |   while(al[1][pos] == '-' && pos>+(len-max_shift)) {
      |                              ~~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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]
   17 |   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]
  166 |   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]
  167 |     for(col=0;col<errMat.ncol();col++) {
      |               ~~~^~~~~~~~~~~~~~
cluster.cpp:156:23: warning: variable ‘cind’ set but not used [-Wunused-but-set-variable]
  156 |   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]
  284 |   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]
  285 |     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]
  288 |       if(raw->reads < min_abund) { continue; }
      |          ~~~~~~~~~~~^~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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]
  141 |   for(int i=0;i<b->nclust;i++) { bi_free(b->bi[i]); }
      |               ~^~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c error.cpp -o error.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c evaluate.cpp -o evaluate.o
evaluate.cpp: In function ‘Rcpp::IntegerVector C_eval_pair(std::string, std::string)’:
evaluate.cpp:88:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   88 |   } while((s1gap || s2gap) && start<s1.size());
      |                               ~~~~~^~~~~~~~~~
evaluate.cpp: In function ‘Rcpp::CharacterVector C_pair_consensus(std::string, std::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 unsigned int’} [-Wsign-compare]
  133 |   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 unsigned int’} [-Wsign-compare]
  152 |     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 unsigned int’} [-Wsign-compare]
  163 |   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 unsigned int’} [-Wsign-compare]
  219 |   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 unsigned int’} [-Wsign-compare]
  243 |   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 unsigned int’} [-Wsign-compare]
  255 |   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 unsigned int’} [-Wsign-compare]
  286 |   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 unsigned int’} [-Wsign-compare]
  298 |   for(i=0;i<nseqs;i++) {
      |           ~^~~~~~
evaluate.cpp:310:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  310 |     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:338:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  338 |   for(i=0;i<nseqs;i++) {
      |           ~^~~~~~
evaluate.cpp:345:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  345 |     for(j=0;j<n_kmers;j++) {
      |             ~^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c filter.cpp -o filter.o
filter.cpp: In function ‘Rcpp::IntegerVector C_matchRef(std::vector<std::__cxx11::basic_string<char> >, std::string, unsigned int, bool)’:
filter.cpp:16:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   16 |   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 unsigned int’} [-Wsign-compare]
   20 |   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]
   24 |     for(j=0;j<=(len-word_size);j++) {
      |             ~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c kmers.cpp -o kmers.o
kmers.cpp: In function ‘double kmer_dist_SSEi_8(uint8_t*, int, uint8_t*, int, int)’:
kmers.cpp:85:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   85 |   for(i=0;i<STEP;i++) {
      |           ~^~~~~
kmers.cpp: In function ‘double kord_dist(uint16_t*, int, uint16_t*, int, int)’:
kmers.cpp:110:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  110 |   for(i=0;i<klen;i++) {
      |           ~^~~~~
kmers.cpp: In function ‘double kord_dist_SSEi(uint16_t*, int, uint16_t*, int, int)’:
kmers.cpp:141:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  141 |   for(i=0;i<STEP;i++) {
      |           ~^~~~~
kmers.cpp:144:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |   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:162:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  162 |   if(k >= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
      |      ~~^~~~~~
kmers.cpp:174:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  174 |   for(i=0; i<klen; i++) {
      |            ~^~~~~
kmers.cpp: In function ‘void assign_kmer(uint16_t*, const char*, int)’:
kmers.cpp:211:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  211 |   if(k >= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
      |      ~~^~~~~~
kmers.cpp:221:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  221 |   for(i=0; i<klen; i++) {
      |            ~^~~~~
kmers.cpp: In function ‘void assign_kmer_order(uint16_t*, char*, int)’:
kmers.cpp:250:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  250 |   if(k >= len || k < 1 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
      |      ~~^~~~~~
kmers.cpp:255:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |   for(i=0;i<klen;i++) { kord[i] = 0; }
      |           ~^~~~~
kmers.cpp:257:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  257 |   for(i=0; i<klen; i++) {
      |            ~^~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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 unsigned int’} [-Wsign-compare]
   24 |   for(int i=0;i<strlen(al0);i++) {
      |               ~^~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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 unsigned int’} [-Wsign-compare]
   89 |   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 unsigned int’} [-Wsign-compare]
   95 |   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 unsigned int’} [-Wsign-compare]
  114 |   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 unsigned int’} [-Wsign-compare]
  114 |   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 unsigned int’} [-Wsign-compare]
  115 |     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 unsigned int’} [-Wsign-compare]
  117 |       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 unsigned int’} [-Wsign-compare]
  122 |   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 unsigned int’} [-Wsign-compare]
  125 |       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 unsigned int’} [-Wsign-compare]
  130 |       if (i == len1) {
      |           ~~^~~~~~~
nwalign_endsfree.cpp:137:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  137 |       if (j == len2) {
      |           ~~^~~~~~~
nwalign_endsfree.cpp:201:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  201 |   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 unsigned int’} [-Wsign-compare]
  230 |   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 unsigned int’} [-Wsign-compare]
  231 |     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 unsigned int’} [-Wsign-compare]
  244 |   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 unsigned int’} [-Wsign-compare]
  245 |     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 unsigned int’} [-Wsign-compare]
  264 |   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 unsigned int’} [-Wsign-compare]
  270 |   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 unsigned int’} [-Wsign-compare]
  289 |   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 unsigned int’} [-Wsign-compare]
  289 |   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 unsigned int’} [-Wsign-compare]
  290 |     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 unsigned int’} [-Wsign-compare]
  292 |       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 unsigned int’} [-Wsign-compare]
  297 |   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 unsigned int’} [-Wsign-compare]
  300 |       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 unsigned int’} [-Wsign-compare]
  305 |       if (i == len1) {
      |           ~~^~~~~~~
nwalign_endsfree.cpp:314:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  314 |       if (j == len2) {
      |           ~~^~~~~~~
nwalign_endsfree.cpp:379:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  379 |   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 unsigned int’} [-Wsign-compare]
  419 |   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 unsigned int’} [-Wsign-compare]
  425 |   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 unsigned int’} [-Wsign-compare]
  444 |   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 unsigned int’} [-Wsign-compare]
  444 |   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 unsigned int’} [-Wsign-compare]
  445 |     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 unsigned int’} [-Wsign-compare]
  447 |       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 unsigned int’} [-Wsign-compare]
  452 |   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 unsigned int’} [-Wsign-compare]
  455 |       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 unsigned int’} [-Wsign-compare]
  522 |   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 unsigned int’} [-Wsign-compare]
  548 |   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 unsigned int’} [-Wsign-compare]
  549 |     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 unsigned int’} [-Wsign-compare]
  550 |     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]
  658 |       for(s=0;s<sub->nsubs;s++) {
      |               ~^~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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 unsigned int’} [-Wsign-compare]
   96 |   start_col = 1 + (1+(band<len1 ? band : len1))/2;
      |                       ~~~~^~~~~
nwalign_vectorized.cpp:124:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  124 |   while(row < (1 + (band < len1 ? band : len1))) {
      |                     ~~~~~^~~~~~
nwalign_vectorized.cpp:177:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  177 |     if(row==(band<len1 ? band : len1)) {
      |              ~~~~^~~~~
nwalign_vectorized.cpp:217:12: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  217 |     if(row < band && row < len1) { // upper tri for seq1
      |        ~~~~^~~~~~
nwalign_vectorized.cpp:279:27: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  279 |         Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
      |                          ~^                                                                         ~~~~
      |                           |                                                                         |
      |                           int                                                                       size_t {aka long unsigned int}
      |                          %li
nwalign_vectorized.cpp:279:31: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  279 |         Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
      |                              ~^                                                                           ~~~~
      |                               |                                                                           |
      |                               int                                                                         size_t {aka long unsigned int}
      |                              %li
nwalign_vectorized.cpp:279:47: warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  279 |         Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
      |                                              ~^                                                                 ~~~~
      |                                               |                                                                 |
      |                                               int                                                               size_t {aka long unsigned int}
      |                                              %li
nwalign_vectorized.cpp:279:50: warning: format ‘%i’ expects argument of type ‘int’, but argument 5 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  279 |         Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
      |                                                 ~^                                                                    ~~~~
      |                                                  |                                                                    |
      |                                                  int                                                                  size_t {aka long unsigned int}
      |                                                 %li
nwalign_vectorized.cpp:279:59: warning: format ‘%i’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  279 |         Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
      |                                                          ~^                                                                 ~
      |                                                           |                                                                 |
      |                                                           int                                                               size_t {aka long unsigned int}
      |                                                          %li
nwalign_vectorized.cpp:279:62: warning: format ‘%i’ expects argument of type ‘int’, but argument 7 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  279 |         Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
      |                                                             ~^                                                                ~
      |                                                              |                                                                |
      |                                                              int                                                              size_t {aka long unsigned int}
      |                                                             %li
nwalign_vectorized.cpp:279:71: warning: format ‘%i’ expects argument of type ‘int’, but argument 8 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  279 |         Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
      |                                                                      ~^                                                         ~~~
      |                                                                       |                                                          |
      |                                                                       int                                                        size_t {aka long unsigned int}
      |                                                                      %li
nwalign_vectorized.cpp:279:74: warning: format ‘%i’ expects argument of type ‘int’, but argument 9 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  279 |         Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
      |                                                                         ~^                                                          ~~~~~~~~~~~~~~~~~~~
      |                                                                          |                                                                           |
      |                                                                          int                                                                         size_t {aka long unsigned int}
      |                                                                         %li
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:329:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  329 |   for(i=0;i<s1.size();i++) {
      |           ~^~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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]
  121 |   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]
  123 |     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]
  177 |   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]
  179 |     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-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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 unsigned int’} [-Wsign-compare]
   48 |     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]
   84 |   for(g=0;g<ngenus;g++) {
      |           ~^~~~~~~
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:221:45: 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 unsigned int’} [-Wsign-compare]
  221 |     if(ref_to_genus[i]<0 || ref_to_genus[i] >= ngenus) {
taxonomy.cpp:251:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  251 |     for(kmer=0;kmer<n_kmers;kmer++) {
      |                ~~~~^~~~~~~~
taxonomy.cpp:260:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  260 |   for(kmer=0;kmer<n_kmers;kmer++) {
      |              ~~~~^~~~~~~~
taxonomy.cpp:267:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  267 |     for(kmer=0;kmer<n_kmers;kmer++) {
      |                ~~~~^~~~~~~~
taxonomy.cpp:286:12: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  286 |   for(i=0;i<unifs.size();i++) { C_unifs[i] = unifs(i); }
      |           ~^~~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.22-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-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-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)