Package: dada2

Version: 1.11.3

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:dada2.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings dada2_1.11.3.tar.gz

StartedAt: 2019-04-08 23:50:40 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:54:59 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 258.9 seconds

RetCode: 0

Status:  OK

CheckDir: dada2.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:dada2.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings dada2_1.11.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/dada2.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dada2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dada2’ version ‘1.11.3’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  7.8Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      6.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 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.
* 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
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 ‘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’
samdf_to_qiime2: no visible global function definition for
  ‘write.table’
seqtab_to_mothur: no visible global function definition for
  ‘write.table’
seqtab_to_mothur: no visible binding for global variable ‘four’
seqtab_to_qiime: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  Count Cum Cycle Estimated Input Mean Nominal Observed Q25 Q50 Q75
  Qual Score complexity four write.table
Consider adding
  importFrom("utils", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
PacBioErrfun 11.638  0.036  11.772
learnErrors   7.767  0.050   6.482
dada          5.188  0.024   5.256
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/dada2.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### 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)

name	user	system	elapsed
PacBioErrfun	11.638	0.036	11.772
addSpecies	1.434	0.008	1.455
assignSpecies	0.667	0.004	0.687
assignTaxonomy	0.210	0.019	0.230
collapseNoMismatch	1.099	0.008	1.118
dada	5.188	0.024	5.256
derepFastq	0.865	0.016	0.883
fastqFilter	0.707	0.000	0.711
fastqPairedFilter	1.010	0.000	1.018
filterAndTrim	1.175	0.008	1.192
getDadaOpt	0.000	0.001	0.001
getErrors	1.713	0.010	1.734
getSequences	0.617	0.007	0.624
getUniques	0.619	0.008	0.663
inflateErr	0.000	0.000	0.001
isBimera	0.071	0.000	0.072
isBimeraDenovo	2.951	0.008	2.960
isBimeraDenovoTable	4.009	0.016	4.060
isPhiX	0.253	0.004	0.259
isShiftDenovo	1.818	0.004	1.826
learnErrors	7.767	0.050	6.482
loessErrfun	0.597	0.000	0.597
makeSequenceTable	1.062	0.000	1.062
mergePairs	2.952	0.012	2.965
mergeSequenceTables	0	0	0
noqualErrfun	0.885	0.004	0.889
nwalign	0.000	0.000	0.001
nwhamming	0	0	0
plotComplexity	0.363	0.004	0.366
plotErrors	2.782	0.088	2.874
plotQualityProfile	1.022	0.253	1.395
removeBimeraDenovo	3.236	0.092	3.357
seqComplexity	0.032	0.000	0.032
setDadaOpt	0.001	0.000	0.001
uniquesToFasta	0.086	0.008	0.095