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BioC 3.3: CHECK report for dada2 on zin2

This page was generated on 2016-10-13 12:46:27 -0700 (Thu, 13 Oct 2016).

Package 268/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dada2 1.0.3
Benjamin Callahan
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/dada2
Last Changed Rev: 117763 / Revision: 122332
Last Changed Date: 2016-05-22 14:30:54 -0700 (Sun, 22 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: dada2
Version: 1.0.3
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings dada2_1.0.3.tar.gz
StartedAt: 2016-10-13 01:03:49 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 01:07:18 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 209.2 seconds
RetCode: 0
Status:  OK 
CheckDir: dada2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings dada2_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/dada2.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.0.3’
* 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 ... OK
* 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  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getBadBases: no visible global function definition for ‘ppois’
loessErrfun: no visible global function definition for ‘loess’
loessErrfun: no visible global function definition for ‘predict’
mergePairsByID: no visible binding for global variable ‘seqF’
mergePairsByID: no visible binding for global variable ‘seqR’
mergePairsByID: no visible binding for global variable ‘abundance’
mergePairsByID: no visible binding for global variable ‘accept’
mergePairsByID: no visible binding for global variable ‘als1’
mergePairsByID: no visible binding for global variable ‘als2’
mergePairsByID: no visible binding for global variable ‘prefer’
mergePairsByID: no visible binding for global variable ‘n0R’
mergePairsByID: no visible binding for global variable ‘n0F’
mergePairsByID: no visible binding for global variable ‘allMismatch’
mergePairsByID: no visible binding for global variable ‘mismatch’
mergePairsByID: no visible binding for global variable ‘indel’
plotComplementarySubstitutions: no visible binding for global variable
  ‘Sub1’
plotComplementarySubstitutions: no visible binding for global variable
  ‘Substitution’
plotComplementarySubstitutions: no visible binding for global variable
  ‘Sub2’
plotComplementarySubstitutions: no visible binding for global variable
  ‘SubGrp’
plotComplementarySubstitutions: no visible binding for global variable
  ‘Direction’
plotComplementarySubstitutions: no visible binding for global variable
  ‘Count’
plotComplementarySubstitutions: no visible binding for global variable
  ‘Forward’
plotComplementarySubstitutions: no visible binding for global variable
  ‘Reverse’
plotComplementarySubstitutions: no visible binding for global variable
  ‘Quality’
plotErrors: no visible binding for global variable ‘Qual’
plotErrors: no visible binding for global variable ‘Observed’
plotErrors: no visible binding for global variable ‘Estimated’
plotErrors: no visible binding for global variable ‘Input’
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’
show,derep: no visible global function definition for ‘median’
Undefined global functions or variables:
  Count Cycle Direction Estimated Forward Input Mean Nominal Observed
  Q25 Q50 Q75 Qual Quality Reverse Score Sub1 Sub2 SubGrp Substitution
  abundance accept allMismatch als1 als2 indel loess median mismatch
  n0F n0R ppois predict prefer seqF seqR
Consider adding
  importFrom("stats", "loess", "median", "ppois", "predict")
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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/dada2.Rcheck/00check.log’
for details.

dada2.Rcheck/00install.out:

* installing *source* package ‘dada2’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c Rmain.cpp -o Rmain.o
Rmain.cpp: In function ‘Rcpp::List dada_uniques(std::vector<std::basic_string<char> >, std::vector<int>, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, bool, double, int, double, int, double, int, bool, int, bool, bool, int, bool)’:
Rmain.cpp:56:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(quals.nrow() != seqlen) {
                        ^
Rmain.cpp: In function ‘B* run_dada(Raw**, int, Rcpp::NumericMatrix, int (*)[4], int, int, bool, double, int, double, int, double, int, bool, int, bool, bool, bool)’:
Rmain.cpp:164:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while( (bb->nclust < max_clust) && (newi = b_bud(bb, min_fold, min_hamming, verbose)) ) {
                        ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c chimera.cpp -o chimera.o
chimera.cpp: In function ‘bool C_is_bimera(std::string, std::vector<std::basic_string<char> >, bool, int, Rcpp::NumericMatrix, int, int)’:
chimera.cpp:30:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<pars.size();i++) {
                       ^
chimera.cpp:43:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<pars.size() && rval==false;i++) {
                       ^
chimera.cpp:88:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if((left+right) >= sq.size()) { // Toss id/pure-shift/internal-indel "parents"
                                ^
chimera.cpp:103:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if((max_right+max_left)>=sq.size()) {
                                      ^
chimera.cpp:107:49: 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:107:93: 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:17:35: warning: ‘right_oo’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   int i, j, left, right, left_oo, right_oo, pos, len, max_len;
                                   ^
chimera.cpp:17:26: warning: ‘left_oo’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   int i, j, left, right, left_oo, right_oo, pos, len, max_len;
                          ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c cluster.cpp -o cluster.o
cluster.cpp: In function ‘void b_free(B*)’:
cluster.cpp:160:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<b->nclust;i++) { bi_free(b->bi[i]); }
                    ^
cluster.cpp: In function ‘int b_bud(B*, double, int, bool)’:
cluster.cpp:403:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<b->nclust;i++) {
                ^
cluster.cpp:404:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(r=0; r<b->bi[i]->nraw; r++) {
                          ^
cluster.cpp:414:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             ((raw->p == minp && raw->reads > minreads))) { // Most significant
                                              ^
cluster.cpp:435:29: warning: ‘mine’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     b->bi[i]->birth_e = mine;
                             ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/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:154:51: warning: variable ‘ncol’ set but not used [-Wunused-but-set-variable]
   unsigned int i, pos, pos1, qind, j, r, s, nti0, ncol;
                                                   ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c evaluate.cpp -o evaluate.o
evaluate.cpp: In function ‘Rcpp::IntegerVector C_eval_pair(std::string, std::string)’:
evaluate.cpp:87:45: 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::string, std::string, int)’:
evaluate.cpp:132:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<s1.size();i++) {
                     ^
evaluate.cpp:151:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<s1.size();i++) {
                     ^
evaluate.cpp: In function ‘Rcpp::DataFrame evaluate_kmers(std::vector<std::basic_string<char> >, int, Rcpp::NumericMatrix, int, int, unsigned int)’:
evaluate.cpp:235:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(max_aligns < (nseqs * (nseqs-1)/2)) { // More potential comparisons than max
                                       ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c filter.cpp -o filter.o
filter.cpp: In function ‘Rcpp::IntegerVector C_matchRef(std::vector<std::basic_string<char> >, std::string, unsigned int, bool)’:
filter.cpp:17:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<len;i++) {
             ^
filter.cpp:21:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<seqs.size();i++) {
                       ^
filter.cpp:25:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(j=0;j<=(len-word_size);j++) {
                              ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c misc.cpp -o misc.o
misc.cpp: In function ‘void align_print(char**)’:
misc.cpp:24:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i<strlen(al0);i++) {
                           ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c nwalign_endsfree.cpp -o nwalign_endsfree.o
nwalign_endsfree.cpp: In function ‘char** nwalign_endsfree(const char*, const char*, int (*)[4], int, int)’:
nwalign_endsfree.cpp:103:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i <= len1; i++) {
                    ^
nwalign_endsfree.cpp:109:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (j = 0; j <= len2; j++) {
                    ^
nwalign_endsfree.cpp:128:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                       ^
nwalign_endsfree.cpp:128:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                                    ^
nwalign_endsfree.cpp:129:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(i=0;i<=len1;i++) {
                ^
nwalign_endsfree.cpp:131:23: 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:136:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
                    ^
nwalign_endsfree.cpp:139:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       r = i+rband; if(r>len2) { r = len2; }
                         ^
nwalign_endsfree.cpp:144:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (i == len1) {
                ^
nwalign_endsfree.cpp:151:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (j == len2) {
                ^
nwalign_endsfree.cpp:215:14: 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*, const char*, int (*)[4], int, int, int)’:
nwalign_endsfree.cpp:246:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0,j=0;j<len1;j++) {
                  ^
nwalign_endsfree.cpp:247:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (j==len1-1 || s1[j]!=s1[j+1]) {
                 ^
nwalign_endsfree.cpp:260:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0,j=0;j<len2;j++) {
                  ^
nwalign_endsfree.cpp:261:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (j==len2-1 || s2[j]!=s2[j+1]) {
                 ^
nwalign_endsfree.cpp:280:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i <= len1; i++) {
                    ^
nwalign_endsfree.cpp:286:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (j = 0; j <= len2; j++) {
                    ^
nwalign_endsfree.cpp:305:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                       ^
nwalign_endsfree.cpp:305:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                                    ^
nwalign_endsfree.cpp:306:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(i=0;i<=len1;i++) {
                ^
nwalign_endsfree.cpp:308:23: 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:313:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
                    ^
nwalign_endsfree.cpp:316:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       r = i+rband; if(r>len2) { r = len2; }
                         ^
nwalign_endsfree.cpp:321:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (i == len1) {
                ^
nwalign_endsfree.cpp:330:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (j == len2) {
                ^
nwalign_endsfree.cpp:395:14: 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*, const char*, int (*)[4], int, int)’:
nwalign_endsfree.cpp:435:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
                    ^
nwalign_endsfree.cpp:441:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (j = 1; j <= len2; j++) {
                    ^
nwalign_endsfree.cpp:460:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                       ^
nwalign_endsfree.cpp:460:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                                    ^
nwalign_endsfree.cpp:461:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(i=0;i<=len1;i++) {
                ^
nwalign_endsfree.cpp:463:23: 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:468:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
                    ^
nwalign_endsfree.cpp:471:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       r = i+rband; if(r>len2) { r = len2; }
                         ^
nwalign_endsfree.cpp:538:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0;i<len_al;i++) {
              ^
nwalign_endsfree.cpp: In function ‘Sub* sub_new(Raw*, Raw*, int (*)[4], int, int, bool, double, int, bool)’:
nwalign_endsfree.cpp:672:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(s=0;s<sub->nsubs;s++) {
                      ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c nwalign_vectorized.cpp -o nwalign_vectorized.o
nwalign_vectorized.cpp: In function ‘char** nwalign_endsfree_vectorized(char*, char*, int16_t, int16_t, int16_t, int)’:
nwalign_vectorized.cpp:51:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band<0 || band>len1) {
                     ^
nwalign_vectorized.cpp:71:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(row<band+1) {
                  ^
nwalign_vectorized.cpp:83:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(row<band+1) {
                  ^
nwalign_vectorized.cpp:124:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(row <= band) {
                ^
nwalign_vectorized.cpp:136:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(++row > band) break;
                ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/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:93:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(s=0;s<sub->nsubs;s++) {
                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c strmap.cpp -o strmap.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/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:41:24: 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*, unsigned int, unsigned int, unsigned int*, unsigned int, double*, double*)’:
taxonomy.cpp:65:13: 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::basic_string<char> >, std::vector<std::basic_string<char> >, std::vector<int>, Rcpp::IntegerMatrix, bool)’:
taxonomy.cpp:112:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(ref_to_genus[i]<0 || ref_to_genus[i] >= ngenus) {
                                                ^
taxonomy.cpp:141:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(kmer=0;kmer<n_kmers;kmer++) {
                     ^
taxonomy.cpp:150:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(kmer=0;kmer<n_kmers;kmer++) {
                   ^
taxonomy.cpp:200:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(i=0;i<(genusmat.ncol());i++) {
                                 ^
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o dada2.so RcppExports.o Rmain.o chimera.o cluster.o error.o evaluate.o filter.o misc.o nwalign_endsfree.o nwalign_vectorized.o pval.o strmap.o taxonomy.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/dada2.Rcheck/dada2/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (dada2)

dada2.Rcheck/dada2-Ex.timings:

nameusersystemelapsed
assignTaxonomy0.0010.0000.001
collapseNoMismatch1.4600.0281.413
dada3.5010.0163.452
dada_to_seq_table1.3140.0001.272
derepFastq2.8790.0121.866
evaluate_kmers0.2220.0000.187
fastqFilter0.5850.0010.458
fastqPairedFilter1.4440.0241.242
getDadaOpt0.0010.0000.001
getSequences0.8000.0030.757
getUniques0.5690.0080.530
inflateErr0.0010.0000.000
isBimera0.1350.0000.089
isBimeraDenovo1.2440.0041.209
isPhiX0.5180.0040.487
isShiftDenovo1.1810.0041.137
loessErrfun0.5180.1800.659
makeSequenceTable1.0470.0361.084
mergePairs2.4240.0132.388
mergePairsByID3.7570.0003.699
nwalign0.0010.0000.001
nwhamming0.0020.0000.002
plotComplementarySubstitutions2.2590.0032.251
plotErrors2.5410.1612.784
plotQualityProfile1.1220.0231.120
removeBimeraDenovo1.5150.0041.498
setDadaOpt0.0010.0000.001
show-methods0.0010.0000.000
uniquesToFasta0.3950.0000.383