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BioC 3.4: CHECK report for dada2 on moscato1

This page was generated on 2016-09-21 03:48:04 -0700 (Wed, 21 Sep 2016).

Package 285/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dada2 1.1.5
Benjamin Callahan
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/dada2
Last Changed Rev: 119878 / Revision: 121152
Last Changed Date: 2016-08-03 17:28:37 -0700 (Wed, 03 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: dada2
Version: 1.1.5
Command: rm -rf dada2.buildbin-libdir dada2.Rcheck && mkdir dada2.buildbin-libdir dada2.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=dada2.buildbin-libdir dada2_1.1.5.tar.gz >dada2.Rcheck\00install.out 2>&1 && cp dada2.Rcheck\00install.out dada2-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=dada2.buildbin-libdir --install="check:dada2-install.out" --force-multiarch --no-vignettes --timings dada2_1.1.5.tar.gz
StartedAt: 2016-09-20 06:47:05 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 06:55:17 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 491.6 seconds
RetCode: 0
Status:  OK  
CheckDir: dada2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf dada2.buildbin-libdir dada2.Rcheck && mkdir dada2.buildbin-libdir dada2.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=dada2.buildbin-libdir dada2_1.1.5.tar.gz >dada2.Rcheck\00install.out 2>&1 && cp dada2.Rcheck\00install.out dada2-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=dada2.buildbin-libdir --install="check:dada2-install.out" --force-multiarch --no-vignettes --timings dada2_1.1.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/dada2.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'dada2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dada2' version '1.1.5'
* 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 whether package 'dada2' can be installed ... OK
* checking installed package size ... OK
* 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
* loading checks for arch 'i386'
** 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 ... NOTE
Warning: no function found corresponding to methods exports from 'dada2' for: 'show'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 ... NOTE
Warning: no function found corresponding to methods exports from 'dada2' for: 'show'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
** 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
assignSpecies: no visible global function definition for 'as'
combineDereps2: no visible global function definition for 'as'
dada: no visible global function definition for 'as'
derepFastq: no visible global function definition for 'as'
fastqFilter: no visible global function definition for 'as'
fastqPairedFilter: no visible global function definition for 'as'
getBadBases: no visible global function definition for 'ppois'
getSequences: no visible global function definition for 'is'
is.list.of: no visible binding for global variable 'is'
isPhiX: no visible global function definition for 'as'
loessErrfun: no visible global function definition for 'loess'
loessErrfun: no visible global function definition for 'predict'
maxEEFilter : <anonymous>: no visible global function definition for
  'as'
mergePairs: no visible global function definition for 'is'
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'
minQFilter : <anonymous>: no visible global function definition for
  'as'
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 global function definition for 'is'
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'
qtables2: no visible global function definition for 'as'
rc: no visible global function definition for 'as'
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 as indel is loess median
  mismatch n0F n0R ppois predict prefer seqF seqR
Consider adding
  importFrom("methods", "as", "is")
  importFrom("stats", "loess", "median", "ppois", "predict")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.4-bioc/meat/dada2.buildbin-libdir/dada2/libs/i386/dada2.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
dada           5.65   0.00    5.64
mergePairsByID 5.16   0.49    5.65
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mergePairsByID 5.21   0.45    5.66
dada           5.32   0.08    5.39
* 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: 6 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/dada2.Rcheck/00check.log'
for details.

dada2.Rcheck/00install.out:


install for i386

* installing *source* package 'dada2' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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) {
              ^
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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, bool, bool, int, bool, bool)':
Rmain.cpp:56:21: 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, bool, bool, bool, bool)':
Rmain.cpp:165:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while( (bb->nclust < max_clust) && (newi = b_bud(bb, min_fold, min_hamming, verbose)) ) {
                      ^
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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:30:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<pars.size();i++) {
            ^
chimera.cpp:43:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<pars.size() && rval==false;i++) {
            ^
chimera.cpp:89:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if((left+right) >= sq.size()) { // Toss id/pure-shift/internal-indel "parents"
                     ^
chimera.cpp:104:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if((max_right+max_left)>=sq.size()) {
                            ^
chimera.cpp:108:39: 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:108:83: 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: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;
                          ^
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c cluster.cpp -o cluster.o
cluster.cpp: In function 'void b_free(B*)':
cluster.cpp:161:16: 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 'void b_compare_parallel(B*, unsigned int, bool, double, Rcpp::NumericMatrix, bool)':
cluster.cpp:477:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(row=0;row<errMat.nrow();row++) {
                ^
cluster.cpp:478:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(col=0;col<errMat.ncol();col++) {
                  ^
cluster.cpp: In function 'int b_bud(B*, double, int, bool)':
cluster.cpp:618:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<b->nclust;i++) {
            ^
cluster.cpp:619:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(r=0; r<b->bi[i]->nraw; r++) {
               ^
cluster.cpp:630:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             ((raw->p == minp && raw->reads > minreads))) { // Most significant
                                            ^
cluster.cpp:651:29: warning: 'mine' may be used uninitialized in this function [-Wmaybe-uninitialized]
     b->bi[i]->birth_e = mine;
                             ^
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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:155:51: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
   unsigned int i, pos, pos1, qind, j, r, s, nti0, ncol;
                                                   ^
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c evaluate.cpp -o evaluate.o
evaluate.cpp: In function 'Rcpp::IntegerVector C_eval_pair(std::string, std::string)':
evaluate.cpp:87:36: 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::string, std::string, int)':
evaluate.cpp:132:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<s1.size();i++) {
            ^
evaluate.cpp:151:12: 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:235:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(max_aligns < (nseqs * (nseqs-1)/2)) { // More potential comparisons than max
                 ^
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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: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++) {
              ^
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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++) {
                ^
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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:104:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i <= len1; i++) {
                 ^
nwalign_endsfree.cpp:110:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (j = 0; j <= len2; j++) {
                 ^
nwalign_endsfree.cpp:129:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                      ^
nwalign_endsfree.cpp:129:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                                   ^
nwalign_endsfree.cpp:130:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(i=0;i<=len1;i++) {
              ^
nwalign_endsfree.cpp:132:20: 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:137:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
                 ^
nwalign_endsfree.cpp:140:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       r = i+rband; if(r>len2) { r = len2; }
                        ^
nwalign_endsfree.cpp:145:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (i == len1) {
             ^
nwalign_endsfree.cpp:152:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (j == len2) {
             ^
nwalign_endsfree.cpp:216:13: 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*, const char*, int (*)[4], int, int, int)':
nwalign_endsfree.cpp:247:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0,j=0;j<len1;j++) {
                 ^
nwalign_endsfree.cpp:248:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (j==len1-1 || s1[j]!=s1[j+1]) {
          ^
nwalign_endsfree.cpp:261:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0,j=0;j<len2;j++) {
                 ^
nwalign_endsfree.cpp:262:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (j==len2-1 || s2[j]!=s2[j+1]) {
          ^
nwalign_endsfree.cpp:281:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i <= len1; i++) {
                 ^
nwalign_endsfree.cpp:287:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (j = 0; j <= len2; j++) {
                 ^
nwalign_endsfree.cpp:306:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                      ^
nwalign_endsfree.cpp:306:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                                   ^
nwalign_endsfree.cpp:307:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(i=0;i<=len1;i++) {
              ^
nwalign_endsfree.cpp:309:20: 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:314:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
                 ^
nwalign_endsfree.cpp:317:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       r = i+rband; if(r>len2) { r = len2; }
                        ^
nwalign_endsfree.cpp:322:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (i == len1) {
             ^
nwalign_endsfree.cpp:331:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (j == len2) {
             ^
nwalign_endsfree.cpp:396:13: 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*, const char*, int (*)[4], int, int)':
nwalign_endsfree.cpp:436:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
                 ^
nwalign_endsfree.cpp:442:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (j = 1; j <= len2; j++) {
                 ^
nwalign_endsfree.cpp:461:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                      ^
nwalign_endsfree.cpp:461:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                                   ^
nwalign_endsfree.cpp:462:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(i=0;i<=len1;i++) {
              ^
nwalign_endsfree.cpp:464:20: 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:469:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
                 ^
nwalign_endsfree.cpp:472:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       r = i+rband; if(r>len2) { r = len2; }
                        ^
nwalign_endsfree.cpp:539:13: 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:673:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(s=0;s<sub->nsubs;s++) {
                ^
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c nwalign_vectorized.cpp -o nwalign_vectorized.o
nwalign_vectorized.cpp: In function 'char** nwalign_vectorized2(char*, char*, int16_t, int16_t, int16_t, int16_t, int)':
nwalign_vectorized.cpp:98:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   start_col = 1 + (1+(band<len1 ? band : len1))/2;
                           ^
nwalign_vectorized.cpp:127:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(row < (1 + (band < len1 ? band : len1))) {
                          ^
nwalign_vectorized.cpp:180:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(row==(band<len1 ? band : len1)) { 
                  ^
nwalign_vectorized.cpp:220:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(row < band && row < len1) { // upper tri for seq1
            ^
nwalign_vectorized.cpp:76:21: warning: variable 'end_col' set but not used [-Wunused-but-set-variable]
   size_t start_col, end_col;
                     ^
nwalign_vectorized.cpp:79:43: warning: unused variable 'ptr_index' [-Wunused-variable]
   int16_t *ptr_left, *ptr_diag, *ptr_up, *ptr_index, *ptr_d, *ptr_p;
                                           ^
nwalign_vectorized.cpp: In function 'char** nwalign_endsfree_vectorized(char*, char*, int16_t, int16_t, int16_t, int)':
nwalign_vectorized.cpp:343:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band<0 || band>len1) {
                    ^
nwalign_vectorized.cpp:363:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(row<band+1) {
            ^
nwalign_vectorized.cpp:375:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(row<band+1) {
            ^
nwalign_vectorized.cpp:416:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(row <= band) {
             ^
nwalign_vectorized.cpp:428:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(++row > band) break;
              ^
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c pval.cpp -o pval.o
pval.cpp: In function 'double compute_lambda(Raw*, Sub*, Rcpp::NumericMatrix, bool, unsigned int)':
pval.cpp:86:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( qind[pos1] > (ncol-1) ) {
                    ^
pval.cpp:92:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(s=0;s<sub->nsubs;s++) {
            ^
pval.cpp: In function 'double compute_lambda_ts(Raw*, Sub*, unsigned int, double*, bool)':
pval.cpp:142:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( qind[pos1] > (ncol-1) ) {
                    ^
pval.cpp:148:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(s=0;s<sub->nsubs;s++) {
            ^
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c strmap.cpp -o strmap.o
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c taxonomy.cpp -o taxonomy.o
taxonomy.cpp: In function 'void tax_kvec(const char*, unsigned int, unsigned char*)':
taxonomy.cpp:41:23: 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*, unsigned int, unsigned int, unsigned int*, unsigned int, double*, double*)':
taxonomy.cpp:65:12: 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::basic_string<char> >, std::vector<std::basic_string<char> >, std::vector<int>, Rcpp::IntegerMatrix, bool)':
taxonomy.cpp:112:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(ref_to_genus[i]<0 || ref_to_genus[i] >= ngenus) {
                                             ^
taxonomy.cpp:141:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(kmer=0;kmer<n_kmers;kmer++) {
                    ^
taxonomy.cpp:150:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(kmer=0;kmer<n_kmers;kmer++) {
                  ^
taxonomy.cpp:200:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(i=0;i<(genusmat.ncol());i++) {
                ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o dada2.dll tmp.def 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 -LD:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/dada2.buildbin-libdir/dada2/libs/i386
** 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

install for x64

* installing *source* package 'dada2' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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) {
              ^
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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, bool, bool, int, bool, bool)':
Rmain.cpp:56:21: 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, bool, bool, bool, bool)':
Rmain.cpp:165:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while( (bb->nclust < max_clust) && (newi = b_bud(bb, min_fold, min_hamming, verbose)) ) {
                      ^
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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:30:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<pars.size();i++) {
            ^
chimera.cpp:43:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<pars.size() && rval==false;i++) {
            ^
chimera.cpp:89:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if((left+right) >= sq.size()) { // Toss id/pure-shift/internal-indel "parents"
                     ^
chimera.cpp:104:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if((max_right+max_left)>=sq.size()) {
                            ^
chimera.cpp:108:39: 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:108:83: 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: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;
                          ^
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c cluster.cpp -o cluster.o
cluster.cpp: In function 'void b_free(B*)':
cluster.cpp:161:16: 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 'void b_compare_parallel(B*, unsigned int, bool, double, Rcpp::NumericMatrix, bool)':
cluster.cpp:477:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(row=0;row<errMat.nrow();row++) {
                ^
cluster.cpp:478:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(col=0;col<errMat.ncol();col++) {
                  ^
cluster.cpp: In function 'int b_bud(B*, double, int, bool)':
cluster.cpp:618:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<b->nclust;i++) {
            ^
cluster.cpp:619:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(r=0; r<b->bi[i]->nraw; r++) {
               ^
cluster.cpp:630:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             ((raw->p == minp && raw->reads > minreads))) { // Most significant
                                            ^
cluster.cpp:651:29: warning: 'mine' may be used uninitialized in this function [-Wmaybe-uninitialized]
     b->bi[i]->birth_e = mine;
                             ^
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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:155:51: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
   unsigned int i, pos, pos1, qind, j, r, s, nti0, ncol;
                                                   ^
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c evaluate.cpp -o evaluate.o
evaluate.cpp: In function 'Rcpp::IntegerVector C_eval_pair(std::string, std::string)':
evaluate.cpp:87:36: 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::string, std::string, int)':
evaluate.cpp:132:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i<s1.size();i++) {
            ^
evaluate.cpp:151:12: 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:235:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(max_aligns < (nseqs * (nseqs-1)/2)) { // More potential comparisons than max
                 ^
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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: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++) {
              ^
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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++) {
                ^
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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:104:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i <= len1; i++) {
                 ^
nwalign_endsfree.cpp:110:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (j = 0; j <= len2; j++) {
                 ^
nwalign_endsfree.cpp:129:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                      ^
nwalign_endsfree.cpp:129:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                                   ^
nwalign_endsfree.cpp:130:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(i=0;i<=len1;i++) {
              ^
nwalign_endsfree.cpp:132:20: 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:137:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
                 ^
nwalign_endsfree.cpp:140:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       r = i+rband; if(r>len2) { r = len2; }
                        ^
nwalign_endsfree.cpp:145:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (i == len1) {
             ^
nwalign_endsfree.cpp:152:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (j == len2) {
             ^
nwalign_endsfree.cpp:216:13: 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*, const char*, int (*)[4], int, int, int)':
nwalign_endsfree.cpp:247:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0,j=0;j<len1;j++) {
                 ^
nwalign_endsfree.cpp:248:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (j==len1-1 || s1[j]!=s1[j+1]) {
          ^
nwalign_endsfree.cpp:261:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0,j=0;j<len2;j++) {
                 ^
nwalign_endsfree.cpp:262:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (j==len2-1 || s2[j]!=s2[j+1]) {
          ^
nwalign_endsfree.cpp:281:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i <= len1; i++) {
                 ^
nwalign_endsfree.cpp:287:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (j = 0; j <= len2; j++) {
                 ^
nwalign_endsfree.cpp:306:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                      ^
nwalign_endsfree.cpp:306:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                                   ^
nwalign_endsfree.cpp:307:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(i=0;i<=len1;i++) {
              ^
nwalign_endsfree.cpp:309:20: 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:314:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
                 ^
nwalign_endsfree.cpp:317:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       r = i+rband; if(r>len2) { r = len2; }
                        ^
nwalign_endsfree.cpp:322:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (i == len1) {
             ^
nwalign_endsfree.cpp:331:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (j == len2) {
             ^
nwalign_endsfree.cpp:396:13: 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*, const char*, int (*)[4], int, int)':
nwalign_endsfree.cpp:436:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
                 ^
nwalign_endsfree.cpp:442:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (j = 1; j <= len2; j++) {
                 ^
nwalign_endsfree.cpp:461:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                      ^
nwalign_endsfree.cpp:461:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band>=0 && (band<len1 || band<len2)) {
                                   ^
nwalign_endsfree.cpp:462:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(i=0;i<=len1;i++) {
              ^
nwalign_endsfree.cpp:464:20: 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:469:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 1; i <= len1; i++) {
                 ^
nwalign_endsfree.cpp:472:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       r = i+rband; if(r>len2) { r = len2; }
                        ^
nwalign_endsfree.cpp:539:13: 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:673:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(s=0;s<sub->nsubs;s++) {
                ^
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c nwalign_vectorized.cpp -o nwalign_vectorized.o
nwalign_vectorized.cpp: In function 'char** nwalign_vectorized2(char*, char*, int16_t, int16_t, int16_t, int16_t, int)':
nwalign_vectorized.cpp:98:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   start_col = 1 + (1+(band<len1 ? band : len1))/2;
                           ^
nwalign_vectorized.cpp:127:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(row < (1 + (band < len1 ? band : len1))) {
                          ^
nwalign_vectorized.cpp:180:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(row==(band<len1 ? band : len1)) { 
                  ^
nwalign_vectorized.cpp:220:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(row < band && row < len1) { // upper tri for seq1
            ^
nwalign_vectorized.cpp:76:21: warning: variable 'end_col' set but not used [-Wunused-but-set-variable]
   size_t start_col, end_col;
                     ^
nwalign_vectorized.cpp:79:43: warning: unused variable 'ptr_index' [-Wunused-variable]
   int16_t *ptr_left, *ptr_diag, *ptr_up, *ptr_index, *ptr_d, *ptr_p;
                                           ^
nwalign_vectorized.cpp: In function 'char** nwalign_endsfree_vectorized(char*, char*, int16_t, int16_t, int16_t, int)':
nwalign_vectorized.cpp:343:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(band<0 || band>len1) {
                    ^
nwalign_vectorized.cpp:363:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(row<band+1) {
            ^
nwalign_vectorized.cpp:375:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(row<band+1) {
            ^
nwalign_vectorized.cpp:416:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(row <= band) {
             ^
nwalign_vectorized.cpp:428:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(++row > band) break;
              ^
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c pval.cpp -o pval.o
pval.cpp: In function 'double compute_lambda(Raw*, Sub*, Rcpp::NumericMatrix, bool, unsigned int)':
pval.cpp:86:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( qind[pos1] > (ncol-1) ) {
                    ^
pval.cpp:92:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(s=0;s<sub->nsubs;s++) {
            ^
pval.cpp: In function 'double compute_lambda_ts(Raw*, Sub*, unsigned int, double*, bool)':
pval.cpp:142:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( qind[pos1] > (ncol-1) ) {
                    ^
pval.cpp:148:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(s=0;s<sub->nsubs;s++) {
            ^
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c strmap.cpp -o strmap.o
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c taxonomy.cpp -o taxonomy.o
taxonomy.cpp: In function 'void tax_kvec(const char*, unsigned int, unsigned char*)':
taxonomy.cpp:41:23: 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*, unsigned int, unsigned int, unsigned int*, unsigned int, double*, double*)':
taxonomy.cpp:65:12: 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::basic_string<char> >, std::vector<std::basic_string<char> >, std::vector<int>, Rcpp::IntegerMatrix, bool)':
taxonomy.cpp:112:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(ref_to_genus[i]<0 || ref_to_genus[i] >= ngenus) {
                                             ^
taxonomy.cpp:141:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(kmer=0;kmer<n_kmers;kmer++) {
                    ^
taxonomy.cpp:150:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(kmer=0;kmer<n_kmers;kmer++) {
                  ^
taxonomy.cpp:200:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(i=0;i<(genusmat.ncol());i++) {
                ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o dada2.dll tmp.def 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 -LD:/biocbld/bbs-3.4-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/dada2.buildbin-libdir/dada2/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dada2' as dada2_1.1.5.zip
* DONE (dada2)

dada2.Rcheck/examples_i386/dada2-Ex.timings:

nameusersystemelapsed
addSpecies000
assignSpecies000
assignTaxonomy000
collapseNoMismatch1.980.022.00
dada5.650.005.64
dada_to_seq_table2.120.212.34
derepFastq0.660.050.70
evaluate_kmers0.120.030.16
fastqFilter0.380.020.39
fastqPairedFilter1.070.031.12
getDadaOpt000
getSequences0.80.00.8
getUniques0.800.010.81
inflateErr000
isBimera0.060.000.06
isBimeraDenovo1.990.002.00
isPhiX0.240.040.27
isShiftDenovo2.120.012.13
loessErrfun0.830.020.84
makeSequenceTable1.450.011.47
mergePairs3.790.063.85
mergePairsByID5.160.495.65
mergeSequenceTables000
nwalign000
nwhamming000
plotComplementarySubstitutions3.40.03.4
plotErrors3.670.033.70
plotQualityProfile0.590.030.63
removeBimeraDenovo2.080.002.07
setDadaOpt000
show-methods000
uniquesToFasta0.080.000.08

dada2.Rcheck/examples_x64/dada2-Ex.timings:

nameusersystemelapsed
addSpecies000
assignSpecies000
assignTaxonomy000
collapseNoMismatch2.080.012.34
dada5.320.085.39
dada_to_seq_table1.990.282.28
derepFastq0.740.020.75
evaluate_kmers0.120.010.14
fastqFilter0.420.020.44
fastqPairedFilter1.230.041.30
getDadaOpt000
getSequences1.020.001.01
getUniques0.680.030.72
inflateErr000
isBimera0.040.030.06
isBimeraDenovo1.720.021.73
isPhiX0.200.030.23
isShiftDenovo1.810.031.84
loessErrfun0.720.000.72
makeSequenceTable1.320.001.33
mergePairs3.390.023.40
mergePairsByID5.210.455.66
mergeSequenceTables000
nwalign000
nwhamming000
plotComplementarySubstitutions3.450.003.45
plotErrors2.590.022.60
plotQualityProfile0.700.010.72
removeBimeraDenovo1.790.001.80
setDadaOpt000
show-methods000
uniquesToFasta0.080.020.09