Package: dada2

Version: 1.12.1

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dada2.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings dada2_1.12.1.tar.gz

StartedAt: 2019-10-16 03:02:58 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:10:07 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 428.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: dada2.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dada2.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings dada2_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/dada2.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.12.1'
* 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 whether package 'dada2' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/dada.Rd:13: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/derepFastq.Rd:37: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/derepFastq.Rd:12: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/derepFastq.Rd:19: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/fastqFilter.Rd:71: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/fastqFilter.Rd:74: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/fastqFilter.Rd:76: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/fastqFilter.Rd:112: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/fastqPairedFilter.Rd:101: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/fastqPairedFilter.Rd:104: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/fastqPairedFilter.Rd:106: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/fastqPairedFilter.Rd:145: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/filterAndTrim.Rd:107: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/filterAndTrim.Rd:108: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/filterAndTrim.Rd:117: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/filterAndTrim.Rd:120: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/filterAndTrim.Rd:164: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/learnErrors.Rd:14: file link 'FastqStreamer' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/plotComplexity.Rd:52: file link 'oligonucleotideFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/rc.Rd:11: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/rc.Rd:11: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/removePrimers.Rd:35: file link 'vmatchPattern' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/seqComplexity.Rd:61: file link 'oligonucleotideFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/uniquesToFasta.Rd:22: file link 'writeFasta' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/uniquesToFasta.Rd:27: file link 'writeFasta' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/uniquesToFasta.Rd:29: file link 'writeFasta' in package 'ShortRead' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/writeFasta.Rd:21: file link 'writeXStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0IaqVn/R.INSTALL260059175229/dada2/man/writeFasta.Rd:31: file link 'writeXStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/dada2.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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 ... OK
** checking whether the namespace can be unloaded cleanly ... 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 ... 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'
seqtab_to_mothur: no visible binding for global variable 'four'
Undefined global functions or variables:
  Count Cum Cycle Estimated Input Mean Nominal Observed Q25 Q50 Q75
  Qual Score complexity four
* 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 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/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)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/dada2/libs/x64/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 use Fortran I/O
nor system RNGs. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
PacBioErrfun 10.64   0.36   11.12
learnErrors   9.92   0.57    8.34
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
PacBioErrfun 11.06   0.03   11.17
learnErrors   9.01   0.34    7.89
* 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: 1 WARNING, 7 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/dada2.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/dada2_1.12.1.tar.gz && rm -rf dada2.buildbin-libdir && mkdir dada2.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dada2.buildbin-libdir dada2_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL dada2_1.12.1.zip && rm dada2_1.12.1.tar.gz dada2_1.12.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1325k  100 1325k    0     0  15.4M      0 --:--:-- --:--:-- --:--:-- 16.6M

install for i386

* installing *source* package 'dada2' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -c Rmain.cpp -o Rmain.o
Rmain.cpp: In function 'Rcpp::List dada_uniques(std::vector >, std::vector, std::vector, 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::vector, std::vector, 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:282:15: warning: 'kord' may be used uninitialized in this function [-Wmaybe-uninitialized]
     free(kord);
               ^
Rmain.cpp:281:14: warning: 'k16' may be used uninitialized in this function [-Wmaybe-uninitialized]
     free(k16);
              ^
Rmain.cpp:280:13: warning: 'k8' may be used uninitialized in this function [-Wmaybe-uninitialized]
     free(k8);
             ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -c chimera.cpp -o chimera.o
chimera.cpp: In function 'bool C_is_bimera(std::string, std::vector >, bool, int, int, int, int, int)':
chimera.cpp:25:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i= 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-max_shift)) {
                                 ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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;rownclust;i++) {
            ^
cluster.cpp:318:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(r=1; rbi[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; }
                     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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;inclust;i++) { bi_free(b->bi[i]); }
                ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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;
                                                   ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -c evaluate.cpp -o evaluate.o
evaluate.cpp: In function 'Rcpp::IntegerVector C_eval_pair(std::string, std::string)':
evaluate.cpp:88:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   } while((s1gap || s2gap) && start >, std::vector >, int)':
evaluate.cpp:219:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i >, std::vector >, int, int)':
evaluate.cpp:243:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i >, std::vector >, int)':
evaluate.cpp:286:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i >, std::vector >, int)':
evaluate.cpp:339:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i >, std::string, unsigned int, bool)':
filter.cpp:16:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i= 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= 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= 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=0 && (band=0 && (bandlen2) { 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=0 && (band=0 && (bandlen2) { 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=0 && (band=0 && (bandlen2) { r = len2; }
                        ^
nwalign_endsfree.cpp:522:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0;insubs;s++) {
                ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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 >, std::vector >, 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;insubs;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;snsubs;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); }
                         ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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 >, std::vector >, std::vector >, std::vector, 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 >, std::vector >, std::vector >, std::vector, 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 >, std::vector, std::vector, 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::vector, std::vector, 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:282:15: warning: 'kord' may be used uninitialized in this function [-Wmaybe-uninitialized]
     free(kord);
               ^
Rmain.cpp:281:14: warning: 'k16' may be used uninitialized in this function [-Wmaybe-uninitialized]
     free(k16);
              ^
Rmain.cpp:280:13: warning: 'k8' may be used uninitialized in this function [-Wmaybe-uninitialized]
     free(k8);
             ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -c chimera.cpp -o chimera.o
chimera.cpp: In function 'bool C_is_bimera(std::string, std::vector >, bool, int, int, int, int, int)':
chimera.cpp:25:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i= 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-max_shift)) {
                                 ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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;rownclust;i++) {
            ^
cluster.cpp:318:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(r=1; rbi[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; }
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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;inclust;i++) { bi_free(b->bi[i]); }
                ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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;
                                                   ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -c evaluate.cpp -o evaluate.o
evaluate.cpp: In function 'Rcpp::IntegerVector C_eval_pair(std::string, std::string)':
evaluate.cpp:88:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   } while((s1gap || s2gap) && start >, std::vector >, int)':
evaluate.cpp:219:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i >, std::vector >, int, int)':
evaluate.cpp:243:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i >, std::vector >, int)':
evaluate.cpp:286:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i=0;i >, std::vector >, int)':
evaluate.cpp:339:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i >, std::string, unsigned int, bool)':
filter.cpp:16:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(i=0;i= 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= 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= 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=0 && (band=0 && (bandlen2) { 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=0 && (band=0 && (bandlen2) { 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=0 && (band=0 && (bandlen2) { r = len2; }
                        ^
nwalign_endsfree.cpp:522:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i=0;insubs;s++) {
                ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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 >, std::vector >, 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;insubs;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;snsubs;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); }
                         ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -msse2 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"  -msse2   -O2 -Wall  -mtune=generic -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 >, std::vector >, std::vector >, std::vector, 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 >, std::vector >, std::vector >, std::vector, 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