Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-02-28 11:37:30 -0500 (Wed, 28 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4671
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4411
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4438
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4414
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 497/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dada2 1.31.0  (landing page)
Benjamin Callahan
Snapshot Date: 2024-02-26 14:39:26 -0500 (Mon, 26 Feb 2024)
git_url: https://git.bioconductor.org/packages/dada2
git_branch: devel
git_last_commit: b28635a
git_last_commit_date: 2023-10-24 10:47:58 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for dada2 on palomino3


To the developers/maintainers of the dada2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dada2.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: dada2
Version: 1.31.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:dada2.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings dada2_1.31.0.tar.gz
StartedAt: 2024-02-27 03:44:11 -0500 (Tue, 27 Feb 2024)
EndedAt: 2024-02-27 03:49:06 -0500 (Tue, 27 Feb 2024)
EllapsedTime: 294.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: dada2.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:dada2.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings dada2_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/dada2.Rcheck'
* using R Under development (unstable) (2024-01-14 r85805 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'dada2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dada2' version '1.31.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'dada2' can be installed ... WARNING
Found the following significant warnings:
  nwalign_vectorized.cpp:280:27: warning: format '%i' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  nwalign_vectorized.cpp:280:31: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  nwalign_vectorized.cpp:280:47: warning: format '%i' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  nwalign_vectorized.cpp:280:50: warning: format '%i' expects argument of type 'int', but argument 5 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  nwalign_vectorized.cpp:280:59: warning: format '%i' expects argument of type 'int', but argument 6 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  nwalign_vectorized.cpp:280:62: warning: format '%i' expects argument of type 'int', but argument 7 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  nwalign_vectorized.cpp:280:71: warning: format '%i' expects argument of type 'int', but argument 8 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  nwalign_vectorized.cpp:280:74: warning: format '%i' expects argument of type 'int', but argument 9 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
See 'F:/biocbuild/bbs-3.19-bioc/meat/dada2.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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
* 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.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'C_isACGT' 'matchGenera'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call(ShortRead:::.set_omp_threads, ...)
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
tax.check: warning in assignTaxonomy(sq.test, fn.tax, multi = TRUE):
  partial argument match of 'multi' to 'multithread'
plotComplexity: no visible binding for global variable 'complexity'
plotErrors: no visible binding for global variable 'Qual'
plotErrors: no visible binding for global variable 'Observed'
plotErrors: no visible binding for global variable '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'
tax.check: no visible binding for global variable 'fn.spc'
Undefined global functions or variables:
  Count Cum Cycle Estimated Input Mean Nominal Observed Q25 Q50 Q75
  Qual Score complexity fn.spc
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... NOTE
   PKG_CFLAGS set in 'src/Makevars.win' without any corresponding files
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/dada2/libs/x64/dada2.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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 nor [v]sprintf. 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
learnErrors        5.75   0.55    4.16
PacBioErrfun       5.25   0.03    5.39
plotQualityProfile 2.64   0.03   14.81
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 9 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/dada2.Rcheck/00check.log'
for details.



Installation output

dada2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL dada2
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'dada2' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
using C++11
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/dada2.h:7,
                 from RcppExports.cpp:4:
../inst/include/dada2_RcppExports.h:14:14: warning: 'void dada2::{anonymous}::validateSignature(const char*)' defined but not used [-Wunused-function]
   14 |         void validateSignature(const char* sig) {
      |              ^~~~~~~~~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Rmain.cpp -o Rmain.o
Rmain.cpp: In function 'Rcpp::List dada_uniques(std::vector<std::__cxx11::basic_string<char> >, std::vector<int>, std::vector<bool>, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, int, int, bool, double, int, double, double, double, bool, int, double, int, int, bool, bool, bool, int, bool, bool, int, bool, bool)':
Rmain.cpp:71:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   71 |     if(quals.nrow() != maxlen) {
      |        ~~~~~~~~~~~~~^~~~~~~~~
Rmain.cpp: In function 'B* run_dada(Raw**, int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, double, double, bool, int, double, int, int, bool, bool, bool, bool, bool, int, bool, bool)':
Rmain.cpp:316:22: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  316 |   while( (bb->nclust < max_clust) && (newi = b_bud(bb, min_fold, min_hamming, min_abund, verbose)) ) {
      |           ~~~~~~~~~~~^~~~~~~~~~~
Rmain.cpp: In function 'Rcpp::List dada_uniques(std::vector<std::__cxx11::basic_string<char> >, std::vector<int>, std::vector<bool>, Rcpp::NumericMatrix, Rcpp::NumericMatrix, int, int, int, bool, double, int, double, double, double, bool, int, double, int, int, bool, bool, bool, int, bool, bool, int, bool, bool)':
Rmain.cpp:290:9: warning: 'kord' may be used uninitialized [-Wmaybe-uninitialized]
  290 |     free(kord);
      |     ~~~~^~~~~~
Rmain.cpp:124:13: note: 'kord' was declared here
  124 |   uint16_t *kord;
      |             ^~~~
Rmain.cpp:289:9: warning: 'k16' may be used uninitialized [-Wmaybe-uninitialized]
  289 |     free(k16);
      |     ~~~~^~~~~
Rmain.cpp:123:13: note: 'k16' was declared here
  123 |   uint16_t *k16;
      |             ^~~
Rmain.cpp:288:9: warning: 'k8' may be used uninitialized [-Wmaybe-uninitialized]
  288 |     free(k8);
      |     ~~~~^~~~
Rmain.cpp:122:12: note: 'k8' was declared here
  122 |   uint8_t *k8;
      |            ^~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c chimera.cpp -o chimera.o
chimera.cpp: In function 'bool C_is_bimera(std::string, std::vector<std::__cxx11::basic_string<char> >, bool, int, int, int, int, int)':
chimera.cpp:25:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   25 |   for(i=0;i<pars.size() && rval==false;i++) {
      |           ~^~~~~~~~~~~~
chimera.cpp:29:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   29 |     if((left+right) >= sq.size()) { // Toss id/pure-shift/internal-indel "parents"
      |        ~~~~~~~~~~~~~^~~~~~~~~~~~
chimera.cpp:44:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   44 |     if((max_right+max_left)>=sq.size()) {
      |        ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
chimera.cpp:48:39: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   48 |       if((oo_max_left+oo_max_right_oo)>=sq.size() || (oo_max_left_oo+oo_max_right)>=sq.size()) {
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
chimera.cpp:48:83: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   48 |       if((oo_max_left+oo_max_right_oo)>=sq.size() || (oo_max_left_oo+oo_max_right)>=sq.size()) {
      |                                                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
chimera.cpp: In function 'void get_lr(char**, int&, int&, int&, int&, bool, int)':
chimera.cpp:231:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  231 |   while(al[0][pos] == '-' && pos<len) {
      |                              ~~~^~~~
chimera.cpp:237:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  237 |   while(pos<len && al[0][pos] == al[1][pos]) {
      |         ~~~^~~~
chimera.cpp:244:11: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  244 |     if(pos<len && al[0][pos] != '-') { left_oo++; }
      |        ~~~^~~~
chimera.cpp:245:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  245 |     while(pos<len && al[0][pos] == al[1][pos]) {
      |           ~~~^~~~
chimera.cpp:254:33: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  254 |   while(al[1][pos] == '-' && pos>+(len-max_shift)) {
      |                              ~~~^~~~~~~~~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cluster.cpp -o cluster.o
cluster.cpp: In function 'void b_compare(B*, unsigned int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, bool, int, bool, bool, bool)':
cluster.cpp:17:23: warning: variable 'cind' set but not used [-Wunused-but-set-variable]
   17 |   unsigned int index, cind, center_reads;
      |                       ^~~~
cluster.cpp: In function 'void b_compare_parallel(B*, unsigned int, Rcpp::NumericMatrix, int, int, int, int, bool, double, int, bool, int, bool, bool, bool)':
cluster.cpp:166:16: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  166 |   for(row=0;row<errMat.nrow();row++) {
      |             ~~~^~~~~~~~~~~~~~
cluster.cpp:167:18: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  167 |     for(col=0;col<errMat.ncol();col++) {
      |               ~~~^~~~~~~~~~~~~~
cluster.cpp:156:23: warning: variable 'cind' set but not used [-Wunused-but-set-variable]
  156 |   unsigned int index, cind, row, col, ncol;
      |                       ^~~~
cluster.cpp: In function 'int b_bud(B*, double, int, int, bool)':
cluster.cpp:284:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  284 |   for(i=0;i<b->nclust;i++) {
      |           ~^~~~~~~~~~
cluster.cpp:285:15: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  285 |     for(r=1; r<b->bi[i]->nraw; r++) { // r=0 is the center
      |              ~^~~~~~~~~~~~~~~
cluster.cpp:288:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  288 |       if(raw->reads < min_abund) { continue; }
      |          ~~~~~~~~~~~^~~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c containers.cpp -o containers.o
containers.cpp: In function 'void b_free(B*)':
containers.cpp:141:16: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  141 |   for(int i=0;i<b->nclust;i++) { bi_free(b->bi[i]); }
      |               ~^~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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:178:51: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
  178 |   unsigned int i, pos, pos1, qind, j, r, s, nti0, ncol;
      |                                                   ^~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c evaluate.cpp -o evaluate.o
evaluate.cpp: In function 'Rcpp::IntegerVector C_eval_pair(std::string, std::string)':
evaluate.cpp:88:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   88 |   } while((s1gap || s2gap) && start<s1.size());
      |                               ~~~~~^~~~~~~~~~
evaluate.cpp: In function 'Rcpp::CharacterVector C_pair_consensus(std::string, std::string, int, bool)':
evaluate.cpp:133:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  133 |   for(i=0;i<s1.size();i++) {
      |           ~^~~~~~~~~~
evaluate.cpp:152:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  152 |     for(i=0;i<s1.size();i++) {
      |             ~^~~~~~~~~~
evaluate.cpp:163:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  163 |   for(i=0;i<s1.size();i++) {
      |           ~^~~~~~~~~~
evaluate.cpp: In function 'Rcpp::NumericVector kmer_dist(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)':
evaluate.cpp:219:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  219 |   for(int i=0;i<nseqs;i++) {
      |               ~^~~~~~
evaluate.cpp: In function 'Rcpp::NumericVector kord_dist(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int, int)':
evaluate.cpp:243:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  243 |   for(int i=0;i<nseqs;i++) {
      |               ~^~~~~~
evaluate.cpp:255:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  255 |   for(int i=0;i<nseqs;i++) {
      |               ~^~~~~~
evaluate.cpp: In function 'Rcpp::IntegerVector kmer_matches(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)':
evaluate.cpp:286:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  286 |   for(int i=0;i<nseqs;i++) {
      |               ~^~~~~~
evaluate.cpp:298:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  298 |   for(i=0;i<nseqs;i++) {
      |           ~^~~~~~
evaluate.cpp:310:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  310 |     for(j=0;j<klen_min;j++) {
      |             ~^~~~~~~~~
evaluate.cpp: In function 'Rcpp::IntegerVector kdist_matches(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)':
evaluate.cpp:339:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  339 |   for(i=0;i<nseqs;i++) {
      |           ~^~~~~~
evaluate.cpp:348:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  348 |     for(j=0;j<n_kmers;j++) {
      |             ~^~~~~~~~
evaluate.cpp:327:10: warning: variable 'len1' set but not used [-Wunused-but-set-variable]
  327 |   size_t len1 = 0, len2 = 0;
      |          ^~~~
evaluate.cpp:327:20: warning: variable 'len2' set but not used [-Wunused-but-set-variable]
  327 |   size_t len1 = 0, len2 = 0;
      |                    ^~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c filter.cpp -o filter.o
filter.cpp: In function 'Rcpp::IntegerVector C_matchRef(std::vector<std::__cxx11::basic_string<char> >, std::string, unsigned int, bool)':
filter.cpp:16:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   16 |   for(i=0;i<len;i++) {
      |           ~^~~~
filter.cpp:20:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   20 |   for(i=0;i<seqs.size();i++) {
      |           ~^~~~~~~~~~~~
filter.cpp:24:14: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   24 |     for(j=0;j<=(len-word_size);j++) {
      |             ~^~~~~~~~~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c kmers.cpp -o kmers.o
kmers.cpp: In function 'double kmer_dist_SSEi_8(uint8_t*, int, uint8_t*, int, int)':
kmers.cpp:85:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   85 |   for(i=0;i<STEP;i++) {
      |           ~^~~~~
kmers.cpp: In function 'double kord_dist(uint16_t*, int, uint16_t*, int, int)':
kmers.cpp:110:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  110 |   for(i=0;i<klen;i++) {
      |           ~^~~~~
kmers.cpp: In function 'double kord_dist_SSEi(uint16_t*, int, uint16_t*, int, int)':
kmers.cpp:141:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  141 |   for(i=0;i<STEP;i++) {
      |           ~^~~~~
kmers.cpp:144:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  144 |   for(i=n_vec;i<klen;i++,kord1++,kord2++) { // kord starts pointing to where it was left
      |               ~^~~~~
kmers.cpp: In function 'void assign_kmer8(uint8_t*, const char*, int)':
kmers.cpp:162:8: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  162 |   if(k >= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
      |      ~~^~~~~~
kmers.cpp:174:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  174 |   for(i=0; i<klen; i++) {
      |            ~^~~~~
kmers.cpp: In function 'void assign_kmer(uint16_t*, const char*, int)':
kmers.cpp:211:8: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  211 |   if(k >= len || k < 3 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
      |      ~~^~~~~~
kmers.cpp:221:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  221 |   for(i=0; i<klen; i++) {
      |            ~^~~~~
kmers.cpp: In function 'void assign_kmer_order(uint16_t*, char*, int)':
kmers.cpp:250:8: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  250 |   if(k >= len || k < 1 || k > 8) { Rcpp::stop("Invalid kmer-size."); }
      |      ~~^~~~~~
kmers.cpp:255:12: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  255 |   for(i=0;i<klen;i++) { kord[i] = 0; }
      |           ~^~~~~
kmers.cpp:257:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  257 |   for(i=0; i<klen; i++) {
      |            ~^~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c misc.cpp -o misc.o
misc.cpp: In function 'void align_print(char**)':
misc.cpp:24:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   24 |   for(int i=0;i<strlen(al0);i++) {
      |               ~^~~~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nwalign_endsfree.cpp -o nwalign_endsfree.o
nwalign_endsfree.cpp: In function 'char** nwalign_endsfree(const char*, size_t, const char*, size_t, int (*)[4], int, int)':
nwalign_endsfree.cpp:89:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   89 |   for (i = 0; i <= len1; i++) {
      |               ~~^~~~~~~
nwalign_endsfree.cpp:95:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   95 |   for (j = 0; j <= len2; j++) {
      |               ~~^~~~~~~
nwalign_endsfree.cpp:114:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  114 |   if(band>=0 && (band<len1 || band<len2)) {
      |                  ~~~~^~~~~
nwalign_endsfree.cpp:114:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  114 |   if(band>=0 && (band<len1 || band<len2)) {
      |                               ~~~~^~~~~
nwalign_endsfree.cpp:115:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  115 |     for(i=0;i<=len1;i++) {
      |             ~^~~~~~
nwalign_endsfree.cpp:117:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  117 |       if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
      |          ~~~~~~~~~~^~~~~~~
nwalign_endsfree.cpp:122:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  122 |   for (i = 1; i <= len1; i++) {
      |               ~~^~~~~~~
nwalign_endsfree.cpp:125:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  125 |       r = i+rband; if(r>len2) { r = len2; }
      |                       ~^~~~~
nwalign_endsfree.cpp:130:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  130 |       if (i == len1) {
      |           ~~^~~~~~~
nwalign_endsfree.cpp:137:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  137 |       if (j == len2) {
      |           ~~^~~~~~~
nwalign_endsfree.cpp:201:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  201 |   for (i=0;i<len_al;i++) {
      |            ~^~~~~~~
nwalign_endsfree.cpp: In function 'char** nwalign_endsfree_homo(const char*, size_t, const char*, size_t, int (*)[4], int, int, int)':
nwalign_endsfree.cpp:230:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  230 |   for (i=0,j=0;j<len1;j++) {
      |                ~^~~~~
nwalign_endsfree.cpp:231:10: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  231 |     if (j==len1-1 || s1[j]!=s1[j+1]) {
      |         ~^~~~~~~~
nwalign_endsfree.cpp:244:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  244 |   for (i=0,j=0;j<len2;j++) {
      |                ~^~~~~
nwalign_endsfree.cpp:245:10: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  245 |     if (j==len2-1 || s2[j]!=s2[j+1]) {
      |         ~^~~~~~~~
nwalign_endsfree.cpp:264:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  264 |   for (i = 0; i <= len1; i++) {
      |               ~~^~~~~~~
nwalign_endsfree.cpp:270:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  270 |   for (j = 0; j <= len2; j++) {
      |               ~~^~~~~~~
nwalign_endsfree.cpp:289:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  289 |   if(band>=0 && (band<len1 || band<len2)) {
      |                  ~~~~^~~~~
nwalign_endsfree.cpp:289:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  289 |   if(band>=0 && (band<len1 || band<len2)) {
      |                               ~~~~^~~~~
nwalign_endsfree.cpp:290:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  290 |     for(i=0;i<=len1;i++) {
      |             ~^~~~~~
nwalign_endsfree.cpp:292:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  292 |       if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
      |          ~~~~~~~~~~^~~~~~~
nwalign_endsfree.cpp:297:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  297 |   for (i = 1; i <= len1; i++) {
      |               ~~^~~~~~~
nwalign_endsfree.cpp:300:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  300 |       r = i+rband; if(r>len2) { r = len2; }
      |                       ~^~~~~
nwalign_endsfree.cpp:305:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  305 |       if (i == len1) {
      |           ~~^~~~~~~
nwalign_endsfree.cpp:314:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  314 |       if (j == len2) {
      |           ~~^~~~~~~
nwalign_endsfree.cpp:379:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  379 |   for (i=0;i<len_al;i++) {
      |            ~^~~~~~~
nwalign_endsfree.cpp: In function 'char** nwalign(const char*, size_t, const char*, size_t, int (*)[4], int, int)':
nwalign_endsfree.cpp:419:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  419 |   for (i = 1; i <= len1; i++) {
      |               ~~^~~~~~~
nwalign_endsfree.cpp:425:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  425 |   for (j = 1; j <= len2; j++) {
      |               ~~^~~~~~~
nwalign_endsfree.cpp:444:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  444 |   if(band>=0 && (band<len1 || band<len2)) {
      |                  ~~~~^~~~~
nwalign_endsfree.cpp:444:35: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  444 |   if(band>=0 && (band<len1 || band<len2)) {
      |                               ~~~~^~~~~
nwalign_endsfree.cpp:445:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  445 |     for(i=0;i<=len1;i++) {
      |             ~^~~~~~
nwalign_endsfree.cpp:447:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  447 |       if(i+rband+1 <= len2) { d[i*ncol + i+rband+1] = -9999; }
      |          ~~~~~~~~~~^~~~~~~
nwalign_endsfree.cpp:452:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  452 |   for (i = 1; i <= len1; i++) {
      |               ~~^~~~~~~
nwalign_endsfree.cpp:455:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  455 |       r = i+rband; if(r>len2) { r = len2; }
      |                       ~^~~~~
nwalign_endsfree.cpp:522:13: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  522 |   for (i=0;i<len_al;i++) {
      |            ~^~~~~~~
nwalign_endsfree.cpp: In function 'char** nwalign_gapless(const char*, size_t, const char*, size_t)':
nwalign_endsfree.cpp:548:17: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  548 |   for (int i=0;i<len_al;i++) {
      |                ~^~~~~~~
nwalign_endsfree.cpp:549:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  549 |     al[0][i] = i < len1 ? s1[i] : '-';
      |                ~~^~~~~~
nwalign_endsfree.cpp:550:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  550 |     al[1][i] = i < len2 ? s2[i] : '-';
      |                ~~^~~~~~
nwalign_endsfree.cpp: In function 'Sub* sub_new(Raw*, Raw*, int, int, int, int, bool, double, int, bool, int, bool)':
nwalign_endsfree.cpp:658:16: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  658 |       for(s=0;s<sub->nsubs;s++) {
      |               ~^~~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nwalign_vectorized.cpp -o nwalign_vectorized.o
nwalign_vectorized.cpp: In function 'char** nwalign_vectorized2(const char*, size_t, const char*, size_t, int16_t, int16_t, int16_t, int16_t, int)':
nwalign_vectorized.cpp:96:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   96 |   start_col = 1 + (1+(band<len1 ? band : len1))/2;
      |                       ~~~~^~~~~
nwalign_vectorized.cpp:125:26: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  125 |   while(row < (1 + (band < len1 ? band : len1))) {
      |                     ~~~~~^~~~~~
nwalign_vectorized.cpp:178:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  178 |     if(row==(band<len1 ? band : len1)) {
      |              ~~~~^~~~~
nwalign_vectorized.cpp:218:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  218 |     if(row < band && row < len1) { // upper tri for seq1
      |        ~~~~^~~~~~
nwalign_vectorized.cpp:280:27: warning: format '%i' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  280 |         Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
      |                          ~^                                                                         ~~~~
      |                           |                                                                         |
      |                           int                                                                       size_t {aka long long unsigned int}
      |                          %lli
nwalign_vectorized.cpp:280:31: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  280 |         Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
      |                              ~^                                                                           ~~~~
      |                               |                                                                           |
      |                               int                                                                         size_t {aka long long unsigned int}
      |                              %lli
nwalign_vectorized.cpp:280:47: warning: format '%i' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  280 |         Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
      |                                              ~^                                                                 ~~~~
      |                                               |                                                                 |
      |                                               int                                                               size_t {aka long long unsigned int}
      |                                              %lli
nwalign_vectorized.cpp:280:50: warning: format '%i' expects argument of type 'int', but argument 5 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  280 |         Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
      |                                                 ~^                                                                    ~~~~
      |                                                  |                                                                    |
      |                                                  int                                                                  size_t {aka long long unsigned int}
      |                                                 %lli
nwalign_vectorized.cpp:280:59: warning: format '%i' expects argument of type 'int', but argument 6 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  280 |         Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
      |                                                          ~^                                                                 ~
      |                                                           |                                                                 |
      |                                                           int                                                               size_t {aka long long unsigned int}
      |                                                          %lli
nwalign_vectorized.cpp:280:62: warning: format '%i' expects argument of type 'int', but argument 7 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  280 |         Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
      |                                                             ~^                                                                ~
      |                                                              |                                                                |
      |                                                              int                                                              size_t {aka long long unsigned int}
      |                                                             %lli
nwalign_vectorized.cpp:280:71: warning: format '%i' expects argument of type 'int', but argument 8 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  280 |         Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
      |                                                                      ~^                                                         ~~~
      |                                                                       |                                                          |
      |                                                                       int                                                        size_t {aka long long unsigned int}
      |                                                                      %lli
nwalign_vectorized.cpp:280:74: warning: format '%i' expects argument of type 'int', but argument 9 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
  280 |         Rprintf("len1/2=(%i, %i), nrow,ncol=(%i,%i), ij=(%i,%i), rc=(%i,%i), d[][]=%i, p[][]=%i\n", len1, len2, nrow, ncol, i,j,i+j,(2*start_col+j-i)/2, d[(i+j)*ncol + (2*start_col+j-i)/2], p[(i+j)*ncol + (2*start_col+j-i)/2]);
      |                                                                         ~^                                                          ~~~~~~~~~~~~~~~~~~~
      |                                                                          |                                                                           |
      |                                                                          int                                                                         size_t {aka long long unsigned int}
      |                                                                         %lli
nwalign_vectorized.cpp:75:21: warning: variable 'end_col' set but not used [-Wunused-but-set-variable]
   75 |   size_t start_col, end_col;
      |                     ^~~~~~~
nwalign_vectorized.cpp: In function 'Rcpp::CharacterVector C_nwvec(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int16_t, int16_t, int16_t, int, bool)':
nwalign_vectorized.cpp:330:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  330 |   for(i=0;i<s1.size();i++) {
      |           ~^~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pval.cpp -o pval.o
pval.cpp: In function 'double compute_lambda(Raw*, Sub*, Rcpp::NumericMatrix, bool, unsigned int)':
pval.cpp:121:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  121 |   for(s=0;s<sub->nsubs;s++) {
      |           ~^~~~~~~~~~~
pval.cpp:123:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  123 |     if(pos0 < 0 || pos0 >= sub->len0) { Rcpp::stop("CL: Bad pos0: %i (len0=%i).", pos0, sub->len0); }
      |                    ~~~~~^~~~~~~~~~~~
pval.cpp: In function 'double compute_lambda_ts(Raw*, Sub*, unsigned int, double*, bool)':
pval.cpp:177:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  177 |   for(s=0;s<sub->nsubs;s++) {
      |           ~^~~~~~~~~~~
pval.cpp:179:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  179 |     if(pos0 < 0 || pos0 >= sub->len0) { Rcpp::stop("CL: Bad pos0: %i (len0=%i).", pos0, sub->len0); }
      |                    ~~~~~^~~~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -msse2 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -msse2   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c taxonomy.cpp -o taxonomy.o
taxonomy.cpp: In function 'void tax_kvec(const char*, unsigned int, unsigned char*)':
taxonomy.cpp:48:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   48 |     if(kmer>=0 && kmer<n_kmers) {
      |                   ~~~~^~~~~~~~
taxonomy.cpp: In function 'int get_best_genus(int*, float*, unsigned int, unsigned int, unsigned int, float*)':
taxonomy.cpp:84:12: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   84 |   for(g=0;g<ngenus;g++) {
      |           ~^~~~~~~
taxonomy.cpp: In member function 'virtual void AssignParallel::operator()(std::size_t, std::size_t)':
taxonomy.cpp:145:31: warning: variable 'boot_match' set but not used [-Wunused-but-set-variable]
  145 |     unsigned int boot, booti, boot_match, arraylen, arraylen_rc;
      |                               ^~~~~~~~~~
taxonomy.cpp: In function 'Rcpp::List C_assign_taxonomy2(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<int>, Rcpp::IntegerMatrix, bool, bool)':
taxonomy.cpp:222:45: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type' {aka 'int'} and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  222 |     if(ref_to_genus[i]<0 || ref_to_genus[i] >= ngenus) {
taxonomy.cpp:252:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  252 |     for(kmer=0;kmer<n_kmers;kmer++) {
      |                ~~~~^~~~~~~~
taxonomy.cpp:261:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  261 |   for(kmer=0;kmer<n_kmers;kmer++) {
      |              ~~~~^~~~~~~~
taxonomy.cpp:268:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
  268 |     for(kmer=0;kmer<n_kmers;kmer++) {
      |                ~~~~^~~~~~~~
taxonomy.cpp:287:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
  287 |   for(i=0;i<unifs.size();i++) { C_unifs[i] = unifs(i); }
      |           ~^~~~~~~~~~~~~
g++ -shared -s -static-libgcc -o dada2.dll tmp.def RcppExports.o Rmain.o chimera.o cluster.o containers.o error.o evaluate.o filter.o kmers.o misc.o nwalign_endsfree.o nwalign_vectorized.o pval.o taxonomy.o -LF:/biocbuild/bbs-3.19-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-dada2/00new/dada2/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (dada2)

Tests output


Example timings

dada2.Rcheck/dada2-Ex.timings

nameusersystemelapsed
PacBioErrfun5.250.035.39
addSpecies3.030.033.08
assignSpecies1.390.001.39
assignTaxonomy0.450.002.44
collapseNoMismatch1.410.031.50
dada2.460.112.86
derepFastq0.820.030.88
fastqFilter0.500.020.62
fastqPairedFilter1.560.081.81
filterAndTrim1.130.051.39
getDadaOpt000
getErrors1.120.031.19
getSequences0.300.000.31
getUniques0.280.000.30
inflateErr000
isBimera0.080.000.09
isBimeraDenovo2.360.062.42
isBimeraDenovoTable2.280.052.35
isPhiX0.240.030.26
isShiftDenovo1.230.041.30
learnErrors5.750.554.16
loessErrfun0.360.000.37
makeSequenceTable0.560.020.57
mergePairs3.810.264.13
mergeSequenceTables000
noqualErrfun0.630.030.67
nwalign000
nwhamming000
plotComplexity0.290.020.36
plotErrors2.160.082.25
plotQualityProfile 2.64 0.0314.81
rc0.010.000.02
removeBimeraDenovo2.470.032.53
removePrimers0.190.020.22
seqComplexity0.020.000.01
setDadaOpt000
uniquesToFasta0.060.030.10