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This page was generated on 2022-01-17 13:06:53 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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

CHECK results for Rfastp on tokay2


To the developers/maintainers of the Rfastp package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rfastp.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1586/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rfastp 1.4.0  (landing page)
Thomas Carroll
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/Rfastp
git_branch: RELEASE_3_14
git_last_commit: 81990f1
git_last_commit_date: 2021-10-26 13:02:08 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Rfastp
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rfastp.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Rfastp_1.4.0.tar.gz
StartedAt: 2022-01-17 02:30:02 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 02:31:36 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 93.6 seconds
RetCode: 0
Status:   OK  
CheckDir: Rfastp.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rfastp.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Rfastp_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/Rfastp.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rfastp/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rfastp' version '1.4.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'Rfastp' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      3.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 line endings in shell scripts ... 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 ... 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-3.14-bioc/R/library/Rfastp/libs/i386/Rfastp.dll':
  Found '_exit', possibly from '_exit' (C)
  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-3.14-bioc/R/library/Rfastp/libs/x64/Rfastp.dll':
  Found '_exit', possibly from '_exit' (C)
  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
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/Rfastp.Rcheck/00check.log'
for details.



Installation output

Rfastp.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/Rfastp_1.4.0.tar.gz && rm -rf Rfastp.buildbin-libdir && mkdir Rfastp.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rfastp.buildbin-libdir Rfastp_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Rfastp_1.4.0.zip && rm Rfastp_1.4.0.tar.gz Rfastp_1.4.0.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
 99 2205k   99 2189k    0     0  5053k      0 --:--:-- --:--:-- --:--:-- 5057k
100 2205k  100 2205k    0     0  5063k      0 --:--:-- --:--:-- --:--:-- 5057k

install for i386

* installing *source* package 'Rfastp' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c main_fastp.cpp -o main_fastp.o
In file included from main_fastp.cpp:9:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
main_fastp.cpp: In function 'int runFastp(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, bool, std::__cxx11::string, bool, bool, bool, bool, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, int, int, int, int, int, int, bool, bool, int, bool, int, bool, bool, bool, int, int, int, int, int, int, int, int, bool, int, int, int, int, bool, int, int, bool, int, std::__cxx11::string, std::__cxx11::string, int, bool, int, int, int, bool, bool, std::__cxx11::string, int, std::__cxx11::string, int, bool, int, int, int, int, bool)':
main_fastp.cpp:289:12: warning: unused variable 't1' [-Wunused-variable]
     time_t t1 = time(NULL);
            ^~
main_fastp.cpp:291:10: warning: unused variable 'supportEvaluation' [-Wunused-variable]
     bool supportEvaluation = true;
          ^~~~~~~~~~~~~~~~~
main_fastp.cpp:366:12: warning: unused variable 't2' [-Wunused-variable]
     time_t t2 = time(NULL);
            ^~
In file included from FASTP/fastqreader.h:12,
                 from main_fastp.cpp:4:
FASTP/common.h: At global scope:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/adaptertrimmer.cpp -o FASTP/adaptertrimmer.o
FASTP/adaptertrimmer.cpp: In static member function 'static bool AdapterTrimmer::trimByMultiSequences(Read*, FilterResult*, std::vector<std::__cxx11::basic_string<char> >&, bool, bool)':
FASTP/adaptertrimmer.cpp:58:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i=0; i<adapterList.size(); i++) {
                  ~^~~~~~~~~~~~~~~~~~~
FASTP/adaptertrimmer.cpp: In static member function 'static bool AdapterTrimmer::test()':
FASTP/adaptertrimmer.cpp:145:10: warning: variable 'trimmed' set but not used [-Wunused-but-set-variable]
     bool trimmed = AdapterTrimmer::trimBySequence(&r, NULL, adapter);
          ^~~~~~~
In file included from FASTP/overlapanalysis.h:9,
                 from FASTP/adaptertrimmer.h:7,
                 from FASTP/adaptertrimmer.cpp:1:
FASTP/common.h: At global scope:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/basecorrector.cpp -o FASTP/basecorrector.o
In file included from FASTP/basecorrector.cpp:2:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
In file included from FASTP/overlapanalysis.h:9,
                 from FASTP/basecorrector.h:7,
                 from FASTP/basecorrector.cpp:1:
FASTP/common.h: At global scope:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/duplicate.cpp -o FASTP/duplicate.o
In file included from FASTP/duplicate.h:9,
                 from FASTP/duplicate.cpp:1:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/evaluator.cpp -o FASTP/evaluator.o
In file included from FASTP/evaluator.h:8,
                 from FASTP/evaluator.cpp:1:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
FASTP/evaluator.cpp: In member function 'int Evaluator::computeSeqLen(std::__cxx11::string)':
FASTP/evaluator.cpp:46:10: warning: variable 'reachedEOF' set but not used [-Wunused-but-set-variable]
     bool reachedEOF = false;
          ^~~~~~~~~~
FASTP/evaluator.cpp: In member function 'void Evaluator::computeOverRepSeq(std::__cxx11::string, std::map<std::__cxx11::basic_string<char>, long int>&, int)':
FASTP/evaluator.cpp:108:25: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
         if(seq.length() >= seqlen-1) {
            ~~~~~~~~~~~~~^~~~~~~~~~~
FASTP/evaluator.cpp:74:10: warning: variable 'reachedEOF' set but not used [-Wunused-but-set-variable]
     bool reachedEOF = false;
          ^~~~~~~~~~
FASTP/evaluator.cpp: In member function 'std::__cxx11::string Evaluator::evalAdapterAndReadNumDepreciated(long int&)':
FASTP/evaluator.cpp:304:22: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
         if(counts[i] >= repeatReq) {
            ~~~~~~~~~~^~~~~~~~~~~~
FASTP/evaluator.cpp:308:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
             for(int s=0; s<seq.length() - 1; s++) {
                          ~^~~~~~~~~~~~~~~~~
FASTP/evaluator.cpp:336:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i=0; i<needToDelete.size(); i++) {
                  ~^~~~~~~~~~~~~~~~~~~~
FASTP/evaluator.cpp:389:25: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
         if(iter->second > largest) {
            ~~~~~~~~~~~~~^~~~~~~~~
FASTP/evaluator.cpp: In member function 'std::__cxx11::string Evaluator::evalAdapterAndReadNum(long int&, bool)':
FASTP/evaluator.cpp:479:21: warning: unused variable 'data' [-Wunused-variable]
         const char* data = r->mSeq.mStr.c_str();
                     ^~~~
FASTP/evaluator.cpp:549:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         for(int s=0; s<seq.length() - 1; s++) {
                      ~^~~~~~~~~~~~~~~~~
FASTP/evaluator.cpp: In member function 'std::__cxx11::string Evaluator::getAdapterWithSeed(int, Read**, long int, int)':
FASTP/evaluator.cpp:585:21: warning: unused variable 'data' [-Wunused-variable]
         const char* data = r->mSeq.mStr.c_str();
                     ^~~~
FASTP/evaluator.cpp:601:21: warning: unused variable 'data' [-Wunused-variable]
         const char* data = r->mSeq.mStr.c_str();
                     ^~~~
FASTP/evaluator.cpp: In static member function 'static std::__cxx11::string Evaluator::matchKnownAdapter(std::__cxx11::string)':
FASTP/evaluator.cpp:643:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         for(int i=0; i<adapter.length() && i<seq.length(); i++) {
                      ~^~~~~~~~~~~~~~~~~
FASTP/evaluator.cpp:643:45: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         for(int i=0; i<adapter.length() && i<seq.length(); i++) {
                                            ~^~~~~~~~~~~~~
FASTP/evaluator.cpp: In member function 'int Evaluator::seq2int(std::__cxx11::string&, int, int, int)':
FASTP/evaluator.cpp:666:9: warning: unused variable 'rlen' [-Wunused-variable]
     int rlen = seq.length();
         ^~~~
In file included from FASTP/fastqreader.h:12,
                 from FASTP/evaluator.cpp:3:
FASTP/common.h: At global scope:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/fastareader.cpp -o FASTP/fastareader.o
In file included from FASTP/fastareader.cpp:3:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/fastqreader.cpp -o FASTP/fastqreader.o
In file included from FASTP/fastqreader.cpp:2:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
FASTP/fastqreader.cpp: In member function 'std::__cxx11::string FastqReader::getLine()':
FASTP/fastqreader.cpp:98:9: warning: unused variable 'copied' [-Wunused-variable]
     int copied = 0;
         ^~~~~~
In file included from FASTP/fastqreader.h:12,
                 from FASTP/fastqreader.cpp:1:
FASTP/common.h: At global scope:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/filter.cpp -o FASTP/filter.o
FASTP/filter.cpp: In member function 'bool Filter::match(std::vector<std::__cxx11::basic_string<char> >&, std::__cxx11::string, int)':
FASTP/filter.cpp:239:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i=0; i<list.size(); i++) {
                  ~^~~~~~~~~~~~
In file included from FASTP/writer.h:11,
                 from FASTP/threadconfig.h:9,
                 from FASTP/peprocessor.h:13,
                 from FASTP/filter.cpp:2:
FASTP/common.h: At global scope:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/filterresult.cpp -o FASTP/filterresult.o
FASTP/filterresult.cpp: In static member function 'static FilterResult* FilterResult::merge(std::vector<FilterResult*>&)':
FASTP/filterresult.cpp:43:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<FilterResult*>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i=0; i<list.size(); i++) {
                  ~^~~~~~~~~~~~
FASTP/filterresult.cpp:75:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<FilterResult*>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i=0; i<list.size(); i++) {
                  ~^~~~~~~~~~~~
In file included from FASTP/filterresult.h:9,
                 from FASTP/filterresult.cpp:3:
FASTP/common.h: At global scope:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/htmlreporter.cpp -o FASTP/htmlreporter.o
In file included from FASTP/filterresult.h:9,
                 from FASTP/htmlreporter.h:10,
                 from FASTP/htmlreporter.cpp:1:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/jsonreporter.cpp -o FASTP/jsonreporter.o
In file included from FASTP/filterresult.h:9,
                 from FASTP/jsonreporter.h:10,
                 from FASTP/jsonreporter.cpp:1:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/nucleotidetree.cpp -o FASTP/nucleotidetree.o
FASTP/nucleotidetree.cpp: In member function 'void NucleotideTree::addSeq(std::__cxx11::string)':
FASTP/nucleotidetree.cpp:45:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i=0; i<seq.length(); i++) {
                  ~^~~~~~~~~~~~~
FASTP/nucleotidetree.cpp:49:34: warning: array subscript has type 'char' [-Wchar-subscripts]
         if(curNode->children[base] == NULL) {
                                  ^
FASTP/nucleotidetree.cpp:50:35: warning: array subscript has type 'char' [-Wchar-subscripts]
             curNode->children[base] = new NucleotideNode();
                                   ^
FASTP/nucleotidetree.cpp:51:35: warning: array subscript has type 'char' [-Wchar-subscripts]
             curNode->children[base]->base = seq[i];
                                   ^
FASTP/nucleotidetree.cpp:53:31: warning: array subscript has type 'char' [-Wchar-subscripts]
         curNode->children[base]->count++;
                               ^
FASTP/nucleotidetree.cpp:54:41: warning: array subscript has type 'char' [-Wchar-subscripts]
         curNode = curNode->children[base];
                                         ^
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/options.cpp -o FASTP/options.o
In file included from FASTP/options.cpp:4:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
FASTP/options.cpp: In member function 'bool Options::validate()':
FASTP/options.cpp:360:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         for(int i=0; i<adapter.sequence.length(); i++) {
                      ~^~~~~~~~~~~~~~~~~~~~~~~~~~
FASTP/options.cpp:376:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         for(int i=0; i<adapter.sequenceR2.length(); i++) {
                      ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
FASTP/options.cpp:406:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
             for(int i=0; i<umi.prefix.length(); i++) {
                          ~^~~~~~~~~~~~~~~~~~~~
FASTP/options.cpp:417:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
             for(int i=0; i<umi.separator.length(); i++) {
                          ~^~~~~~~~~~~~~~~~~~~~~~~
FASTP/options.cpp: In member function 'std::vector<std::__cxx11::basic_string<char> > Options::makeListFromFileByLine(std::__cxx11::string)':
FASTP/options.cpp:486:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         for(int i=0; i<linestr.length(); i++) {
                      ~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/overlapanalysis.cpp -o FASTP/overlapanalysis.o
In file included from FASTP/overlapanalysis.h:9,
                 from FASTP/overlapanalysis.cpp:1:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/peprocessor.cpp -o FASTP/peprocessor.o
In file included from FASTP/peprocessor.cpp:9:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
FASTP/peprocessor.cpp: In member function 'bool PairEndProcessor::process()':
FASTP/peprocessor.cpp:126:9: warning: unused variable 'cycle' [-Wunused-variable]
     int cycle = 151;
         ^~~~~
FASTP/peprocessor.cpp:228:13: warning: unused variable 'dupMeanTlen' [-Wunused-variable]
     double* dupMeanTlen = NULL;
             ^~~~~~~~~~~
FASTP/peprocessor.cpp: In member function 'bool PairEndProcessor::processPairEnd(ReadPairPack*, ThreadConfig*)':
FASTP/peprocessor.cpp:345:13: warning: unused variable 'lowQualNum1' [-Wunused-variable]
         int lowQualNum1 = 0;
             ^~~~~~~~~~~
FASTP/peprocessor.cpp:346:13: warning: unused variable 'nBaseNum1' [-Wunused-variable]
         int nBaseNum1 = 0;
             ^~~~~~~~~
FASTP/peprocessor.cpp:347:13: warning: unused variable 'lowQualNum2' [-Wunused-variable]
         int lowQualNum2 = 0;
             ^~~~~~~~~~~
FASTP/peprocessor.cpp:348:13: warning: unused variable 'nBaseNum2' [-Wunused-variable]
         int nBaseNum2 = 0;
             ^~~~~~~~~
FASTP/peprocessor.cpp: In member function 'void PairEndProcessor::producerTask()':
FASTP/peprocessor.cpp:718:10: warning: unused variable 'splitSizeReEvaluated' [-Wunused-variable]
     bool splitSizeReEvaluated = false;
          ^~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/polyx.cpp -o FASTP/polyx.o
In file included from FASTP/overlapanalysis.h:9,
                 from FASTP/polyx.h:7,
                 from FASTP/polyx.cpp:1:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
FASTP/polyx.cpp: In static member function 'static void PolyX::trimPolyX(Read*, FilterResult*, int)':
FASTP/polyx.cpp:114:30: warning: 'poly' may be used uninitialized in this function [-Wmaybe-uninitialized]
           fr->addPolyXTrimmed(poly, pos + 1);
           ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/processor.cpp -o FASTP/processor.o
In file included from FASTP/writer.h:11,
                 from FASTP/threadconfig.h:9,
                 from FASTP/peprocessor.h:13,
                 from FASTP/processor.cpp:2:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/read.cpp -o FASTP/read.o
In file included from FASTP/read.cpp:4:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
FASTP/read.cpp: In member function 'void Read::convertPhred64To33()':
FASTP/read.cpp:41:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i=0; i<mQuality.length(); i++) {
                  ~^~~~~~~~~~~~~~~~~~
FASTP/read.cpp: In member function 'int Read::lowQualCount(int)':
FASTP/read.cpp:120:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int q=0;q<mQuality.size();q++){
                 ~^~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/seprocessor.cpp -o FASTP/seprocessor.o
In file included from FASTP/seprocessor.cpp:9:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
FASTP/seprocessor.cpp: In member function 'bool SingleEndProcessor::process()':
FASTP/seprocessor.cpp:76:9: warning: unused variable 'cycle' [-Wunused-variable]
     int cycle = 151;
         ^~~~~
FASTP/seprocessor.cpp:142:13: warning: unused variable 'dupMeanTlen' [-Wunused-variable]
     double* dupMeanTlen = NULL;
             ^~~~~~~~~~~
FASTP/seprocessor.cpp: In member function 'void SingleEndProcessor::producerTask()':
FASTP/seprocessor.cpp:388:10: warning: unused variable 'splitSizeReEvaluated' [-Wunused-variable]
     bool splitSizeReEvaluated = false;
          ^~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/sequence.cpp -o FASTP/sequence.o
FASTP/sequence.cpp: In member function 'Sequence Sequence::reverseComplement()':
FASTP/sequence.cpp:21:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int c=0;c<mStr.length();c++){
                 ~^~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/stats.cpp -o FASTP/stats.o
In file included from FASTP/stats.cpp:5:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
FASTP/stats.cpp: In member function 'void Stats::summarize(bool)':
FASTP/stats.cpp:187:36: warning: array subscript has type 'char' [-Wchar-subscripts]
             if(mCycleBaseContents[b][c] == 0)
                                    ^
FASTP/stats.cpp:190:56: warning: array subscript has type 'char' [-Wchar-subscripts]
                 qualCurve[c] = (double)mCycleBaseQual[b][c] / (double)mCycleBaseContents[b][c];
                                                        ^
FASTP/stats.cpp:190:91: warning: array subscript has type 'char' [-Wchar-subscripts]
                 qualCurve[c] = (double)mCycleBaseQual[b][c] / (double)mCycleBaseContents[b][c];
                                                                                           ^
FASTP/stats.cpp:191:59: warning: array subscript has type 'char' [-Wchar-subscripts]
             contentCurve[c] = (double)mCycleBaseContents[b][c] / (double)mCycleTotalBase[c];
                                                           ^
FASTP/stats.cpp:203:62: warning: array subscript has type 'char' [-Wchar-subscripts]
         gcContentCurve[c] = (double)(mCycleBaseContents[gBase][c] + mCycleBaseContents[cBase][c]) / (double)mCycleTotalBase[c];
                                                              ^
FASTP/stats.cpp:203:93: warning: array subscript has type 'char' [-Wchar-subscripts]
         gcContentCurve[c] = (double)(mCycleBaseContents[gBase][c] + mCycleBaseContents[cBase][c]) / (double)mCycleTotalBase[c];
                                                                                             ^
FASTP/stats.cpp: In member function 'void Stats::statRead(Read*)':
FASTP/stats.cpp:249:29: warning: array subscript has type 'char' [-Wchar-subscripts]
             mCycleQ30Bases[b][i]++;
                             ^
FASTP/stats.cpp:250:29: warning: array subscript has type 'char' [-Wchar-subscripts]
             mCycleQ20Bases[b][i]++;
                             ^
FASTP/stats.cpp:252:29: warning: array subscript has type 'char' [-Wchar-subscripts]
             mCycleQ20Bases[b][i]++;
                             ^
FASTP/stats.cpp:255:29: warning: array subscript has type 'char' [-Wchar-subscripts]
         mCycleBaseContents[b][i]++;
                             ^
FASTP/stats.cpp:256:25: warning: array subscript has type 'char' [-Wchar-subscripts]
         mCycleBaseQual[b][i] += (qual-33);
                         ^
FASTP/stats.cpp:313:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
                         for(int p = i; p < seq.length() + i && p < mEvaluatedSeqLen; p++) {
                                        ~~^~~~~~~~~~~~~~~~~~
FASTP/stats.cpp: In member function 'void Stats::reportHtmlORA(std::ofstream&, std::__cxx11::string, std::__cxx11::string)':
FASTP/stats.cpp:551:9: warning: unused variable 'displayed' [-Wunused-variable]
     int displayed = 0;
         ^~~~~~~~~
FASTP/stats.cpp: In member function 'void Stats::reportHtmlContents(std::ofstream&, std::__cxx11::string, std::__cxx11::string)':
FASTP/stats.cpp:850:36: warning: array subscript has type 'char' [-Wchar-subscripts]
             count = mBaseContents[b];
                                    ^
FASTP/stats.cpp: In static member function 'static Stats* Stats::merge(std::vector<Stats*>&)':
FASTP/stats.cpp:888:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Stats*>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int t=0; t<list.size(); t++) {
                  ~^~~~~~~~~~~~
FASTP/stats.cpp:898:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Stats*>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int t=0; t<list.size(); t++) {
                  ~^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/threadconfig.cpp -o FASTP/threadconfig.o
In file included from FASTP/threadconfig.cpp:2:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
FASTP/threadconfig.cpp: In member function 'void ThreadConfig::initWriterForSplit()':
FASTP/threadconfig.cpp:96:26: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
         while(num.size() < mOptions->split.digits)
               ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from FASTP/writer.h:11,
                 from FASTP/threadconfig.h:9,
                 from FASTP/threadconfig.cpp:1:
FASTP/common.h: At global scope:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/umiprocessor.cpp -o FASTP/umiprocessor.o
FASTP/umiprocessor.cpp: In member function 'void UmiProcessor::addUmiToName(Read*, std::__cxx11::string)':
FASTP/umiprocessor.cpp:70:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i=0; i<r->mName.length(); i++) {
                  ~^~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/unittest.cpp -o FASTP/unittest.o
In file included from FASTP/evaluator.h:8,
                 from FASTP/unittest.cpp:12:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
In file included from FASTP/fastqreader.h:12,
                 from FASTP/unittest.cpp:4:
FASTP/common.h: At global scope:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/writer.cpp -o FASTP/writer.o
In file included from FASTP/writer.cpp:2:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
In file included from FASTP/writer.h:11,
                 from FASTP/writer.cpp:1:
FASTP/common.h: At global scope:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/writerthread.cpp -o FASTP/writerthread.o
In file included from FASTP/writerthread.cpp:2:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
In file included from FASTP/writer.h:11,
                 from FASTP/writerthread.h:8,
                 from FASTP/writerthread.cpp:1:
FASTP/common.h: At global scope:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
sh:  C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/R: No such file or directory
sh:  C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/R: No such file or directory
sh:  C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/R: No such file or directory
sh:  C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/R: No such file or directory
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Rfastp.dll tmp.def ./RcppExports.o ./main_fastp.o ./FASTP/adaptertrimmer.o ./FASTP/basecorrector.o ./FASTP/duplicate.o ./FASTP/evaluator.o ./FASTP/fastareader.o ./FASTP/fastqreader.o ./FASTP/filter.o ./FASTP/filterresult.o ./FASTP/htmlreporter.o ./FASTP/jsonreporter.o ./FASTP/nucleotidetree.o ./FASTP/options.o ./FASTP/overlapanalysis.o ./FASTP/peprocessor.o ./FASTP/polyx.o ./FASTP/processor.o ./FASTP/read.o ./FASTP/seprocessor.o ./FASTP/sequence.o ./FASTP/stats.o ./FASTP/threadconfig.o ./FASTP/umiprocessor.o ./FASTP/unittest.o ./FASTP/writer.o ./FASTP/writerthread.o C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/Rfastp.buildbin-libdir/00LOCK-Rfastp/00new/Rfastp/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Rfastp'
    finding HTML links ... done
    catfastq                                html  
    curvePlot                               html  
    qcSummary                               html  
    rfastp                                  html  
    trimSummary                             html  
** 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

install for x64

* installing *source* package 'Rfastp' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c main_fastp.cpp -o main_fastp.o
In file included from main_fastp.cpp:9:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
main_fastp.cpp: In function 'int runFastp(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, bool, std::__cxx11::string, bool, bool, bool, bool, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, int, int, int, int, int, int, bool, bool, int, bool, int, bool, bool, bool, int, int, int, int, int, int, int, int, bool, int, int, int, int, bool, int, int, bool, int, std::__cxx11::string, std::__cxx11::string, int, bool, int, int, int, bool, bool, std::__cxx11::string, int, std::__cxx11::string, int, bool, int, int, int, int, bool)':
main_fastp.cpp:289:12: warning: unused variable 't1' [-Wunused-variable]
     time_t t1 = time(NULL);
            ^~
main_fastp.cpp:291:10: warning: unused variable 'supportEvaluation' [-Wunused-variable]
     bool supportEvaluation = true;
          ^~~~~~~~~~~~~~~~~
main_fastp.cpp:366:12: warning: unused variable 't2' [-Wunused-variable]
     time_t t2 = time(NULL);
            ^~
In file included from FASTP/fastqreader.h:12,
                 from main_fastp.cpp:4:
FASTP/common.h: At global scope:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/adaptertrimmer.cpp -o FASTP/adaptertrimmer.o
FASTP/adaptertrimmer.cpp: In static member function 'static bool AdapterTrimmer::trimByMultiSequences(Read*, FilterResult*, std::vector<std::__cxx11::basic_string<char> >&, bool, bool)':
FASTP/adaptertrimmer.cpp:58:19: 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]
     for(int i=0; i<adapterList.size(); i++) {
                  ~^~~~~~~~~~~~~~~~~~~
FASTP/adaptertrimmer.cpp: In static member function 'static bool AdapterTrimmer::test()':
FASTP/adaptertrimmer.cpp:145:10: warning: variable 'trimmed' set but not used [-Wunused-but-set-variable]
     bool trimmed = AdapterTrimmer::trimBySequence(&r, NULL, adapter);
          ^~~~~~~
In file included from FASTP/overlapanalysis.h:9,
                 from FASTP/adaptertrimmer.h:7,
                 from FASTP/adaptertrimmer.cpp:1:
FASTP/common.h: At global scope:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/basecorrector.cpp -o FASTP/basecorrector.o
In file included from FASTP/basecorrector.cpp:2:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
In file included from FASTP/overlapanalysis.h:9,
                 from FASTP/basecorrector.h:7,
                 from FASTP/basecorrector.cpp:1:
FASTP/common.h: At global scope:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/duplicate.cpp -o FASTP/duplicate.o
In file included from FASTP/duplicate.h:9,
                 from FASTP/duplicate.cpp:1:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/evaluator.cpp -o FASTP/evaluator.o
In file included from FASTP/evaluator.h:8,
                 from FASTP/evaluator.cpp:1:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
FASTP/evaluator.cpp: In member function 'int Evaluator::computeSeqLen(std::__cxx11::string)':
FASTP/evaluator.cpp:46:10: warning: variable 'reachedEOF' set but not used [-Wunused-but-set-variable]
     bool reachedEOF = false;
          ^~~~~~~~~~
FASTP/evaluator.cpp: In member function 'void Evaluator::computeOverRepSeq(std::__cxx11::string, std::map<std::__cxx11::basic_string<char>, long int>&, int)':
FASTP/evaluator.cpp:108:25: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
         if(seq.length() >= seqlen-1) {
            ~~~~~~~~~~~~~^~~~~~~~~~~
FASTP/evaluator.cpp:74:10: warning: variable 'reachedEOF' set but not used [-Wunused-but-set-variable]
     bool reachedEOF = false;
          ^~~~~~~~~~
FASTP/evaluator.cpp: In member function 'std::__cxx11::string Evaluator::evalAdapterAndReadNumDepreciated(long int&)':
FASTP/evaluator.cpp:304:22: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
         if(counts[i] >= repeatReq) {
            ~~~~~~~~~~^~~~~~~~~~~~
FASTP/evaluator.cpp:308:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
             for(int s=0; s<seq.length() - 1; s++) {
                          ~^~~~~~~~~~~~~~~~~
FASTP/evaluator.cpp:336:19: 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]
     for(int i=0; i<needToDelete.size(); i++) {
                  ~^~~~~~~~~~~~~~~~~~~~
FASTP/evaluator.cpp:389:25: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
         if(iter->second > largest) {
            ~~~~~~~~~~~~~^~~~~~~~~
FASTP/evaluator.cpp: In member function 'std::__cxx11::string Evaluator::evalAdapterAndReadNum(long int&, bool)':
FASTP/evaluator.cpp:479:21: warning: unused variable 'data' [-Wunused-variable]
         const char* data = r->mSeq.mStr.c_str();
                     ^~~~
FASTP/evaluator.cpp:549:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
         for(int s=0; s<seq.length() - 1; s++) {
                      ~^~~~~~~~~~~~~~~~~
FASTP/evaluator.cpp: In member function 'std::__cxx11::string Evaluator::getAdapterWithSeed(int, Read**, long int, int)':
FASTP/evaluator.cpp:585:21: warning: unused variable 'data' [-Wunused-variable]
         const char* data = r->mSeq.mStr.c_str();
                     ^~~~
FASTP/evaluator.cpp:601:21: warning: unused variable 'data' [-Wunused-variable]
         const char* data = r->mSeq.mStr.c_str();
                     ^~~~
FASTP/evaluator.cpp: In static member function 'static std::__cxx11::string Evaluator::matchKnownAdapter(std::__cxx11::string)':
FASTP/evaluator.cpp:643:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
         for(int i=0; i<adapter.length() && i<seq.length(); i++) {
                      ~^~~~~~~~~~~~~~~~~
FASTP/evaluator.cpp:643:45: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
         for(int i=0; i<adapter.length() && i<seq.length(); i++) {
                                            ~^~~~~~~~~~~~~
FASTP/evaluator.cpp: In member function 'int Evaluator::seq2int(std::__cxx11::string&, int, int, int)':
FASTP/evaluator.cpp:666:9: warning: unused variable 'rlen' [-Wunused-variable]
     int rlen = seq.length();
         ^~~~
In file included from FASTP/fastqreader.h:12,
                 from FASTP/evaluator.cpp:3:
FASTP/common.h: At global scope:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/fastareader.cpp -o FASTP/fastareader.o
In file included from FASTP/fastareader.cpp:3:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/fastqreader.cpp -o FASTP/fastqreader.o
In file included from FASTP/fastqreader.cpp:2:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
FASTP/fastqreader.cpp: In member function 'std::__cxx11::string FastqReader::getLine()':
FASTP/fastqreader.cpp:98:9: warning: unused variable 'copied' [-Wunused-variable]
     int copied = 0;
         ^~~~~~
In file included from FASTP/fastqreader.h:12,
                 from FASTP/fastqreader.cpp:1:
FASTP/common.h: At global scope:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/filter.cpp -o FASTP/filter.o
FASTP/filter.cpp: In member function 'bool Filter::match(std::vector<std::__cxx11::basic_string<char> >&, std::__cxx11::string, int)':
FASTP/filter.cpp:239:19: 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]
     for(int i=0; i<list.size(); i++) {
                  ~^~~~~~~~~~~~
In file included from FASTP/writer.h:11,
                 from FASTP/threadconfig.h:9,
                 from FASTP/peprocessor.h:13,
                 from FASTP/filter.cpp:2:
FASTP/common.h: At global scope:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/filterresult.cpp -o FASTP/filterresult.o
FASTP/filterresult.cpp: In static member function 'static FilterResult* FilterResult::merge(std::vector<FilterResult*>&)':
FASTP/filterresult.cpp:43:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<FilterResult*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i=0; i<list.size(); i++) {
                  ~^~~~~~~~~~~~
FASTP/filterresult.cpp:75:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<FilterResult*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i=0; i<list.size(); i++) {
                  ~^~~~~~~~~~~~
In file included from FASTP/filterresult.h:9,
                 from FASTP/filterresult.cpp:3:
FASTP/common.h: At global scope:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/htmlreporter.cpp -o FASTP/htmlreporter.o
In file included from FASTP/filterresult.h:9,
                 from FASTP/htmlreporter.h:10,
                 from FASTP/htmlreporter.cpp:1:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/jsonreporter.cpp -o FASTP/jsonreporter.o
In file included from FASTP/filterresult.h:9,
                 from FASTP/jsonreporter.h:10,
                 from FASTP/jsonreporter.cpp:1:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/nucleotidetree.cpp -o FASTP/nucleotidetree.o
FASTP/nucleotidetree.cpp: In member function 'void NucleotideTree::addSeq(std::__cxx11::string)':
FASTP/nucleotidetree.cpp:45:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i=0; i<seq.length(); i++) {
                  ~^~~~~~~~~~~~~
FASTP/nucleotidetree.cpp:49:34: warning: array subscript has type 'char' [-Wchar-subscripts]
         if(curNode->children[base] == NULL) {
                                  ^
FASTP/nucleotidetree.cpp:50:35: warning: array subscript has type 'char' [-Wchar-subscripts]
             curNode->children[base] = new NucleotideNode();
                                   ^
FASTP/nucleotidetree.cpp:51:35: warning: array subscript has type 'char' [-Wchar-subscripts]
             curNode->children[base]->base = seq[i];
                                   ^
FASTP/nucleotidetree.cpp:53:31: warning: array subscript has type 'char' [-Wchar-subscripts]
         curNode->children[base]->count++;
                               ^
FASTP/nucleotidetree.cpp:54:41: warning: array subscript has type 'char' [-Wchar-subscripts]
         curNode = curNode->children[base];
                                         ^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/options.cpp -o FASTP/options.o
In file included from FASTP/options.cpp:4:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
FASTP/options.cpp: In member function 'bool Options::validate()':
FASTP/options.cpp:360:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
         for(int i=0; i<adapter.sequence.length(); i++) {
                      ~^~~~~~~~~~~~~~~~~~~~~~~~~~
FASTP/options.cpp:376:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
         for(int i=0; i<adapter.sequenceR2.length(); i++) {
                      ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
FASTP/options.cpp:406:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
             for(int i=0; i<umi.prefix.length(); i++) {
                          ~^~~~~~~~~~~~~~~~~~~~
FASTP/options.cpp:417:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
             for(int i=0; i<umi.separator.length(); i++) {
                          ~^~~~~~~~~~~~~~~~~~~~~~~
FASTP/options.cpp: In member function 'std::vector<std::__cxx11::basic_string<char> > Options::makeListFromFileByLine(std::__cxx11::string)':
FASTP/options.cpp:486:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
         for(int i=0; i<linestr.length(); i++) {
                      ~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/overlapanalysis.cpp -o FASTP/overlapanalysis.o
In file included from FASTP/overlapanalysis.h:9,
                 from FASTP/overlapanalysis.cpp:1:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/peprocessor.cpp -o FASTP/peprocessor.o
In file included from FASTP/peprocessor.cpp:9:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
FASTP/peprocessor.cpp: In member function 'bool PairEndProcessor::process()':
FASTP/peprocessor.cpp:126:9: warning: unused variable 'cycle' [-Wunused-variable]
     int cycle = 151;
         ^~~~~
FASTP/peprocessor.cpp:228:13: warning: unused variable 'dupMeanTlen' [-Wunused-variable]
     double* dupMeanTlen = NULL;
             ^~~~~~~~~~~
FASTP/peprocessor.cpp: In member function 'bool PairEndProcessor::processPairEnd(ReadPairPack*, ThreadConfig*)':
FASTP/peprocessor.cpp:345:13: warning: unused variable 'lowQualNum1' [-Wunused-variable]
         int lowQualNum1 = 0;
             ^~~~~~~~~~~
FASTP/peprocessor.cpp:346:13: warning: unused variable 'nBaseNum1' [-Wunused-variable]
         int nBaseNum1 = 0;
             ^~~~~~~~~
FASTP/peprocessor.cpp:347:13: warning: unused variable 'lowQualNum2' [-Wunused-variable]
         int lowQualNum2 = 0;
             ^~~~~~~~~~~
FASTP/peprocessor.cpp:348:13: warning: unused variable 'nBaseNum2' [-Wunused-variable]
         int nBaseNum2 = 0;
             ^~~~~~~~~
FASTP/peprocessor.cpp: In member function 'void PairEndProcessor::producerTask()':
FASTP/peprocessor.cpp:718:10: warning: unused variable 'splitSizeReEvaluated' [-Wunused-variable]
     bool splitSizeReEvaluated = false;
          ^~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/polyx.cpp -o FASTP/polyx.o
In file included from FASTP/overlapanalysis.h:9,
                 from FASTP/polyx.h:7,
                 from FASTP/polyx.cpp:1:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
FASTP/polyx.cpp: In static member function 'static void PolyX::trimPolyX(Read*, FilterResult*, int)':
FASTP/polyx.cpp:114:30: warning: 'poly' may be used uninitialized in this function [-Wmaybe-uninitialized]
           fr->addPolyXTrimmed(poly, pos + 1);
           ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/processor.cpp -o FASTP/processor.o
In file included from FASTP/writer.h:11,
                 from FASTP/threadconfig.h:9,
                 from FASTP/peprocessor.h:13,
                 from FASTP/processor.cpp:2:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/read.cpp -o FASTP/read.o
In file included from FASTP/read.cpp:4:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
FASTP/read.cpp: In member function 'void Read::convertPhred64To33()':
FASTP/read.cpp:41:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i=0; i<mQuality.length(); i++) {
                  ~^~~~~~~~~~~~~~~~~~
FASTP/read.cpp: In member function 'int Read::lowQualCount(int)':
FASTP/read.cpp:120:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int q=0;q<mQuality.size();q++){
                 ~^~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/seprocessor.cpp -o FASTP/seprocessor.o
In file included from FASTP/seprocessor.cpp:9:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
FASTP/seprocessor.cpp: In member function 'bool SingleEndProcessor::process()':
FASTP/seprocessor.cpp:76:9: warning: unused variable 'cycle' [-Wunused-variable]
     int cycle = 151;
         ^~~~~
FASTP/seprocessor.cpp:142:13: warning: unused variable 'dupMeanTlen' [-Wunused-variable]
     double* dupMeanTlen = NULL;
             ^~~~~~~~~~~
FASTP/seprocessor.cpp: In member function 'void SingleEndProcessor::producerTask()':
FASTP/seprocessor.cpp:388:10: warning: unused variable 'splitSizeReEvaluated' [-Wunused-variable]
     bool splitSizeReEvaluated = false;
          ^~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/sequence.cpp -o FASTP/sequence.o
FASTP/sequence.cpp: In member function 'Sequence Sequence::reverseComplement()':
FASTP/sequence.cpp:21:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int c=0;c<mStr.length();c++){
                 ~^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/stats.cpp -o FASTP/stats.o
In file included from FASTP/stats.cpp:5:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
FASTP/stats.cpp: In member function 'void Stats::summarize(bool)':
FASTP/stats.cpp:187:36: warning: array subscript has type 'char' [-Wchar-subscripts]
             if(mCycleBaseContents[b][c] == 0)
                                    ^
FASTP/stats.cpp:190:56: warning: array subscript has type 'char' [-Wchar-subscripts]
                 qualCurve[c] = (double)mCycleBaseQual[b][c] / (double)mCycleBaseContents[b][c];
                                                        ^
FASTP/stats.cpp:190:91: warning: array subscript has type 'char' [-Wchar-subscripts]
                 qualCurve[c] = (double)mCycleBaseQual[b][c] / (double)mCycleBaseContents[b][c];
                                                                                           ^
FASTP/stats.cpp:191:59: warning: array subscript has type 'char' [-Wchar-subscripts]
             contentCurve[c] = (double)mCycleBaseContents[b][c] / (double)mCycleTotalBase[c];
                                                           ^
FASTP/stats.cpp:203:62: warning: array subscript has type 'char' [-Wchar-subscripts]
         gcContentCurve[c] = (double)(mCycleBaseContents[gBase][c] + mCycleBaseContents[cBase][c]) / (double)mCycleTotalBase[c];
                                                              ^
FASTP/stats.cpp:203:93: warning: array subscript has type 'char' [-Wchar-subscripts]
         gcContentCurve[c] = (double)(mCycleBaseContents[gBase][c] + mCycleBaseContents[cBase][c]) / (double)mCycleTotalBase[c];
                                                                                             ^
FASTP/stats.cpp: In member function 'void Stats::statRead(Read*)':
FASTP/stats.cpp:249:29: warning: array subscript has type 'char' [-Wchar-subscripts]
             mCycleQ30Bases[b][i]++;
                             ^
FASTP/stats.cpp:250:29: warning: array subscript has type 'char' [-Wchar-subscripts]
             mCycleQ20Bases[b][i]++;
                             ^
FASTP/stats.cpp:252:29: warning: array subscript has type 'char' [-Wchar-subscripts]
             mCycleQ20Bases[b][i]++;
                             ^
FASTP/stats.cpp:255:29: warning: array subscript has type 'char' [-Wchar-subscripts]
         mCycleBaseContents[b][i]++;
                             ^
FASTP/stats.cpp:256:25: warning: array subscript has type 'char' [-Wchar-subscripts]
         mCycleBaseQual[b][i] += (qual-33);
                         ^
FASTP/stats.cpp:313:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
                         for(int p = i; p < seq.length() + i && p < mEvaluatedSeqLen; p++) {
                                        ~~^~~~~~~~~~~~~~~~~~
FASTP/stats.cpp: In member function 'void Stats::reportHtmlORA(std::ofstream&, std::__cxx11::string, std::__cxx11::string)':
FASTP/stats.cpp:551:9: warning: unused variable 'displayed' [-Wunused-variable]
     int displayed = 0;
         ^~~~~~~~~
FASTP/stats.cpp: In member function 'void Stats::reportHtmlContents(std::ofstream&, std::__cxx11::string, std::__cxx11::string)':
FASTP/stats.cpp:850:36: warning: array subscript has type 'char' [-Wchar-subscripts]
             count = mBaseContents[b];
                                    ^
FASTP/stats.cpp: In static member function 'static Stats* Stats::merge(std::vector<Stats*>&)':
FASTP/stats.cpp:888:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Stats*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int t=0; t<list.size(); t++) {
                  ~^~~~~~~~~~~~
FASTP/stats.cpp:898:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Stats*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int t=0; t<list.size(); t++) {
                  ~^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/threadconfig.cpp -o FASTP/threadconfig.o
In file included from FASTP/threadconfig.cpp:2:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
FASTP/threadconfig.cpp: In member function 'void ThreadConfig::initWriterForSplit()':
FASTP/threadconfig.cpp:96:26: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
         while(num.size() < mOptions->split.digits)
               ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from FASTP/writer.h:11,
                 from FASTP/threadconfig.h:9,
                 from FASTP/threadconfig.cpp:1:
FASTP/common.h: At global scope:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/umiprocessor.cpp -o FASTP/umiprocessor.o
FASTP/umiprocessor.cpp: In member function 'void UmiProcessor::addUmiToName(Read*, std::__cxx11::string)':
FASTP/umiprocessor.cpp:70:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i=0; i<r->mName.length(); i++) {
                  ~^~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/unittest.cpp -o FASTP/unittest.o
In file included from FASTP/evaluator.h:8,
                 from FASTP/unittest.cpp:12:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
In file included from FASTP/fastqreader.h:12,
                 from FASTP/unittest.cpp:4:
FASTP/common.h: At global scope:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/writer.cpp -o FASTP/writer.o
In file included from FASTP/writer.cpp:2:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
In file included from FASTP/writer.h:11,
                 from FASTP/writer.cpp:1:
FASTP/common.h: At global scope:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FASTP/writerthread.cpp -o FASTP/writerthread.o
In file included from FASTP/writerthread.cpp:2:
FASTP/util.h: In function 'std::__cxx11::string reverse(const string&)':
FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int pos=0; pos<str.length(); pos++) {
                    ~~~^~~~~~~~~~~~~
In file included from FASTP/writer.h:11,
                 from FASTP/writerthread.h:8,
                 from FASTP/writerthread.cpp:1:
FASTP/common.h: At global scope:
FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable]
 const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = {
                    ^~~~~~~~~~~~
sh:  C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/R: No such file or directory
sh:  C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/R: No such file or directory
sh:  C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/R: No such file or directory
sh:  C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/R: No such file or directory
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Rfastp.dll tmp.def ./RcppExports.o ./main_fastp.o ./FASTP/adaptertrimmer.o ./FASTP/basecorrector.o ./FASTP/duplicate.o ./FASTP/evaluator.o ./FASTP/fastareader.o ./FASTP/fastqreader.o ./FASTP/filter.o ./FASTP/filterresult.o ./FASTP/htmlreporter.o ./FASTP/jsonreporter.o ./FASTP/nucleotidetree.o ./FASTP/options.o ./FASTP/overlapanalysis.o ./FASTP/peprocessor.o ./FASTP/polyx.o ./FASTP/processor.o ./FASTP/read.o ./FASTP/seprocessor.o ./FASTP/sequence.o ./FASTP/stats.o ./FASTP/threadconfig.o ./FASTP/umiprocessor.o ./FASTP/unittest.o ./FASTP/writer.o ./FASTP/writerthread.o C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/Rfastp.buildbin-libdir/Rfastp/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rfastp' as Rfastp_1.4.0.zip
* DONE (Rfastp)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'Rfastp' successfully unpacked and MD5 sums checked

Tests output

Rfastp.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Rfastp)
Rfastp is a wrapper of fastp project: https://github.com/OpenGene/fastp

Please cite fastp in your publication:
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu; fastp: an ultra-fast all-in-one 
    FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 1 September 2018,
    Pages i884-i890, https://doi.org/10.1093/bioinformatics/bty560
> 
> test_check("Rfastp")
Detecting adapter sequence for read1...
No adapter detected for read1

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
   1.87    0.25    2.03 

Rfastp.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Rfastp)
Rfastp is a wrapper of fastp project: https://github.com/OpenGene/fastp

Please cite fastp in your publication:
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu; fastp: an ultra-fast all-in-one 
    FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 1 September 2018,
    Pages i884-i890, https://doi.org/10.1093/bioinformatics/bty560
> 
> test_check("Rfastp")
Detecting adapter sequence for read1...
No adapter detected for read1

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
   1.76    0.34    2.04 

Example timings

Rfastp.Rcheck/examples_i386/Rfastp-Ex.timings

nameusersystemelapsed
catfastq0.000.020.15
curvePlot1.030.181.17
qcSummary0.410.130.45
rfastp1.500.471.48
trimSummary0.390.150.44

Rfastp.Rcheck/examples_x64/Rfastp-Ex.timings

nameusersystemelapsed
catfastq0.000.010.05
curvePlot1.170.241.80
qcSummary0.440.170.51
rfastp1.230.861.70
trimSummary0.420.170.49