##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rfastp.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Rfastp_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/Rfastp.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.5.0'
* 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 ... OK
* 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
* 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 x64 is not available
File 'D:/biocbuild/bbs-3.15-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 ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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: 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/Rfastp.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Rfastp
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'Rfastp' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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:  D:/biocbuild/bbs-3.15-bioc/R/bin/R: No such file or directory
sh:  D:/biocbuild/bbs-3.15-bioc/R/bin/R: No such file or directory
sh:  D:/biocbuild/bbs-3.15-bioc/R/bin/R: No such file or directory
sh:  D:/biocbuild/bbs-3.15-bioc/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 D:/biocbuild/bbs-3.15-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 -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-Rfastp/00new/Rfastp/libs/x64
** 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
* DONE (Rfastp)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'OSAT' is missing or broken
 done

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Platform: x86_64-w64-mingw32/x64 (64-bit)

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> 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 
   1.18    0.39    1.50