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###
### Running command:
###
### 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
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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)
