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INSTALL report for rTANDEM on tokay1

This page was generated on 2021-02-27 12:13:34 -0500 (Sat, 27 Feb 2021).

To the developers/maintainers of the rTANDEM package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1589/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rTANDEM 1.30.0
Frederic Fournier
Snapshot Date: 2021-02-26 14:50:01 -0500 (Fri, 26 Feb 2021)
URL: https://git.bioconductor.org/packages/rTANDEM
Branch: RELEASE_3_12
Last Commit: 96455bf
Last Changed Date: 2020-10-27 10:48:41 -0500 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    ERROR  
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    NA  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    NA  
merida1macOS 10.14.6 Mojave / x86_64  ERROR    ERROR  skippedskipped

Summary

Package: rTANDEM
Version: 1.30.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/rTANDEM_1.30.0.tar.gz && rm -rf rTANDEM.buildbin-libdir && mkdir rTANDEM.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rTANDEM.buildbin-libdir rTANDEM_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL rTANDEM_1.30.0.zip && rm rTANDEM_1.30.0.tar.gz rTANDEM_1.30.0.zip
StartedAt: 2021-02-26 17:25:07 -0500 (Fri, 26 Feb 2021)
EndedAt: 2021-02-26 17:30:18 -0500 (Fri, 26 Feb 2021)
EllapsedTime: 311.3 seconds
RetCode: 0
Status:   OK   

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/rTANDEM_1.30.0.tar.gz && rm -rf rTANDEM.buildbin-libdir && mkdir rTANDEM.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rTANDEM.buildbin-libdir rTANDEM_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL rTANDEM_1.30.0.zip && rm rTANDEM_1.30.0.tar.gz rTANDEM_1.30.0.zip
###
##############################################################################
##############################################################################


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100 1925k  100 1925k    0     0  26.6M      0 --:--:-- --:--:-- --:--:-- 28.4M

install for i386

* installing *source* package 'rTANDEM' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c PTMTreeSearch.cpp -o PTMTreeSearch.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from PTMTreeSearch.h:16,
                 from PTMTreeSearch.cpp:14:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
PTMTreeSearch.cpp: In member function 'virtual bool PTMTreeSearch::refine()':
PTMTreeSearch.cpp:304:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<mi>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for (i = 0; i < m_pProcess->m_vSpectra[a].m_vMI.size(); ++i){
                 ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PTMTreeSearch.cpp:308:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for (i = 1; i < spectraIntTMP.size(); ++i){
                 ~~^~~~~~~~~~~~~~~~~~~~~~
PTMTreeSearch.cpp:382:12: warning: unused variable 'dMaxExpect' [-Wunused-variable]
     double dMaxExpect = atof(strValue.c_str());
            ^~~~~~~~~~
PTMTreeSearch.cpp:402:67: warning: array subscript has type 'char' [-Wchar-subscripts]
    for (unsigned int k = 1; k < m_vmodModificationsDB[itAa->m_cRes].size(); k++){
                                                                   ^
PTMTreeSearch.cpp:403:34: warning: array subscript has type 'char' [-Wchar-subscripts]
      if (floor((mods[itAa->m_cRes][k])*10000) == iModSize){
                                  ^
PTMTreeSearch.cpp:405:37: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_vmodModificationsDB[itAa->m_cRes][k].m_uiCount++;
                                     ^
PTMTreeSearch.cpp:406:41: warning: array subscript has type 'char' [-Wchar-subscripts]
   if (m_vmodModificationsDB[itAa->m_cRes][k].m_dTarget < itAa->m_fPval-1.0)
                                         ^
PTMTreeSearch.cpp:407:39: warning: array subscript has type 'char' [-Wchar-subscripts]
     m_vmodModificationsDB[itAa->m_cRes][k].m_dTarget = itAa->m_fPval-1.0;
                                       ^
PTMTreeSearch.cpp:408:41: warning: array subscript has type 'char' [-Wchar-subscripts]
   if (m_vmodModificationsDB[itAa->m_cRes][k].m_dTargetEval > expect)
                                         ^
PTMTreeSearch.cpp:409:39: warning: array subscript has type 'char' [-Wchar-subscripts]
     m_vmodModificationsDB[itAa->m_cRes][k].m_dTargetEval = expect;
                                       ^
PTMTreeSearch.cpp:585:14: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
   if (modCnt > noptmhitlimit){
       ~~~~~~~^~~~~~~~~~~~~~~
PTMTreeSearch.cpp:54:10: warning: unused variable 'tActiveNow' [-Wunused-variable]
   size_t tActiveNow = 0;
          ^~~~~~~~~~
PTMTreeSearch.cpp:66:10: warning: variable 'dPTMMinEval' set but not used [-Wunused-but-set-variable]
   double dPTMMinEval;
          ^~~~~~~~~~~
PTMTreeSearch.cpp:380:10: warning: unused variable 'dMaxExpect' [-Wunused-variable]
   double dMaxExpect = 0.1;
          ^~~~~~~~~~
PTMTreeSearch.cpp: In member function 'bool PTMTreeSearch::openUniprotPTMs(const char*, std::vector<Modification>*)':
PTMTreeSearch.cpp:751:31: warning: array subscript has type 'char' [-Wchar-subscripts]
    m_vmodModificationsDB[resid].push_back(mod);
                               ^
PTMTreeSearch.cpp:676:16: warning: variable 'm_uiId' set but not used [-Wunused-but-set-variable]
   unsigned int m_uiId;  //unique id of the modification
                ^~~~~~
PTMTreeSearch.cpp: In member function 'virtual void SAXModsHandler::endElement(const XML_Char*)':
PTMTreeSearch.cpp:875:29: warning: array subscript has type 'char' [-Wchar-subscripts]
  m_vmodModificationsDB[resid].push_back(mod);
                             ^
PTMTreeSearch.cpp: In member function 'virtual void SAXResidHandler::endElement(const XML_Char*)':
PTMTreeSearch.cpp:1018:29: warning: array subscript has type 'char' [-Wchar-subscripts]
  m_vmodModificationsDB[resid].push_back(mod);
                             ^
PTMTreeSearch.cpp: In member function 'virtual void SAXUnimodHandler::endElement(const XML_Char*)':
PTMTreeSearch.cpp:1170:34: warning: array subscript has type 'char' [-Wchar-subscripts]
       m_vmodModificationsDB[resid].push_back(mod);
                                  ^
PTMTreeSearch.cpp:1156:10: warning: unused variable 'pos' [-Wunused-variable]
   size_t pos = 0;
          ^~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c PTMTreeSearchScore.cpp -o PTMTreeSearchScore.o
PTMTreeSearchScore.cpp:1264:1: warning: "/*" within comment [-Wcomment]
 /*
  
PTMTreeSearchScore.cpp:1366:1: warning: "/*" within comment [-Wcomment]
 /*
  
In file included from mspectrum.h:142,
                 from PTMTreeSearchScore.cpp:13:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
PTMTreeSearchScore.cpp: In member function 'virtual float PTMTreeSearchScore::score(size_t)':
PTMTreeSearchScore.cpp:369:35: warning: array subscript has type 'char' [-Wchar-subscripts]
    dPTM = m_pdMods[m_pSeq[uiLevel]][uiModIt];
                                   ^
PTMTreeSearchScore.cpp:373:47: warning: array subscript has type 'char' [-Wchar-subscripts]
     if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){ //this was the last modification, so delete this state
                                               ^
PTMTreeSearchScore.cpp:528:47: warning: array subscript has type 'char' [-Wchar-subscripts]
     if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){
                                               ^
PTMTreeSearchScore.cpp:568:47: warning: array subscript has type 'char' [-Wchar-subscripts]
     if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){
                                               ^
PTMTreeSearchScore.cpp:587:47: warning: array subscript has type 'char' [-Wchar-subscripts]
     if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){
                                               ^
PTMTreeSearchScore.cpp:193:9: warning: unused variable 'fMaxIntens' [-Wunused-variable]
   float fMaxIntens = 0;
         ^~~~~~~~~~
PTMTreeSearchScore.cpp:195:8: warning: unused variable 'active' [-Wunused-variable]
   bool active;
        ^~~~~~
PTMTreeSearchScore.cpp:309:16: warning: unused variable 'ScoreOffset' [-Wunused-variable]
   unsigned int ScoreOffset;
                ^~~~~~~~~~~
PTMTreeSearchScore.cpp:724:47: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'long int' [-Wsign-compare]
   if (m_uiSpectraNum + m_uiBatchCnt*MAX_BATCH < m_State.m_lEqualsS){
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
PTMTreeSearchScore.cpp:624:16: warning: unused variable 'lValue' [-Wunused-variable]
  unsigned long lValue = 0;
                ^~~~~~
PTMTreeSearchScore.cpp: In member function 'virtual bool PTMTreeSearchScore::get_aa(std::vector<maa>&, size_t, double&)':
PTMTreeSearchScore.cpp:871:40: warning: array subscript has type 'char' [-Wchar-subscripts]
     aaValue.m_dMod = m_pdMods[m_pSeq[i]][m_pBestGoal->m_uipPTMMap[i]-1];
                                        ^
PTMTreeSearchScore.cpp: In member function 'bool PTMTreeSearchScore::AnchorFixedModification()':
PTMTreeSearchScore.cpp:903:52: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaMod[tC] + m_pSeqUtilFrag->m_pdAaFullMod[tC];
                                                    ^
PTMTreeSearchScore.cpp:903:88: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaMod[tC] + m_pSeqUtilFrag->m_pdAaFullMod[tC];
                                                                                        ^
PTMTreeSearchScore.cpp:905:56: warning: array subscript has type 'char' [-Wchar-subscripts]
    m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaPrompt[tC];
                                                        ^
PTMTreeSearchScore.cpp: In member function 'bool PTMTreeSearchScore::add_dB(long unsigned int, long int)':
PTMTreeSearchScore.cpp:1068:54: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_pfIntens[a] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
                                                      ^
PTMTreeSearchScore.cpp: In member function 'bool PTMTreeSearchScore::add_dC(long unsigned int, long int)':
PTMTreeSearchScore.cpp:1157:54: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_pfIntens[a] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
                                                      ^
PTMTreeSearchScore.cpp: In member function 'bool PTMTreeSearchScore::add_dX(long unsigned int, long int)':
PTMTreeSearchScore.cpp:1199:8: warning: unused variable 'fSub' [-Wunused-variable]
  float fSub = 0.0;
        ^~~~
PTMTreeSearchScore.cpp: In member function 'bool PTMTreeSearchScore::add_dY(long unsigned int, long int)':
PTMTreeSearchScore.cpp:1305:59: warning: array subscript has type 'char' [-Wchar-subscripts]
     m_pfIntens[a-1] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                           ^
PTMTreeSearchScore.cpp:1314:58: warning: array subscript has type 'char' [-Wchar-subscripts]
    m_pfIntens[a-1] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                          ^
PTMTreeSearchScore.cpp:1271:8: warning: unused variable 'fSub' [-Wunused-variable]
  float fSub = 0.0;
        ^~~~
PTMTreeSearchScore.cpp: In member function 'bool PTMTreeSearchScore::add_dZ(long unsigned int, long int)':
PTMTreeSearchScore.cpp:1405:57: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_pfIntens[a-1] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                         ^
PTMTreeSearchScore.cpp:1374:8: warning: unused variable 'fSub' [-Wunused-variable]
  float fSub = 0.0;
        ^~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c base64.cpp -o base64.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c dataLoader.cpp -o dataLoader.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c loadmspectrum.cpp -o loadmspectrum.o
In file included from mspectrum.h:142,
                 from loadmspectrum.cpp:142:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c masscalc.cpp -o masscalc.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mbiomlreport.cpp -o mbiomlreport.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mpam.cpp -o mpam.o
In file included from mspectrum.h:142,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mpam.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mplugin.cpp -o mplugin.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mpmods.cpp -o mpmods.o
In file included from mspectrum.h:142,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mpmods.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mprocess.cpp -o mprocess.o
In file included from mspectrum.h:142,
                 from mprocess.cpp:157:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
mprocess.cpp: In member function 'virtual bool mprocess::create_score(const msequence&, size_t, size_t, long int, bool)':
mprocess.cpp:440:7: warning: unused variable 'bC' [-Wunused-variable]
  bool bC = false;
       ^~
mprocess.cpp: In member function 'bool mprocess::report_valid(double)':
mprocess.cpp:2472:9: warning: unused variable 'c' [-Wunused-variable]
  size_t c = 0;
         ^
mprocess.cpp:2476:9: warning: unused variable 'tLast' [-Wunused-variable]
  size_t tLast = 0;
         ^~~~~
mprocess.cpp: In member function 'bool mprocess::score_single(const msequence&)':
mprocess.cpp:3390:46: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
       if(m_iCurrentRound == 1 && (m_bPermute && m_bCrcCheck || m_bPermuteHigh)) {
                                   ~~~~~~~~~~~^~~~~~~~~~~~~~
mprocess.cpp: In member function 'bool mprocess::initialize_crc()':
mprocess.cpp:4843:14: warning: unused variable 'crc' [-Wunused-variable]
     uint64_t crc = INITIALCRC, part = 0;
              ^~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mrefine.cpp -o mrefine.o
In file included from mspectrum.h:142,
                 from mrefine.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
mrefine.cpp: In member function 'virtual bool mrefine::refine()':
mrefine.cpp:250:9: warning: unused variable 'a' [-Wunused-variable]
  size_t a = 0;
         ^
mrefine.cpp:251:9: warning: unused variable 'tActiveNow' [-Wunused-variable]
  size_t tActiveNow = 0;
         ^~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mreport.cpp -o mreport.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxsaphandler.h:140,
                 from mreport.cpp:143:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
mreport.cpp: In member function 'bool mreport::masses(msequtilities&)':
mreport.cpp:655:78: warning: array subscript has type 'char' [-Wchar-subscripts]
   sprintf(pLine,"\t<aa type=\"%c\" mass=\"%.6lf\" />\n",cAa,_p.m_pdAaMass[cAa]);
                                                                              ^
mreport.cpp:646:9: warning: unused variable 'a' [-Wunused-variable]
  size_t a = 0;
         ^
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mscore.cpp -o mscore.o
In file included from mspectrum.h:142,
                 from mscore.cpp:153:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
mscore.cpp: In constructor 'mscore::mscore()':
mscore.cpp:200:16: warning: iteration 16 invokes undefined behavior [-Waggressive-loop-optimizations]
   m_plCount[a] = 0;
   ~~~~~~~~~~~~~^~~
mscore.cpp:199:10: note: within this loop
  while(a < 20) {
        ~~^~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mscore_hrk.cpp -o mscore_hrk.o
In file included from mspectrum.h:142,
                 from mscore_hrk.cpp:24:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
mscore_hrk.cpp: In member function 'virtual double mscore_hrk::dot(long unsigned int*)':
mscore_hrk.cpp:305:33: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
     if (itType != itEnd && iIon == itType->m_lM) {
                            ~~~~~^~~~~~~~~~~~~~~
mscore_hrk.cpp:314:39: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
     if (itType != itBegin && iIon - 1 == itType[-1].m_lM) {
                              ~~~~~~~~~^~~~~~~~~~~~~~~~~~
mscore_hrk.cpp:321:40: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
     if (itGreater != itEnd && iIon + 1 == itGreater->m_lM) {
                               ~~~~~~~~~^~~~~~~~~~~~~~~~~~
mscore_hrk.cpp: In member function 'bool mscore_hrk::add_mi_hr(mspectrum&)':
mscore_hrk.cpp:443:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MIType>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       if(ii==tempLookup.size()-1) break;
          ~~^~~~~~~~~~~~~~~~~~~~~
mscore_hrk.cpp:352:7: warning: unused variable 'iTotI' [-Wunused-variable]
   int iTotI = 0;
       ^~~~~
mscore_hrk.cpp:371:7: warning: unused variable 'peakCount' [-Wunused-variable]
   int peakCount = 0;
       ^~~~~~~~~
mscore_hrk.cpp: In member function 'double mscore_hrk::dot_hr(long unsigned int*)':
mscore_hrk.cpp:491:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MIType>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       if(i==m_vmiType[m_lId].size()){
          ~^~~~~~~~~~~~~~~~~~~~~~~~~
mscore_hrk.cpp: In member function 'virtual bool mscore_hrk::add_A(long unsigned int, long int)':
mscore_hrk.cpp:550:10: warning: unused variable 'pfScore' [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfAScore;
          ^~~~~~~
mscore_hrk.cpp: In member function 'virtual bool mscore_hrk::add_B(long unsigned int, long int)':
mscore_hrk.cpp:587:10: warning: unused variable 'pfScore' [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfBScore;
          ^~~~~~~
mscore_hrk.cpp:588:10: warning: unused variable 'pfScorePlus' [-Wunused-variable]
   float *pfScorePlus = m_pSeqUtilFrag->m_pfYScore;
          ^~~~~~~~~~~
mscore_hrk.cpp: In member function 'virtual bool mscore_hrk::add_C(long unsigned int, long int)':
mscore_hrk.cpp:622:10: warning: unused variable 'pfScore' [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfBScore;
          ^~~~~~~
mscore_hrk.cpp:623:10: warning: unused variable 'pfScorePlus' [-Wunused-variable]
   float *pfScorePlus = m_pSeqUtilFrag->m_pfYScore;
          ^~~~~~~~~~~
mscore_hrk.cpp: In member function 'virtual bool mscore_hrk::add_X(long unsigned int, long int)':
mscore_hrk.cpp:657:9: warning: unused variable 'fSub' [-Wunused-variable]
   float fSub = 0.0;
         ^~~~
mscore_hrk.cpp:658:10: warning: unused variable 'pfScore' [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfXScore;
          ^~~~~~~
mscore_hrk.cpp: In member function 'virtual bool mscore_hrk::add_Y(long unsigned int, long int)':
mscore_hrk.cpp:691:9: warning: unused variable 'fSub' [-Wunused-variable]
   float fSub = 0.0;
         ^~~~
mscore_hrk.cpp:692:10: warning: unused variable 'pfScore' [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfYScore;
          ^~~~~~~
mscore_hrk.cpp:693:10: warning: unused variable 'pfScoreMinus' [-Wunused-variable]
   float *pfScoreMinus = m_pSeqUtilFrag->m_pfBScore;
          ^~~~~~~~~~~~
mscore_hrk.cpp: In member function 'virtual bool mscore_hrk::add_Z(long unsigned int, long int)':
mscore_hrk.cpp:735:9: warning: unused variable 'fSub' [-Wunused-variable]
   float fSub = 0.0;
         ^~~~
mscore_hrk.cpp:736:10: warning: unused variable 'pfScore' [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfYScore;
          ^~~~~~~
mscore_hrk.cpp:737:10: warning: unused variable 'pfScoreMinus' [-Wunused-variable]
   float *pfScoreMinus = m_pSeqUtilFrag->m_pfBScore;
          ^~~~~~~~~~~~
mscore_hrk.cpp: In member function 'virtual float mscore_hrk::ion_check(long unsigned int, size_t)':
mscore_hrk.cpp:758:17: warning: unused variable 'a' [-Wunused-variable]
   unsigned long a = 0;
                 ^
mscore_hrk.cpp:759:17: warning: unused variable 'lCount' [-Wunused-variable]
   unsigned long lCount = 0;
                 ^~~~~~
mscore_hrk.cpp:760:8: warning: unused variable 'lType' [-Wunused-variable]
   long lType = 0;
        ^~~~~
mscore_hrk.cpp:761:10: warning: unused variable 'b' [-Wunused-variable]
   size_t b = 0;
          ^
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mscore_k.cpp -o mscore_k.o
mscore_k.cpp:677:1: warning: "/*" within comment [-Wcomment]
 /*
  
mscore_k.cpp:753:1: warning: "/*" within comment [-Wcomment]
 /*
  
In file included from mspectrum.h:142,
                 from mscore_k.cpp:24:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
mscore_k.cpp: In member function 'virtual double mscore_k::dot(long unsigned int*)':
mscore_k.cpp:344:37: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
         if (itType != itEnd && iIon == itType->m_lM) {
                                ~~~~~^~~~~~~~~~~~~~~
mscore_k.cpp:355:43: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
         if (itType != itBegin && iIon - 1 == itType[-1].m_lM) {
                                  ~~~~~~~~~^~~~~~~~~~~~~~~~~~
mscore_k.cpp:363:44: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
         if (itGreater != itEnd && iIon + 1 == itGreater->m_lM) {
                                   ~~~~~~~~~^~~~~~~~~~~~~~~~~~
mscore_k.cpp: In member function 'virtual float mscore_k::ion_check(long unsigned int, size_t)':
mscore_k.cpp:378:15: warning: unused variable 'a' [-Wunused-variable]
 unsigned long a = 0;
               ^
mscore_k.cpp:379:15: warning: unused variable 'lCount' [-Wunused-variable]
 unsigned long lCount = 0;
               ^~~~~~
mscore_k.cpp:380:6: warning: unused variable 'lType' [-Wunused-variable]
 long lType = 0;
      ^~~~~
mscore_k.cpp:381:8: warning: unused variable 'b' [-Wunused-variable]
 size_t b = 0;
        ^
mscore_k.cpp: In member function 'virtual bool mscore_k::add_A(long unsigned int, long int)':
mscore_k.cpp:466:14: warning: unused variable 'dZ' [-Wunused-variable]
 const double dZ = (double)_c;
              ^~
mscore_k.cpp: In member function 'virtual bool mscore_k::add_B(long unsigned int, long int)':
mscore_k.cpp:529:54: warning: array subscript has type 'char' [-Wchar-subscripts]
 m_pfSeq[lCount] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
                                                      ^
mscore_k.cpp:523:14: warning: unused variable 'dZ' [-Wunused-variable]
 const double dZ = (double)_c;
              ^~
mscore_k.cpp: In member function 'virtual bool mscore_k::add_C(long unsigned int, long int)':
mscore_k.cpp:591:54: warning: array subscript has type 'char' [-Wchar-subscripts]
 m_pfSeq[lCount] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
                                                      ^
mscore_k.cpp:584:8: warning: unused variable 'dZ' [-Wunused-variable]
 double dZ = (double)_c;
        ^~
mscore_k.cpp: In member function 'virtual bool mscore_k::add_X(long unsigned int, long int)':
mscore_k.cpp:631:7: warning: unused variable 'fSub' [-Wunused-variable]
 float fSub = 0.0;
       ^~~~
mscore_k.cpp:638:8: warning: unused variable 'dZ' [-Wunused-variable]
 double dZ = (double)_c;
        ^~
mscore_k.cpp: In member function 'virtual bool mscore_k::add_Y(long unsigned int, long int)':
mscore_k.cpp:706:55: warning: array subscript has type 'char' [-Wchar-subscripts]
 m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                       ^
mscore_k.cpp:712:55: warning: array subscript has type 'char' [-Wchar-subscripts]
 m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                       ^
mscore_k.cpp:684:7: warning: unused variable 'fSub' [-Wunused-variable]
 float fSub = 0.0;
       ^~~~
mscore_k.cpp:694:8: warning: unused variable 'dZ' [-Wunused-variable]
 double dZ = (double)_c;
        ^~
mscore_k.cpp: In member function 'virtual bool mscore_k::add_Z(long unsigned int, long int)':
mscore_k.cpp:776:55: warning: array subscript has type 'char' [-Wchar-subscripts]
 m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                       ^
mscore_k.cpp:779:55: warning: array subscript has type 'char' [-Wchar-subscripts]
 m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                       ^
mscore_k.cpp:761:7: warning: unused variable 'fSub' [-Wunused-variable]
 float fSub = 0.0;
       ^~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mscore_tandem.cpp -o mscore_tandem.o
In file included from mspectrum.h:142,
                 from mscore_tandem.cpp:135:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
mscore_tandem.cpp: In member function 'bool mscore_tandem::blur(std::vector<mi>&)':
mscore_tandem.cpp:288:19: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'long int' [-Wsign-compare]
     if(uType.m_lM == lValue + a) {
        ~~~~~~~~~~~^~~~~~~~~~~~~
mscore_tandem.cpp: In member function 'virtual double mscore_tandem::dot(long unsigned int*)':
mscore_tandem.cpp:358:8: warning: unused variable 'fValue0' [-Wunused-variable]
  float fValue0 = 0.0;
        ^~~~~~~
mscore_tandem.cpp:362:9: warning: unused variable 'b' [-Wunused-variable]
  size_t b = 0;
         ^
mscore_tandem.cpp: In member function 'virtual float mscore_tandem::ion_check(long unsigned int, size_t)':
mscore_tandem.cpp:581:16: warning: unused variable 'a' [-Wunused-variable]
  unsigned long a = 0;
                ^
mscore_tandem.cpp:582:16: warning: unused variable 'lCount' [-Wunused-variable]
  unsigned long lCount = 0;
                ^~~~~~
mscore_tandem.cpp:583:7: warning: unused variable 'lType' [-Wunused-variable]
  long lType = 0;
       ^~~~~
mscore_tandem.cpp:584:9: warning: unused variable 'b' [-Wunused-variable]
  size_t b = 0;
         ^
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c msequencecollection.cpp -o msequencecollection.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c msequenceserver.cpp -o msequenceserver.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c msequtilities.cpp -o msequtilities.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mspectrumcondition.cpp -o mspectrumcondition.o
In file included from mspectrum.h:142,
                 from mspectrumcondition.cpp:154:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mtermmods.cpp -o mtermmods.o
In file included from mspectrum.h:142,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mtermmods.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mxxcleavage.cpp -o mxxcleavage.o
In file included from mspectrum.h:142,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mxxcleavage.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saxbiomlhandler.cpp -o saxbiomlhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxbiomlhandler.h:140,
                 from saxbiomlhandler.cpp:140:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saxgamlhandler.cpp -o saxgamlhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxgamlhandler.h:140,
                 from saxgamlhandler.cpp:139:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saxhandler.cpp -o saxhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxhandler.cpp:132:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saxmodhandler.cpp -o saxmodhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxmodhandler.h:140,
                 from saxmodhandler.cpp:140:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saxmzdatahandler.cpp -o saxmzdatahandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxmzdatahandler.h:4,
                 from saxmzdatahandler.cpp:28:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saxmzmlhandler.cpp -o saxmzmlhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxmzmlhandler.h:4,
                 from saxmzmlhandler.cpp:33:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saxmzxmlhandler.cpp -o saxmzxmlhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxmzxmlhandler.h:4,
                 from saxmzxmlhandler.cpp:20:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saxsaphandler.cpp -o saxsaphandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxsaphandler.h:140,
                 from saxsaphandler.cpp:140:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saxtandeminputhandler.cpp -o saxtandeminputhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxtandeminputhandler.h:140,
                 from saxtandeminputhandler.cpp:139:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saxtaxhandler.cpp -o saxtaxhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxtaxhandler.h:140,
                 from saxtaxhandler.cpp:139:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c stdafx.cpp -o stdafx.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c tandem.cpp -o tandem.o
In file included from mspectrum.h:142,
                 from tandem.h:15,
                 from tandem.cpp:143:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
tandem.cpp: In function 'SEXPREC* tandem(SEXP, SEXP, SEXP, SEXP, SEXP)':
tandem.cpp:277:12: warning: unused variable 'tCount' [-Wunused-variable]
     size_t tCount = pProcess[0]->m_vSpectra.size();
            ^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c xmlparameter.cpp -o xmlparameter.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxtandeminputhandler.h:140,
                 from xmlparameter.cpp:144:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c xmltaxonomy.cpp -o xmltaxonomy.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxtaxhandler.h:140,
                 from xmltaxonomy.cpp:160:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o rTANDEM.dll tmp.def PTMTreeSearch.o PTMTreeSearchScore.o base64.o dataLoader.o loadmspectrum.o masscalc.o mbiomlreport.o mpam.o mplugin.o mpmods.o mprocess.o mrefine.o mreport.o mscore.o mscore_hrk.o mscore_k.o mscore_tandem.o msequencecollection.o msequenceserver.o msequtilities.o mspectrumcondition.o mtermmods.o mxxcleavage.o saxbiomlhandler.o saxgamlhandler.o saxhandler.o saxmodhandler.o saxmzdatahandler.o saxmzmlhandler.o saxmzxmlhandler.o saxsaphandler.o saxtandeminputhandler.o saxtaxhandler.o stdafx.o tandem.o xmlparameter.o xmltaxonomy.o -L -L -L/lib/i386 -shared -lexpat -lpthread -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/rTANDEM.buildbin-libdir/00LOCK-rTANDEM/00new/rTANDEM/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'rTANDEM'
    finding HTML links ... done
    accessors                               html  
    converters                              html  
    parameters                              html  
    rTANDEM-package                         html  
    rTResult-class                          html  
    tandem                                  html  
    visualizers                             html  
** building package indices
** installing vignettes
   'rTANDEM.Rnw' 
** testing if installed package can be loaded from temporary location
Warning: Package 'rTANDEM' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package can be loaded from final location
Warning: Package 'rTANDEM' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'rTANDEM' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c PTMTreeSearch.cpp -o PTMTreeSearch.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from PTMTreeSearch.h:16,
                 from PTMTreeSearch.cpp:14:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
PTMTreeSearch.cpp: In member function 'virtual bool PTMTreeSearch::refine()':
PTMTreeSearch.cpp:304:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<mi>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for (i = 0; i < m_pProcess->m_vSpectra[a].m_vMI.size(); ++i){
                 ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PTMTreeSearch.cpp:308:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for (i = 1; i < spectraIntTMP.size(); ++i){
                 ~~^~~~~~~~~~~~~~~~~~~~~~
PTMTreeSearch.cpp:382:12: warning: unused variable 'dMaxExpect' [-Wunused-variable]
     double dMaxExpect = atof(strValue.c_str());
            ^~~~~~~~~~
PTMTreeSearch.cpp:402:67: warning: array subscript has type 'char' [-Wchar-subscripts]
    for (unsigned int k = 1; k < m_vmodModificationsDB[itAa->m_cRes].size(); k++){
                                                                   ^
PTMTreeSearch.cpp:403:34: warning: array subscript has type 'char' [-Wchar-subscripts]
      if (floor((mods[itAa->m_cRes][k])*10000) == iModSize){
                                  ^
PTMTreeSearch.cpp:405:37: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_vmodModificationsDB[itAa->m_cRes][k].m_uiCount++;
                                     ^
PTMTreeSearch.cpp:406:41: warning: array subscript has type 'char' [-Wchar-subscripts]
   if (m_vmodModificationsDB[itAa->m_cRes][k].m_dTarget < itAa->m_fPval-1.0)
                                         ^
PTMTreeSearch.cpp:407:39: warning: array subscript has type 'char' [-Wchar-subscripts]
     m_vmodModificationsDB[itAa->m_cRes][k].m_dTarget = itAa->m_fPval-1.0;
                                       ^
PTMTreeSearch.cpp:408:41: warning: array subscript has type 'char' [-Wchar-subscripts]
   if (m_vmodModificationsDB[itAa->m_cRes][k].m_dTargetEval > expect)
                                         ^
PTMTreeSearch.cpp:409:39: warning: array subscript has type 'char' [-Wchar-subscripts]
     m_vmodModificationsDB[itAa->m_cRes][k].m_dTargetEval = expect;
                                       ^
PTMTreeSearch.cpp:585:14: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
   if (modCnt > noptmhitlimit){
       ~~~~~~~^~~~~~~~~~~~~~~
PTMTreeSearch.cpp:54:10: warning: unused variable 'tActiveNow' [-Wunused-variable]
   size_t tActiveNow = 0;
          ^~~~~~~~~~
PTMTreeSearch.cpp:66:10: warning: variable 'dPTMMinEval' set but not used [-Wunused-but-set-variable]
   double dPTMMinEval;
          ^~~~~~~~~~~
PTMTreeSearch.cpp:380:10: warning: unused variable 'dMaxExpect' [-Wunused-variable]
   double dMaxExpect = 0.1;
          ^~~~~~~~~~
PTMTreeSearch.cpp: In member function 'bool PTMTreeSearch::openUniprotPTMs(const char*, std::vector<Modification>*)':
PTMTreeSearch.cpp:751:31: warning: array subscript has type 'char' [-Wchar-subscripts]
    m_vmodModificationsDB[resid].push_back(mod);
                               ^
PTMTreeSearch.cpp:676:16: warning: variable 'm_uiId' set but not used [-Wunused-but-set-variable]
   unsigned int m_uiId;  //unique id of the modification
                ^~~~~~
PTMTreeSearch.cpp: In member function 'virtual void SAXModsHandler::endElement(const XML_Char*)':
PTMTreeSearch.cpp:875:29: warning: array subscript has type 'char' [-Wchar-subscripts]
  m_vmodModificationsDB[resid].push_back(mod);
                             ^
PTMTreeSearch.cpp: In member function 'virtual void SAXResidHandler::endElement(const XML_Char*)':
PTMTreeSearch.cpp:1018:29: warning: array subscript has type 'char' [-Wchar-subscripts]
  m_vmodModificationsDB[resid].push_back(mod);
                             ^
PTMTreeSearch.cpp: In member function 'virtual void SAXUnimodHandler::endElement(const XML_Char*)':
PTMTreeSearch.cpp:1170:34: warning: array subscript has type 'char' [-Wchar-subscripts]
       m_vmodModificationsDB[resid].push_back(mod);
                                  ^
PTMTreeSearch.cpp:1156:10: warning: unused variable 'pos' [-Wunused-variable]
   size_t pos = 0;
          ^~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c PTMTreeSearchScore.cpp -o PTMTreeSearchScore.o
PTMTreeSearchScore.cpp:1264:1: warning: "/*" within comment [-Wcomment]
 /*
  
PTMTreeSearchScore.cpp:1366:1: warning: "/*" within comment [-Wcomment]
 /*
  
In file included from mspectrum.h:142,
                 from PTMTreeSearchScore.cpp:13:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
PTMTreeSearchScore.cpp: In member function 'virtual float PTMTreeSearchScore::score(size_t)':
PTMTreeSearchScore.cpp:369:35: warning: array subscript has type 'char' [-Wchar-subscripts]
    dPTM = m_pdMods[m_pSeq[uiLevel]][uiModIt];
                                   ^
PTMTreeSearchScore.cpp:373:47: warning: array subscript has type 'char' [-Wchar-subscripts]
     if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){ //this was the last modification, so delete this state
                                               ^
PTMTreeSearchScore.cpp:528:47: warning: array subscript has type 'char' [-Wchar-subscripts]
     if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){
                                               ^
PTMTreeSearchScore.cpp:568:47: warning: array subscript has type 'char' [-Wchar-subscripts]
     if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){
                                               ^
PTMTreeSearchScore.cpp:587:47: warning: array subscript has type 'char' [-Wchar-subscripts]
     if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){
                                               ^
PTMTreeSearchScore.cpp:193:9: warning: unused variable 'fMaxIntens' [-Wunused-variable]
   float fMaxIntens = 0;
         ^~~~~~~~~~
PTMTreeSearchScore.cpp:195:8: warning: unused variable 'active' [-Wunused-variable]
   bool active;
        ^~~~~~
PTMTreeSearchScore.cpp:309:16: warning: unused variable 'ScoreOffset' [-Wunused-variable]
   unsigned int ScoreOffset;
                ^~~~~~~~~~~
PTMTreeSearchScore.cpp:724:47: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'long int' [-Wsign-compare]
   if (m_uiSpectraNum + m_uiBatchCnt*MAX_BATCH < m_State.m_lEqualsS){
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
PTMTreeSearchScore.cpp:624:16: warning: unused variable 'lValue' [-Wunused-variable]
  unsigned long lValue = 0;
                ^~~~~~
PTMTreeSearchScore.cpp: In member function 'virtual bool PTMTreeSearchScore::get_aa(std::vector<maa>&, size_t, double&)':
PTMTreeSearchScore.cpp:871:40: warning: array subscript has type 'char' [-Wchar-subscripts]
     aaValue.m_dMod = m_pdMods[m_pSeq[i]][m_pBestGoal->m_uipPTMMap[i]-1];
                                        ^
PTMTreeSearchScore.cpp: In member function 'bool PTMTreeSearchScore::AnchorFixedModification()':
PTMTreeSearchScore.cpp:903:52: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaMod[tC] + m_pSeqUtilFrag->m_pdAaFullMod[tC];
                                                    ^
PTMTreeSearchScore.cpp:903:88: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaMod[tC] + m_pSeqUtilFrag->m_pdAaFullMod[tC];
                                                                                        ^
PTMTreeSearchScore.cpp:905:56: warning: array subscript has type 'char' [-Wchar-subscripts]
    m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaPrompt[tC];
                                                        ^
PTMTreeSearchScore.cpp: In member function 'bool PTMTreeSearchScore::add_dB(long unsigned int, long int)':
PTMTreeSearchScore.cpp:1068:54: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_pfIntens[a] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
                                                      ^
PTMTreeSearchScore.cpp: In member function 'bool PTMTreeSearchScore::add_dC(long unsigned int, long int)':
PTMTreeSearchScore.cpp:1157:54: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_pfIntens[a] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
                                                      ^
PTMTreeSearchScore.cpp: In member function 'bool PTMTreeSearchScore::add_dX(long unsigned int, long int)':
PTMTreeSearchScore.cpp:1199:8: warning: unused variable 'fSub' [-Wunused-variable]
  float fSub = 0.0;
        ^~~~
PTMTreeSearchScore.cpp: In member function 'bool PTMTreeSearchScore::add_dY(long unsigned int, long int)':
PTMTreeSearchScore.cpp:1305:59: warning: array subscript has type 'char' [-Wchar-subscripts]
     m_pfIntens[a-1] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                           ^
PTMTreeSearchScore.cpp:1314:58: warning: array subscript has type 'char' [-Wchar-subscripts]
    m_pfIntens[a-1] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                          ^
PTMTreeSearchScore.cpp:1271:8: warning: unused variable 'fSub' [-Wunused-variable]
  float fSub = 0.0;
        ^~~~
PTMTreeSearchScore.cpp: In member function 'bool PTMTreeSearchScore::add_dZ(long unsigned int, long int)':
PTMTreeSearchScore.cpp:1405:57: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_pfIntens[a-1] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                         ^
PTMTreeSearchScore.cpp:1374:8: warning: unused variable 'fSub' [-Wunused-variable]
  float fSub = 0.0;
        ^~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c base64.cpp -o base64.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c dataLoader.cpp -o dataLoader.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c loadmspectrum.cpp -o loadmspectrum.o
In file included from mspectrum.h:142,
                 from loadmspectrum.cpp:142:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c masscalc.cpp -o masscalc.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mbiomlreport.cpp -o mbiomlreport.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mpam.cpp -o mpam.o
In file included from mspectrum.h:142,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mpam.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mplugin.cpp -o mplugin.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mpmods.cpp -o mpmods.o
In file included from mspectrum.h:142,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mpmods.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mprocess.cpp -o mprocess.o
In file included from mspectrum.h:142,
                 from mprocess.cpp:157:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
mprocess.cpp: In member function 'virtual bool mprocess::create_score(const msequence&, size_t, size_t, long int, bool)':
mprocess.cpp:440:7: warning: unused variable 'bC' [-Wunused-variable]
  bool bC = false;
       ^~
mprocess.cpp: In member function 'bool mprocess::report_valid(double)':
mprocess.cpp:2472:9: warning: unused variable 'c' [-Wunused-variable]
  size_t c = 0;
         ^
mprocess.cpp:2476:9: warning: unused variable 'tLast' [-Wunused-variable]
  size_t tLast = 0;
         ^~~~~
mprocess.cpp: In member function 'bool mprocess::score_single(const msequence&)':
mprocess.cpp:3390:46: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
       if(m_iCurrentRound == 1 && (m_bPermute && m_bCrcCheck || m_bPermuteHigh)) {
                                   ~~~~~~~~~~~^~~~~~~~~~~~~~
mprocess.cpp: In member function 'bool mprocess::initialize_crc()':
mprocess.cpp:4843:14: warning: unused variable 'crc' [-Wunused-variable]
     uint64_t crc = INITIALCRC, part = 0;
              ^~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mrefine.cpp -o mrefine.o
In file included from mspectrum.h:142,
                 from mrefine.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
mrefine.cpp: In member function 'virtual bool mrefine::refine()':
mrefine.cpp:250:9: warning: unused variable 'a' [-Wunused-variable]
  size_t a = 0;
         ^
mrefine.cpp:251:9: warning: unused variable 'tActiveNow' [-Wunused-variable]
  size_t tActiveNow = 0;
         ^~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mreport.cpp -o mreport.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxsaphandler.h:140,
                 from mreport.cpp:143:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
mreport.cpp: In member function 'bool mreport::masses(msequtilities&)':
mreport.cpp:655:78: warning: array subscript has type 'char' [-Wchar-subscripts]
   sprintf(pLine,"\t<aa type=\"%c\" mass=\"%.6lf\" />\n",cAa,_p.m_pdAaMass[cAa]);
                                                                              ^
mreport.cpp:646:9: warning: unused variable 'a' [-Wunused-variable]
  size_t a = 0;
         ^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mscore.cpp -o mscore.o
In file included from mspectrum.h:142,
                 from mscore.cpp:153:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
mscore.cpp: In constructor 'mscore::mscore()':
mscore.cpp:200:16: warning: iteration 16 invokes undefined behavior [-Waggressive-loop-optimizations]
   m_plCount[a] = 0;
   ~~~~~~~~~~~~~^~~
mscore.cpp:199:10: note: within this loop
  while(a < 20) {
        ~~^~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mscore_hrk.cpp -o mscore_hrk.o
In file included from mspectrum.h:142,
                 from mscore_hrk.cpp:24:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
mscore_hrk.cpp: In member function 'virtual double mscore_hrk::dot(long unsigned int*)':
mscore_hrk.cpp:305:33: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
     if (itType != itEnd && iIon == itType->m_lM) {
                            ~~~~~^~~~~~~~~~~~~~~
mscore_hrk.cpp:314:39: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
     if (itType != itBegin && iIon - 1 == itType[-1].m_lM) {
                              ~~~~~~~~~^~~~~~~~~~~~~~~~~~
mscore_hrk.cpp:321:40: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
     if (itGreater != itEnd && iIon + 1 == itGreater->m_lM) {
                               ~~~~~~~~~^~~~~~~~~~~~~~~~~~
mscore_hrk.cpp: In member function 'bool mscore_hrk::add_mi_hr(mspectrum&)':
mscore_hrk.cpp:443:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MIType>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
       if(ii==tempLookup.size()-1) break;
          ~~^~~~~~~~~~~~~~~~~~~~~
mscore_hrk.cpp:352:7: warning: unused variable 'iTotI' [-Wunused-variable]
   int iTotI = 0;
       ^~~~~
mscore_hrk.cpp:371:7: warning: unused variable 'peakCount' [-Wunused-variable]
   int peakCount = 0;
       ^~~~~~~~~
mscore_hrk.cpp: In member function 'double mscore_hrk::dot_hr(long unsigned int*)':
mscore_hrk.cpp:491:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MIType>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
       if(i==m_vmiType[m_lId].size()){
          ~^~~~~~~~~~~~~~~~~~~~~~~~~
mscore_hrk.cpp: In member function 'virtual bool mscore_hrk::add_A(long unsigned int, long int)':
mscore_hrk.cpp:550:10: warning: unused variable 'pfScore' [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfAScore;
          ^~~~~~~
mscore_hrk.cpp: In member function 'virtual bool mscore_hrk::add_B(long unsigned int, long int)':
mscore_hrk.cpp:587:10: warning: unused variable 'pfScore' [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfBScore;
          ^~~~~~~
mscore_hrk.cpp:588:10: warning: unused variable 'pfScorePlus' [-Wunused-variable]
   float *pfScorePlus = m_pSeqUtilFrag->m_pfYScore;
          ^~~~~~~~~~~
mscore_hrk.cpp: In member function 'virtual bool mscore_hrk::add_C(long unsigned int, long int)':
mscore_hrk.cpp:622:10: warning: unused variable 'pfScore' [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfBScore;
          ^~~~~~~
mscore_hrk.cpp:623:10: warning: unused variable 'pfScorePlus' [-Wunused-variable]
   float *pfScorePlus = m_pSeqUtilFrag->m_pfYScore;
          ^~~~~~~~~~~
mscore_hrk.cpp: In member function 'virtual bool mscore_hrk::add_X(long unsigned int, long int)':
mscore_hrk.cpp:657:9: warning: unused variable 'fSub' [-Wunused-variable]
   float fSub = 0.0;
         ^~~~
mscore_hrk.cpp:658:10: warning: unused variable 'pfScore' [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfXScore;
          ^~~~~~~
mscore_hrk.cpp: In member function 'virtual bool mscore_hrk::add_Y(long unsigned int, long int)':
mscore_hrk.cpp:691:9: warning: unused variable 'fSub' [-Wunused-variable]
   float fSub = 0.0;
         ^~~~
mscore_hrk.cpp:692:10: warning: unused variable 'pfScore' [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfYScore;
          ^~~~~~~
mscore_hrk.cpp:693:10: warning: unused variable 'pfScoreMinus' [-Wunused-variable]
   float *pfScoreMinus = m_pSeqUtilFrag->m_pfBScore;
          ^~~~~~~~~~~~
mscore_hrk.cpp: In member function 'virtual bool mscore_hrk::add_Z(long unsigned int, long int)':
mscore_hrk.cpp:735:9: warning: unused variable 'fSub' [-Wunused-variable]
   float fSub = 0.0;
         ^~~~
mscore_hrk.cpp:736:10: warning: unused variable 'pfScore' [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfYScore;
          ^~~~~~~
mscore_hrk.cpp:737:10: warning: unused variable 'pfScoreMinus' [-Wunused-variable]
   float *pfScoreMinus = m_pSeqUtilFrag->m_pfBScore;
          ^~~~~~~~~~~~
mscore_hrk.cpp: In member function 'virtual float mscore_hrk::ion_check(long unsigned int, size_t)':
mscore_hrk.cpp:758:17: warning: unused variable 'a' [-Wunused-variable]
   unsigned long a = 0;
                 ^
mscore_hrk.cpp:759:17: warning: unused variable 'lCount' [-Wunused-variable]
   unsigned long lCount = 0;
                 ^~~~~~
mscore_hrk.cpp:760:8: warning: unused variable 'lType' [-Wunused-variable]
   long lType = 0;
        ^~~~~
mscore_hrk.cpp:761:10: warning: unused variable 'b' [-Wunused-variable]
   size_t b = 0;
          ^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mscore_k.cpp -o mscore_k.o
mscore_k.cpp:677:1: warning: "/*" within comment [-Wcomment]
 /*
  
mscore_k.cpp:753:1: warning: "/*" within comment [-Wcomment]
 /*
  
In file included from mspectrum.h:142,
                 from mscore_k.cpp:24:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
mscore_k.cpp: In member function 'virtual double mscore_k::dot(long unsigned int*)':
mscore_k.cpp:344:37: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
         if (itType != itEnd && iIon == itType->m_lM) {
                                ~~~~~^~~~~~~~~~~~~~~
mscore_k.cpp:355:43: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
         if (itType != itBegin && iIon - 1 == itType[-1].m_lM) {
                                  ~~~~~~~~~^~~~~~~~~~~~~~~~~~
mscore_k.cpp:363:44: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
         if (itGreater != itEnd && iIon + 1 == itGreater->m_lM) {
                                   ~~~~~~~~~^~~~~~~~~~~~~~~~~~
mscore_k.cpp: In member function 'virtual float mscore_k::ion_check(long unsigned int, size_t)':
mscore_k.cpp:378:15: warning: unused variable 'a' [-Wunused-variable]
 unsigned long a = 0;
               ^
mscore_k.cpp:379:15: warning: unused variable 'lCount' [-Wunused-variable]
 unsigned long lCount = 0;
               ^~~~~~
mscore_k.cpp:380:6: warning: unused variable 'lType' [-Wunused-variable]
 long lType = 0;
      ^~~~~
mscore_k.cpp:381:8: warning: unused variable 'b' [-Wunused-variable]
 size_t b = 0;
        ^
mscore_k.cpp: In member function 'virtual bool mscore_k::add_A(long unsigned int, long int)':
mscore_k.cpp:466:14: warning: unused variable 'dZ' [-Wunused-variable]
 const double dZ = (double)_c;
              ^~
mscore_k.cpp: In member function 'virtual bool mscore_k::add_B(long unsigned int, long int)':
mscore_k.cpp:529:54: warning: array subscript has type 'char' [-Wchar-subscripts]
 m_pfSeq[lCount] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
                                                      ^
mscore_k.cpp:523:14: warning: unused variable 'dZ' [-Wunused-variable]
 const double dZ = (double)_c;
              ^~
mscore_k.cpp: In member function 'virtual bool mscore_k::add_C(long unsigned int, long int)':
mscore_k.cpp:591:54: warning: array subscript has type 'char' [-Wchar-subscripts]
 m_pfSeq[lCount] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
                                                      ^
mscore_k.cpp:584:8: warning: unused variable 'dZ' [-Wunused-variable]
 double dZ = (double)_c;
        ^~
mscore_k.cpp: In member function 'virtual bool mscore_k::add_X(long unsigned int, long int)':
mscore_k.cpp:631:7: warning: unused variable 'fSub' [-Wunused-variable]
 float fSub = 0.0;
       ^~~~
mscore_k.cpp:638:8: warning: unused variable 'dZ' [-Wunused-variable]
 double dZ = (double)_c;
        ^~
mscore_k.cpp: In member function 'virtual bool mscore_k::add_Y(long unsigned int, long int)':
mscore_k.cpp:706:55: warning: array subscript has type 'char' [-Wchar-subscripts]
 m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                       ^
mscore_k.cpp:712:55: warning: array subscript has type 'char' [-Wchar-subscripts]
 m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                       ^
mscore_k.cpp:684:7: warning: unused variable 'fSub' [-Wunused-variable]
 float fSub = 0.0;
       ^~~~
mscore_k.cpp:694:8: warning: unused variable 'dZ' [-Wunused-variable]
 double dZ = (double)_c;
        ^~
mscore_k.cpp: In member function 'virtual bool mscore_k::add_Z(long unsigned int, long int)':
mscore_k.cpp:776:55: warning: array subscript has type 'char' [-Wchar-subscripts]
 m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                       ^
mscore_k.cpp:779:55: warning: array subscript has type 'char' [-Wchar-subscripts]
 m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                       ^
mscore_k.cpp:761:7: warning: unused variable 'fSub' [-Wunused-variable]
 float fSub = 0.0;
       ^~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mscore_tandem.cpp -o mscore_tandem.o
In file included from mspectrum.h:142,
                 from mscore_tandem.cpp:135:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
mscore_tandem.cpp: In member function 'bool mscore_tandem::blur(std::vector<mi>&)':
mscore_tandem.cpp:288:19: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'long int' [-Wsign-compare]
     if(uType.m_lM == lValue + a) {
        ~~~~~~~~~~~^~~~~~~~~~~~~
mscore_tandem.cpp: In member function 'virtual double mscore_tandem::dot(long unsigned int*)':
mscore_tandem.cpp:358:8: warning: unused variable 'fValue0' [-Wunused-variable]
  float fValue0 = 0.0;
        ^~~~~~~
mscore_tandem.cpp:362:9: warning: unused variable 'b' [-Wunused-variable]
  size_t b = 0;
         ^
mscore_tandem.cpp: In member function 'virtual float mscore_tandem::ion_check(long unsigned int, size_t)':
mscore_tandem.cpp:581:16: warning: unused variable 'a' [-Wunused-variable]
  unsigned long a = 0;
                ^
mscore_tandem.cpp:582:16: warning: unused variable 'lCount' [-Wunused-variable]
  unsigned long lCount = 0;
                ^~~~~~
mscore_tandem.cpp:583:7: warning: unused variable 'lType' [-Wunused-variable]
  long lType = 0;
       ^~~~~
mscore_tandem.cpp:584:9: warning: unused variable 'b' [-Wunused-variable]
  size_t b = 0;
         ^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c msequencecollection.cpp -o msequencecollection.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c msequenceserver.cpp -o msequenceserver.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c msequtilities.cpp -o msequtilities.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mspectrumcondition.cpp -o mspectrumcondition.o
In file included from mspectrum.h:142,
                 from mspectrumcondition.cpp:154:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mtermmods.cpp -o mtermmods.o
In file included from mspectrum.h:142,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mtermmods.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mxxcleavage.cpp -o mxxcleavage.o
In file included from mspectrum.h:142,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mxxcleavage.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saxbiomlhandler.cpp -o saxbiomlhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxbiomlhandler.h:140,
                 from saxbiomlhandler.cpp:140:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saxgamlhandler.cpp -o saxgamlhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxgamlhandler.h:140,
                 from saxgamlhandler.cpp:139:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saxhandler.cpp -o saxhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxhandler.cpp:132:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saxmodhandler.cpp -o saxmodhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxmodhandler.h:140,
                 from saxmodhandler.cpp:140:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saxmzdatahandler.cpp -o saxmzdatahandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxmzdatahandler.h:4,
                 from saxmzdatahandler.cpp:28:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saxmzmlhandler.cpp -o saxmzmlhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxmzmlhandler.h:4,
                 from saxmzmlhandler.cpp:33:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saxmzxmlhandler.cpp -o saxmzxmlhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxmzxmlhandler.h:4,
                 from saxmzxmlhandler.cpp:20:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saxsaphandler.cpp -o saxsaphandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxsaphandler.h:140,
                 from saxsaphandler.cpp:140:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saxtandeminputhandler.cpp -o saxtandeminputhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxtandeminputhandler.h:140,
                 from saxtandeminputhandler.cpp:139:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c saxtaxhandler.cpp -o saxtaxhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxtaxhandler.h:140,
                 from saxtaxhandler.cpp:139:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c stdafx.cpp -o stdafx.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c tandem.cpp -o tandem.o
In file included from mspectrum.h:142,
                 from tandem.h:15,
                 from tandem.cpp:143:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
tandem.cpp: In function 'SEXPREC* tandem(SEXP, SEXP, SEXP, SEXP, SEXP)':
tandem.cpp:277:12: warning: unused variable 'tCount' [-Wunused-variable]
     size_t tCount = pProcess[0]->m_vSpectra.size();
            ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c xmlparameter.cpp -o xmlparameter.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxtandeminputhandler.h:140,
                 from xmlparameter.cpp:144:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c xmltaxonomy.cpp -o xmltaxonomy.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxtaxhandler.h:140,
                 from xmltaxonomy.cpp:160:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^~~~~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o rTANDEM.dll tmp.def PTMTreeSearch.o PTMTreeSearchScore.o base64.o dataLoader.o loadmspectrum.o masscalc.o mbiomlreport.o mpam.o mplugin.o mpmods.o mprocess.o mrefine.o mreport.o mscore.o mscore_hrk.o mscore_k.o mscore_tandem.o msequencecollection.o msequenceserver.o msequtilities.o mspectrumcondition.o mtermmods.o mxxcleavage.o saxbiomlhandler.o saxgamlhandler.o saxhandler.o saxmodhandler.o saxmzdatahandler.o saxmzmlhandler.o saxmzxmlhandler.o saxsaphandler.o saxtandeminputhandler.o saxtaxhandler.o stdafx.o tandem.o xmlparameter.o xmltaxonomy.o -L -L -L/lib/x64 -shared -lexpat -lpthread -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/rTANDEM.buildbin-libdir/rTANDEM/libs/x64
** testing if installed package can be loaded
Warning: Package 'rTANDEM' is deprecated and will be removed from Bioconductor
  version 3.13
* MD5 sums
packaged installation of 'rTANDEM' as rTANDEM_1.30.0.zip
* DONE (rTANDEM)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'rTANDEM' successfully unpacked and MD5 sums checked