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INSTALL report for rTANDEM on nebbiolo1

This page was generated on 2021-02-27 12:11:19 -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: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL rTANDEM
StartedAt: 2021-02-26 16:32:07 -0500 (Fri, 26 Feb 2021)
EndedAt: 2021-02-26 16:34:28 -0500 (Fri, 26 Feb 2021)
EllapsedTime: 141.1 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL rTANDEM
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘rTANDEM’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   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 unsigned int’} [-Wsign-compare]
  304 |     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 unsigned int’} [-Wsign-compare]
  308 |     for (i = 1; i < spectraIntTMP.size(); ++i){
      |                 ~~^~~~~~~~~~~~~~~~~~~~~~
PTMTreeSearch.cpp:382:12: warning: unused variable ‘dMaxExpect’ [-Wunused-variable]
  382 |     double dMaxExpect = atof(strValue.c_str());
      |            ^~~~~~~~~~
PTMTreeSearch.cpp:402:61: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  402 |    for (unsigned int k = 1; k < m_vmodModificationsDB[itAa->m_cRes].size(); k++){
      |                                                       ~~~~~~^~~~~~
PTMTreeSearch.cpp:403:28: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  403 |      if (floor((mods[itAa->m_cRes][k])*10000) == iModSize){
      |                      ~~~~~~^~~~~~
PTMTreeSearch.cpp:405:31: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  405 |   m_vmodModificationsDB[itAa->m_cRes][k].m_uiCount++;
      |                         ~~~~~~^~~~~~
PTMTreeSearch.cpp:406:35: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  406 |   if (m_vmodModificationsDB[itAa->m_cRes][k].m_dTarget < itAa->m_fPval-1.0)
      |                             ~~~~~~^~~~~~
PTMTreeSearch.cpp:407:33: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  407 |     m_vmodModificationsDB[itAa->m_cRes][k].m_dTarget = itAa->m_fPval-1.0;
      |                           ~~~~~~^~~~~~
PTMTreeSearch.cpp:408:35: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  408 |   if (m_vmodModificationsDB[itAa->m_cRes][k].m_dTargetEval > expect)
      |                             ~~~~~~^~~~~~
PTMTreeSearch.cpp:409:33: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  409 |     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]
  585 |   if (modCnt > noptmhitlimit){
      |       ~~~~~~~^~~~~~~~~~~~~~~
PTMTreeSearch.cpp:54:10: warning: unused variable ‘tActiveNow’ [-Wunused-variable]
   54 |   size_t tActiveNow = 0;
      |          ^~~~~~~~~~
PTMTreeSearch.cpp:66:10: warning: variable ‘dPTMMinEval’ set but not used [-Wunused-but-set-variable]
   66 |   double dPTMMinEval;
      |          ^~~~~~~~~~~
PTMTreeSearch.cpp:380:10: warning: unused variable ‘dMaxExpect’ [-Wunused-variable]
  380 |   double dMaxExpect = 0.1;
      |          ^~~~~~~~~~
PTMTreeSearch.cpp: In member function ‘bool PTMTreeSearch::openUniprotPTMs(const char*, std::vector<Modification>*)’:
PTMTreeSearch.cpp:751:26: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  751 |    m_vmodModificationsDB[resid].push_back(mod);
      |                          ^~~~~
PTMTreeSearch.cpp:676:16: warning: variable ‘m_uiId’ set but not used [-Wunused-but-set-variable]
  676 |   unsigned int m_uiId;  //unique id of the modification
      |                ^~~~~~
PTMTreeSearch.cpp: In member function ‘virtual void SAXModsHandler::endElement(const XML_Char*)’:
PTMTreeSearch.cpp:875:24: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  875 |  m_vmodModificationsDB[resid].push_back(mod);
      |                        ^~~~~
PTMTreeSearch.cpp: In member function ‘virtual void SAXResidHandler::endElement(const XML_Char*)’:
PTMTreeSearch.cpp:1018:24: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 1018 |  m_vmodModificationsDB[resid].push_back(mod);
      |                        ^~~~~
PTMTreeSearch.cpp: In member function ‘virtual void SAXUnimodHandler::endElement(const XML_Char*)’:
PTMTreeSearch.cpp:1170:29: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 1170 |       m_vmodModificationsDB[resid].push_back(mod);
      |                             ^~~~~
PTMTreeSearch.cpp:1156:10: warning: unused variable ‘pos’ [-Wunused-variable]
 1156 |   size_t pos = 0;
      |          ^~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c PTMTreeSearchScore.cpp -o PTMTreeSearchScore.o
PTMTreeSearchScore.cpp:1264:1: warning: "/*" within comment [-Wcomment]
 1264 | /*
      |  
PTMTreeSearchScore.cpp:1366:1: warning: "/*" within comment [-Wcomment]
 1366 | /*
      |  
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]
  446 |   int lZeros = m_lHigh - a - 1;
      |       ^~~~~~
PTMTreeSearchScore.cpp: In member function ‘virtual float PTMTreeSearchScore::score(size_t)’:
PTMTreeSearchScore.cpp:369:34: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  369 |    dPTM = m_pdMods[m_pSeq[uiLevel]][uiModIt];
      |                    ~~~~~~~~~~~~~~^
PTMTreeSearchScore.cpp:373:46: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  373 |     if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){ //this was the last modification, so delete this state
      |                                ~~~~~~~~~~~~~~^
PTMTreeSearchScore.cpp:528:46: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  528 |     if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){
      |                                ~~~~~~~~~~~~~~^
PTMTreeSearchScore.cpp:568:46: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  568 |     if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){
      |                                ~~~~~~~~~~~~~~^
PTMTreeSearchScore.cpp:587:46: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  587 |     if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){
      |                                ~~~~~~~~~~~~~~^
PTMTreeSearchScore.cpp:193:9: warning: unused variable ‘fMaxIntens’ [-Wunused-variable]
  193 |   float fMaxIntens = 0;
      |         ^~~~~~~~~~
PTMTreeSearchScore.cpp:195:8: warning: unused variable ‘active’ [-Wunused-variable]
  195 |   bool active;
      |        ^~~~~~
PTMTreeSearchScore.cpp:309:16: warning: unused variable ‘ScoreOffset’ [-Wunused-variable]
  309 |   unsigned int ScoreOffset;
      |                ^~~~~~~~~~~
PTMTreeSearchScore.cpp:624:16: warning: unused variable ‘lValue’ [-Wunused-variable]
  624 |  unsigned long lValue = 0;
      |                ^~~~~~
PTMTreeSearchScore.cpp: In member function ‘virtual bool PTMTreeSearchScore::get_aa(std::vector<maa>&, size_t, double&)’:
PTMTreeSearchScore.cpp:871:39: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  871 |     aaValue.m_dMod = m_pdMods[m_pSeq[i]][m_pBestGoal->m_uipPTMMap[i]-1];
      |                               ~~~~~~~~^
PTMTreeSearchScore.cpp: In member function ‘bool PTMTreeSearchScore::AnchorFixedModification()’:
PTMTreeSearchScore.cpp:903:50: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  903 |   m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaMod[tC] + m_pSeqUtilFrag->m_pdAaFullMod[tC];
      |                                                  ^~
PTMTreeSearchScore.cpp:903:86: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  903 |   m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaMod[tC] + m_pSeqUtilFrag->m_pdAaFullMod[tC];
      |                                                                                      ^~
PTMTreeSearchScore.cpp:905:54: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  905 |    m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaPrompt[tC];
      |                                                      ^~
PTMTreeSearchScore.cpp: In member function ‘bool PTMTreeSearchScore::add_dB(long unsigned int, long int)’:
PTMTreeSearchScore.cpp:1068:53: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 1068 |   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:1157:53: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 1157 |   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]
 1199 |  float fSub = 0.0;
      |        ^~~~
PTMTreeSearchScore.cpp: In member function ‘bool PTMTreeSearchScore::add_dY(long unsigned int, long int)’:
PTMTreeSearchScore.cpp:1305:58: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 1305 |     m_pfIntens[a-1] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
      |                                                ~~~~~~~~~~^
PTMTreeSearchScore.cpp:1314:57: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 1314 |    m_pfIntens[a-1] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
      |                                               ~~~~~~~~~~^
PTMTreeSearchScore.cpp:1271:8: warning: unused variable ‘fSub’ [-Wunused-variable]
 1271 |  float fSub = 0.0;
      |        ^~~~
PTMTreeSearchScore.cpp: In member function ‘bool PTMTreeSearchScore::add_dZ(long unsigned int, long int)’:
PTMTreeSearchScore.cpp:1405:56: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 1405 |   m_pfIntens[a-1] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
      |                                              ~~~~~~~~~~^
PTMTreeSearchScore.cpp:1374:8: warning: unused variable ‘fSub’ [-Wunused-variable]
 1374 |  float fSub = 0.0;
      |        ^~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c base64.cpp -o base64.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c dataLoader.cpp -o dataLoader.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   int lZeros = m_lHigh - a - 1;
      |       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c masscalc.cpp -o masscalc.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mbiomlreport.cpp -o mbiomlreport.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   int lZeros = m_lHigh - a - 1;
      |       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mplugin.cpp -o mplugin.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   int lZeros = m_lHigh - a - 1;
      |       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   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]
  440 |  bool bC = false;
      |       ^~
mprocess.cpp: In member function ‘bool mprocess::report_valid(double)’:
mprocess.cpp:2472:9: warning: unused variable ‘c’ [-Wunused-variable]
 2472 |  size_t c = 0;
      |         ^
mprocess.cpp:2476:9: warning: unused variable ‘tLast’ [-Wunused-variable]
 2476 |  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]
 3390 |       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]
 4843 |     uint64_t crc = INITIALCRC, part = 0;
      |              ^~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   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]
  250 |  size_t a = 0;
      |         ^
mrefine.cpp:251:9: warning: unused variable ‘tActiveNow’ [-Wunused-variable]
  251 |  size_t tActiveNow = 0;
      |         ^~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   int lZeros = m_lHigh - a - 1;
      |       ^~~~~~
mreport.cpp: In member function ‘bool mreport::masses(msequtilities&)’:
mreport.cpp:655:75: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  655 |   sprintf(pLine,"\t<aa type=\"%c\" mass=\"%.6lf\" />\n",cAa,_p.m_pdAaMass[cAa]);
      |                                                                           ^~~
mreport.cpp:646:9: warning: unused variable ‘a’ [-Wunused-variable]
  646 |  size_t a = 0;
      |         ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   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]
  200 |   m_plCount[a] = 0;
      |   ~~~~~~~~~~~~~^~~
mscore.cpp:199:10: note: within this loop
  199 |  while(a < 20) {
      |        ~~^~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   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]
  305 |     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]
  314 |     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]
  321 |     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 unsigned int’} [-Wsign-compare]
  443 |       if(ii==tempLookup.size()-1) break;
      |          ~~^~~~~~~~~~~~~~~~~~~~~
mscore_hrk.cpp:352:7: warning: unused variable ‘iTotI’ [-Wunused-variable]
  352 |   int iTotI = 0;
      |       ^~~~~
mscore_hrk.cpp:371:7: warning: unused variable ‘peakCount’ [-Wunused-variable]
  371 |   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 unsigned int’} [-Wsign-compare]
  491 |       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]
  550 |   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]
  587 |   float *pfScore = m_pSeqUtilFrag->m_pfBScore;
      |          ^~~~~~~
mscore_hrk.cpp:588:10: warning: unused variable ‘pfScorePlus’ [-Wunused-variable]
  588 |   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]
  622 |   float *pfScore = m_pSeqUtilFrag->m_pfBScore;
      |          ^~~~~~~
mscore_hrk.cpp:623:10: warning: unused variable ‘pfScorePlus’ [-Wunused-variable]
  623 |   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]
  657 |   float fSub = 0.0;
      |         ^~~~
mscore_hrk.cpp:658:10: warning: unused variable ‘pfScore’ [-Wunused-variable]
  658 |   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]
  691 |   float fSub = 0.0;
      |         ^~~~
mscore_hrk.cpp:692:10: warning: unused variable ‘pfScore’ [-Wunused-variable]
  692 |   float *pfScore = m_pSeqUtilFrag->m_pfYScore;
      |          ^~~~~~~
mscore_hrk.cpp:693:10: warning: unused variable ‘pfScoreMinus’ [-Wunused-variable]
  693 |   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]
  735 |   float fSub = 0.0;
      |         ^~~~
mscore_hrk.cpp:736:10: warning: unused variable ‘pfScore’ [-Wunused-variable]
  736 |   float *pfScore = m_pSeqUtilFrag->m_pfYScore;
      |          ^~~~~~~
mscore_hrk.cpp:737:10: warning: unused variable ‘pfScoreMinus’ [-Wunused-variable]
  737 |   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]
  758 |   unsigned long a = 0;
      |                 ^
mscore_hrk.cpp:759:17: warning: unused variable ‘lCount’ [-Wunused-variable]
  759 |   unsigned long lCount = 0;
      |                 ^~~~~~
mscore_hrk.cpp:760:8: warning: unused variable ‘lType’ [-Wunused-variable]
  760 |   long lType = 0;
      |        ^~~~~
mscore_hrk.cpp:761:10: warning: unused variable ‘b’ [-Wunused-variable]
  761 |   size_t b = 0;
      |          ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mscore_k.cpp -o mscore_k.o
mscore_k.cpp:677:1: warning: "/*" within comment [-Wcomment]
  677 | /*
      |  
mscore_k.cpp:753:1: warning: "/*" within comment [-Wcomment]
  753 | /*
      |  
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]
  446 |   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]
  344 |         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]
  355 |         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]
  363 |         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]
  378 | unsigned long a = 0;
      |               ^
mscore_k.cpp:379:15: warning: unused variable ‘lCount’ [-Wunused-variable]
  379 | unsigned long lCount = 0;
      |               ^~~~~~
mscore_k.cpp:380:6: warning: unused variable ‘lType’ [-Wunused-variable]
  380 | long lType = 0;
      |      ^~~~~
mscore_k.cpp:381:8: warning: unused variable ‘b’ [-Wunused-variable]
  381 | 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]
  466 | 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:529:53: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  529 | m_pfSeq[lCount] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
      |                                           ~~~~~~~~~~^
mscore_k.cpp:523:14: warning: unused variable ‘dZ’ [-Wunused-variable]
  523 | 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:591:53: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  591 | m_pfSeq[lCount] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
      |                                           ~~~~~~~~~~^
mscore_k.cpp:584:8: warning: unused variable ‘dZ’ [-Wunused-variable]
  584 | 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]
  631 | float fSub = 0.0;
      |       ^~~~
mscore_k.cpp:638:8: warning: unused variable ‘dZ’ [-Wunused-variable]
  638 | double dZ = (double)_c;
      |        ^~
mscore_k.cpp: In member function ‘virtual bool mscore_k::add_Y(long unsigned int, long int)’:
mscore_k.cpp:706:54: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  706 | m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
      |                                            ~~~~~~~~~~^
mscore_k.cpp:712:54: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  712 | m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
      |                                            ~~~~~~~~~~^
mscore_k.cpp:684:7: warning: unused variable ‘fSub’ [-Wunused-variable]
  684 | float fSub = 0.0;
      |       ^~~~
mscore_k.cpp:694:8: warning: unused variable ‘dZ’ [-Wunused-variable]
  694 | double dZ = (double)_c;
      |        ^~
mscore_k.cpp: In member function ‘virtual bool mscore_k::add_Z(long unsigned int, long int)’:
mscore_k.cpp:776:54: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  776 | m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
      |                                            ~~~~~~~~~~^
mscore_k.cpp:779:54: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  779 | m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
      |                                            ~~~~~~~~~~^
mscore_k.cpp:761:7: warning: unused variable ‘fSub’ [-Wunused-variable]
  761 | float fSub = 0.0;
      |       ^~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   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]
  288 |     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]
  358 |  float fValue0 = 0.0;
      |        ^~~~~~~
mscore_tandem.cpp:362:9: warning: unused variable ‘b’ [-Wunused-variable]
  362 |  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]
  581 |  unsigned long a = 0;
      |                ^
mscore_tandem.cpp:582:16: warning: unused variable ‘lCount’ [-Wunused-variable]
  582 |  unsigned long lCount = 0;
      |                ^~~~~~
mscore_tandem.cpp:583:7: warning: unused variable ‘lType’ [-Wunused-variable]
  583 |  long lType = 0;
      |       ^~~~~
mscore_tandem.cpp:584:9: warning: unused variable ‘b’ [-Wunused-variable]
  584 |  size_t b = 0;
      |         ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c msequencecollection.cpp -o msequencecollection.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c msequenceserver.cpp -o msequenceserver.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c msequtilities.cpp -o msequtilities.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   int lZeros = m_lHigh - a - 1;
      |       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   int lZeros = m_lHigh - a - 1;
      |       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   int lZeros = m_lHigh - a - 1;
      |       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   int lZeros = m_lHigh - a - 1;
      |       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   int lZeros = m_lHigh - a - 1;
      |       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   int lZeros = m_lHigh - a - 1;
      |       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   int lZeros = m_lHigh - a - 1;
      |       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   int lZeros = m_lHigh - a - 1;
      |       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   int lZeros = m_lHigh - a - 1;
      |       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   int lZeros = m_lHigh - a - 1;
      |       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   int lZeros = m_lHigh - a - 1;
      |       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   int lZeros = m_lHigh - a - 1;
      |       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   int lZeros = m_lHigh - a - 1;
      |       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c stdafx.cpp -o stdafx.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   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]
  277 |     size_t tCount = pProcess[0]->m_vSpectra.size();
      |            ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   int lZeros = m_lHigh - a - 1;
      |       ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
  446 |   int lZeros = m_lHigh - a - 1;
      |       ^~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o rTANDEM.so 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 -lpthread -lexpat -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-rTANDEM/00new/rTANDEM/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
** checking absolute paths in shared objects and dynamic libraries
** 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
* DONE (rTANDEM)